From 9166400aa2c1d18c431ea7f409e1357a0823d73b Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 20 Oct 2023 21:58:43 +0200
Subject: [PATCH 001/203] Easyconfig that can extend EESSI

---
 EESSI-2023.06-extend.eb | 85 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 EESSI-2023.06-extend.eb

diff --git a/EESSI-2023.06-extend.eb b/EESSI-2023.06-extend.eb
new file mode 100644
index 0000000000..e4fafb860c
--- /dev/null
+++ b/EESSI-2023.06-extend.eb
@@ -0,0 +1,85 @@
+easyblock = 'Binary'
+
+name = 'EESSI'
+version = '2023.06'
+versionsuffix = '-extend'
+
+homepage = 'https://eessi.github.io/docs/'
+
+description = """
+ The goal of the European Environment for Scientific Software Installations
+ (EESSI, pronounced as "easy") is to build a common stack of scientific
+ software installations for HPC systems and beyond, including laptops,
+ personal workstations and cloud infrastructure.
+
+ This module allows you to extend EESSI using the same configuration for
+ EasyBuild as EESSI itself uses. It installs the modules in a special location
+ that is configurable in the CVMFS configuration (so can be on a shared
+ filesystem), and automatically found when using the default EESSI environment. 
+"""
+
+toolchain = SYSTEM
+
+source_urls = None
+sources = ['eb_hooks.py']
+checksums = ['8ae609f99b6953beae89aa1945913686c86c156509dbc55e2b6b8017b13fcf66']
+
+# Don't extend the PATH
+prepend_to_path = None
+
+# All the dependencies we filter in EESSI
+local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,Lua,M4,makeinfo,ncurses,util-linux,XZ,zlib"
+local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
+local_deps_to_filter += local_arch_specific_deps_to_filter[ARCH]
+
+modextravars = {
+    'EASYBUILD_FILTER_DEPS': local_deps_to_filter,
+    'EASYBUILD_IGNORE_OSDEPS': '1',
+    'EASYBUILD_DEBUG': '1',
+    'EASYBUILD_TRACE': '1',
+    'EASYBUILD_ZIP_LOGS': 'bzip2',
+    'EASYBUILD_RPATH': '1',
+    'EASYBUILD_FILTER_ENV_VARS': 'LD_LIBRARY_PATH',
+    'EASYBUILD_READ_ONLY_INSTALLDIR': '1',
+    'EASYBUILD_MODULE_EXTENSIONS': '1',
+    'EASYBUILD_EXPERIMENTAL': '1',
+    'EASYBUILD_HOOKS': '%(installdir)s/eb_hooks.py',
+}
+
+# Need a few other variables, but they are more dynamic
+# EASYBUILD_SYSROOT=${EPREFIX}
+# EASYBUILD_PREFIX=${WORKDIR}/easybuild
+# EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
+# EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
+modluafooter = """
+if (mode() == "load") then
+  -- Use a working directory for temporary build files
+  if (os.getenv("WORKING_DIR") == nil) then
+    LmodMessage("-- Using /tmp as a temporary working directory for installations, you can override this by setting the environment variable WORKING_DIR and reloading the module (e.g., /dev/shm is a common option)")
+  end
+end
+working_dir = os.getenv("WORKING_DIR") or "/tmp"
+-- Gather the EPREFIX to use as a sysroot
+sysroot = os.getenv("EPREFIX")
+-- Use an installation prefix that we _should_ have write access to
+easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
+if (mode() == "load") then
+  LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)
+  -- Advise them to reuse sources
+  if (os.getenv("EASYBUILD_SOURCEPATH") == nil) then
+    LmodMessage("-- You may wish to configure a sources directory for EasyBuild (for example, via setting the environment variable EASYBUILD_SOURCEPATH) to allow you to reuse existing sources for packages.")
+  end
+end
+-- Set the relevant environment variables for EasyBuild
+setenv ("EASYBUILD_SYSROOT", sysroot)
+setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
+setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
+always_load("EasyBuild")
+"""
+
+sanity_check_paths = {
+    'files': ['eb_hooks.py'],
+    'dirs': ['']
+}
+
+moduleclass = 'devel'

From f1a0e71a4b1f01c3b9937a302f50dc87b252c99f Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 20 Oct 2023 22:00:21 +0200
Subject: [PATCH 002/203] Add extension of EESSI to MODULEPATH

---
 init/Magic_Castle/bash           | 2 +-
 init/bash                        | 2 ++
 init/eessi_environment_variables | 2 ++
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/init/Magic_Castle/bash b/init/Magic_Castle/bash
index 85e4d54241..219c6d3a85 100644
--- a/init/Magic_Castle/bash
+++ b/init/Magic_Castle/bash
@@ -10,7 +10,7 @@ source $(dirname "$BASH_SOURCE")/../eessi_environment_variables
 
 # Provide a clean MODULEPATH
 export MODULEPATH_ROOT=$EESSI_MODULEPATH
-export MODULEPATH=$EESSI_MODULEPATH
+export MODULEPATH=$EESSI_EXTEND_MODULEPATH:$EESSI_MODULEPATH
 
 # Extensions are too many, let's not print them by default (requires Lmod 8.4.12)
 export LMOD_AVAIL_EXTENSIONS=no
diff --git a/init/bash b/init/bash
index ea605db0b5..bf8ada4fd2 100644
--- a/init/bash
+++ b/init/bash
@@ -26,6 +26,8 @@ if [ $? -eq 0 ]; then
     # prepend location of modules for EESSI software stack to $MODULEPATH
     echo "Prepending $EESSI_MODULEPATH to \$MODULEPATH..." >> $output
     module use $EESSI_MODULEPATH
+    echo "Prepending $EESSI_EXTEND_MODULEPATH to \$MODULEPATH..." >> $output
+    module use $EESSI_EXTEND_MODULEPATH
 
     #echo >> $output
     #echo "*** Known problems in the ${EESSI_PILOT_VERSION} pilot software stack ***" >> $output
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 10ac1926f4..7b4f82bbd3 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -60,6 +60,8 @@ if [ -d $EESSI_PREFIX ]; then
           if [ -d $EESSI_MODULEPATH ]; then
             export EESSI_MODULEPATH=$EESSI_MODULEPATH
             echo "Using ${EESSI_MODULEPATH} as the directory to be added to MODULEPATH." >> $output
+            export EESSI_EXTEND_MODULEPATH=${EESSI_MODULEPATH/versions/host_injections}
+            echo "Using ${EESSI_EXTEND_MODULEPATH} as the extension directory to be added to MODULEPATH." >> $output
           else
             error "EESSI module path at $EESSI_MODULEPATH not found!"
             false

From 98f20cdd9dd83c481065f30ab6657367d06b869b Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 7 Nov 2023 13:14:24 +0100
Subject: [PATCH 003/203] Allow for both site and user extensions to EESSI

---
 ...nd.eb => EESSI-extend-2023.06-easybuild.eb | 30 ++++++++++++-------
 init/Magic_Castle/bash                        |  2 +-
 init/bash                                     |  6 ++--
 init/eessi_environment_variables              |  6 ++--
 4 files changed, 29 insertions(+), 15 deletions(-)
 rename EESSI-2023.06-extend.eb => EESSI-extend-2023.06-easybuild.eb (69%)

diff --git a/EESSI-2023.06-extend.eb b/EESSI-extend-2023.06-easybuild.eb
similarity index 69%
rename from EESSI-2023.06-extend.eb
rename to EESSI-extend-2023.06-easybuild.eb
index e4fafb860c..fd9f897326 100644
--- a/EESSI-2023.06-extend.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -1,8 +1,9 @@
 easyblock = 'Binary'
 
-name = 'EESSI'
+name = 'EESSI-extend'
 version = '2023.06'
-versionsuffix = '-extend'
+# May have different ways to extend EESSI in future (manually, other tools,...)
+versionsuffix = '-easybuild'
 
 homepage = 'https://eessi.github.io/docs/'
 
@@ -13,9 +14,10 @@ description = """
  personal workstations and cloud infrastructure.
 
  This module allows you to extend EESSI using the same configuration for
- EasyBuild as EESSI itself uses. It installs the modules in a special location
- that is configurable in the CVMFS configuration (so can be on a shared
- filesystem), and automatically found when using the default EESSI environment. 
+ EasyBuild as EESSI itself uses. The default installation is the users
+ home directory, but this can be overridden for a site installation (by setting
+ EESSI_SITE_INSTALL) or for a direct installation under CVMFS (by setting
+ EESSI_CVMFS_INSTALL). 
 """
 
 toolchain = SYSTEM
@@ -55,14 +57,20 @@ modluafooter = """
 if (mode() == "load") then
   -- Use a working directory for temporary build files
   if (os.getenv("WORKING_DIR") == nil) then
-    LmodMessage("-- Using /tmp as a temporary working directory for installations, you can override this by setting the environment variable WORKING_DIR and reloading the module (e.g., /dev/shm is a common option)")
+    LmodMessage("-- Using /tmp/$USER as a temporary working directory for installations, you can override this by setting the environment variable WORKING_DIR and reloading the module (e.g., /dev/shm is a common option)")
   end
 end
-working_dir = os.getenv("WORKING_DIR") or "/tmp"
+working_dir = os.getenv("WORKING_DIR") or pathJoin("/tmp", os.getenv("USER"))
 -- Gather the EPREFIX to use as a sysroot
-sysroot = os.getenv("EPREFIX")
+sysroot = os.getenv("EESSI_EPREFIX")
 -- Use an installation prefix that we _should_ have write access to
-easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
+if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
+  easybuild_installpath = os.getenv("EESSI_SOFTWARE_PATH")
+elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then 
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
+else
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
+end
 if (mode() == "load") then
   LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)
   -- Advise them to reuse sources
@@ -74,7 +82,9 @@ end
 setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
-always_load("EasyBuild")
+if not ( isloaded("EasyBuild") ) then
+    load("EasyBuild")
+end
 """
 
 sanity_check_paths = {
diff --git a/init/Magic_Castle/bash b/init/Magic_Castle/bash
index 219c6d3a85..0ee9d612f3 100644
--- a/init/Magic_Castle/bash
+++ b/init/Magic_Castle/bash
@@ -10,7 +10,7 @@ source $(dirname "$BASH_SOURCE")/../eessi_environment_variables
 
 # Provide a clean MODULEPATH
 export MODULEPATH_ROOT=$EESSI_MODULEPATH
-export MODULEPATH=$EESSI_EXTEND_MODULEPATH:$EESSI_MODULEPATH
+export MODULEPATH=$EESSI_USER_MODULEPATH:$EESSI_SITE_MODULEPATH:$EESSI_MODULEPATH
 
 # Extensions are too many, let's not print them by default (requires Lmod 8.4.12)
 export LMOD_AVAIL_EXTENSIONS=no
diff --git a/init/bash b/init/bash
index bf8ada4fd2..76c1e9154a 100644
--- a/init/bash
+++ b/init/bash
@@ -26,8 +26,10 @@ if [ $? -eq 0 ]; then
     # prepend location of modules for EESSI software stack to $MODULEPATH
     echo "Prepending $EESSI_MODULEPATH to \$MODULEPATH..." >> $output
     module use $EESSI_MODULEPATH
-    echo "Prepending $EESSI_EXTEND_MODULEPATH to \$MODULEPATH..." >> $output
-    module use $EESSI_EXTEND_MODULEPATH
+    echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
+    module use $EESSI_SITE_MODULEPATH
+    echo "Prepending user path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
+    module use $EESSI_USER_MODULEPATH
 
     #echo >> $output
     #echo "*** Known problems in the ${EESSI_PILOT_VERSION} pilot software stack ***" >> $output
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 7b4f82bbd3..656fbc6637 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -60,8 +60,10 @@ if [ -d $EESSI_PREFIX ]; then
           if [ -d $EESSI_MODULEPATH ]; then
             export EESSI_MODULEPATH=$EESSI_MODULEPATH
             echo "Using ${EESSI_MODULEPATH} as the directory to be added to MODULEPATH." >> $output
-            export EESSI_EXTEND_MODULEPATH=${EESSI_MODULEPATH/versions/host_injections}
-            echo "Using ${EESSI_EXTEND_MODULEPATH} as the extension directory to be added to MODULEPATH." >> $output
+            export EESSI_SITE_MODULEPATH=${EESSI_MODULEPATH/versions/host_injections}
+            echo "Using ${EESSI_SITE_MODULEPATH} as the site extension directory to be added to MODULEPATH." >> $output
+            export EESSI_USER_MODULEPATH=${EESSI_MODULEPATH/${EESSI_CVMFS_REPO}/${HOME}\/eessi}
+            echo "Using ${EESSI_USER_MODULEPATH} as the user extension directory to be added to MODULEPATH." >> $output
           else
             error "EESSI module path at $EESSI_MODULEPATH not found!"
             false

From 60cb5dc90187b8b8506933a74cc51e07b67cfe0a Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 7 Nov 2023 13:15:20 +0100
Subject: [PATCH 004/203] Update EESSI-extend-2023.06-easybuild.eb

---
 EESSI-extend-2023.06-easybuild.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index fd9f897326..ce55f619fb 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -30,7 +30,7 @@ checksums = ['8ae609f99b6953beae89aa1945913686c86c156509dbc55e2b6b8017b13fcf66']
 prepend_to_path = None
 
 # All the dependencies we filter in EESSI
-local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,Lua,M4,makeinfo,ncurses,util-linux,XZ,zlib"
+local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,M4,makeinfo,ncurses,util-linux,XZ,zlib"
 local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
 local_deps_to_filter += local_arch_specific_deps_to_filter[ARCH]
 

From 8fe3892e8bb41a8054bd8cfeea34e96888235db3 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 7 Nov 2023 13:48:53 +0100
Subject: [PATCH 005/203] Escape hyphen for gsub

---
 EESSI-extend-2023.06-easybuild.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index ce55f619fb..8993c63cc3 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -69,7 +69,8 @@ if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
 elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then 
   easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
 else
-  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
+  -- Would have liked to use os.getenv("EESSI_CVMFS_REPO") here but the hypen needs to be escaped
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), "/cvmfs/pilot.eessi%-hpc.org", pathJoin(os.getenv("HOME"), "eessi"))
 end
 if (mode() == "load") then
   LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)

From fdf0d9a1ee712f2d46eaeaaf6614eb15846441d7 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:18:22 +0100
Subject: [PATCH 006/203] add zen4 / AMD Genoa

---
 init/arch_specs/eessi_arch_x86.spec           |  7 ++---
 .../x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo | 27 +++++++++++++++++++
 .../x86_64/amd/zen4/Azure-Alma8-9V33X.output  |  1 +
 .../x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo  | 27 +++++++++++++++++++
 .../x86_64/amd/zen4/Shinx-RHEL8-9654.output   |  1 +
 5 files changed, 60 insertions(+), 3 deletions(-)
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output

diff --git a/init/arch_specs/eessi_arch_x86.spec b/init/arch_specs/eessi_arch_x86.spec
index 8d01cb0c03..bfbc5b4be1 100755
--- a/init/arch_specs/eessi_arch_x86.spec
+++ b/init/arch_specs/eessi_arch_x86.spec
@@ -1,6 +1,7 @@
 # x86_64 CPU architecture specifications
 # Software path in EESSI 	| Vendor ID 	| List of defining CPU features
-"x86_64/intel/haswell"		"GenuineIntel"	"avx2 fma" 		# Intel Haswell, Broadwell
+"x86_64/intel/haswell"		"GenuineIntel"	"avx2 fma" 						# Intel Haswell, Broadwell
 "x86_64/intel/skylake_avx512"	"GenuineIntel"	"avx2 fma avx512f avx512bw avx512cd avx512dq avx512vl"	# Intel Skylake, Cascade Lake
-"x86_64/amd/zen2"		"AuthenticAMD"	"avx2 fma"		# AMD Rome
-"x86_64/amd/zen3"		"AuthenticAMD"	"avx2 fma vaes"		# AMD Milan, Milan-X
+"x86_64/amd/zen2"		"AuthenticAMD"	"avx2 fma"						# AMD Rome
+"x86_64/amd/zen3"		"AuthenticAMD"	"avx2 fma vaes"						# AMD Milan, Milan-X
+"x86_64/amd/zen4"		"AuthenticAMD"	"avx2 fma vaes avx512f avx512ifma"			# AMD Genoa, Genoa-X
diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
new file mode 100644
index 0000000000..4a97da862c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo
@@ -0,0 +1,27 @@
+processor       : 0
+vendor_id       : AuthenticAMD
+cpu family      : 25
+model           : 17
+model name      : AMD EPYC 9V33X 96-Core Processor
+stepping        : 1
+microcode       : 0xffffffff
+cpu MHz         : 3705.853
+cache size      : 1024 KB
+physical id     : 0
+siblings        : 88
+core id         : 0
+cpu cores       : 88
+apicid          : 0
+initial apicid  : 0
+fpu             : yes
+fpu_exception   : yes
+cpuid level     : 13
+wp              : yes
+flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext perfctr_core invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves avx512_bf16 clzero xsaveerptr arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload avx512vbmi umip avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq rdpid fsrm
+bugs            : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
+bogomips        : 5100.08
+TLB size        : 3584 4K pages
+clflush size    : 64
+cache_alignment : 64
+address sizes   : 48 bits physical, 48 bits virtual
+power management:
diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
new file mode 100644
index 0000000000..950740a78c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output
@@ -0,0 +1 @@
+x86_64/amd/zen4
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
new file mode 100644
index 0000000000..f28381d7a2
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo
@@ -0,0 +1,27 @@
+processor	: 0
+vendor_id	: AuthenticAMD
+cpu family	: 25
+model		: 17
+model name	: AMD EPYC 9654 96-Core Processor
+stepping	: 1
+microcode	: 0xa10113e
+cpu MHz		: 3699.993
+cache size	: 1024 KB
+physical id	: 0
+siblings	: 96
+core id		: 0
+cpu cores	: 96
+apicid		: 0
+initial apicid	: 0
+fpu		: yes
+fpu_exception	: yes
+cpuid level	: 16
+wp		: yes
+flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 invpcid_single hw_pstate ssbd mba perfmon_v2 ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a avx512f avx512dq rdseed adx avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local avx512_bf16 clzero irperf xsaveerptr wbnoinvd amd_ppin cppc arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif v_spec_ctrl avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq la57 rdpid overflow_recov succor smca fsrm flush_l1d
+bugs		: sysret_ss_attrs spectre_v1 spectre_v2 spec_store_bypass
+bogomips	: 4799.99
+TLB size	: 3584 4K pages
+clflush size	: 64
+cache_alignment	: 64
+address sizes	: 52 bits physical, 57 bits virtual
+power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output
new file mode 100644
index 0000000000..950740a78c
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output
@@ -0,0 +1 @@
+x86_64/amd/zen4

From 1ee221bdbfe0ae6015ca3765a8e23b0760a2323f Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:24:21 +0100
Subject: [PATCH 007/203] add all.output tests

---
 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output | 1 +
 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output  | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
 create mode 100644 tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output

diff --git a/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
new file mode 100644
index 0000000000..e1bbd79e4a
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output
@@ -0,0 +1 @@
+x86_64/amd/zen4:x86_64/amd/zen3:x86_64/amd/zen2:x86_64/generic
diff --git a/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output
new file mode 100644
index 0000000000..e1bbd79e4a
--- /dev/null
+++ b/tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output
@@ -0,0 +1 @@
+x86_64/amd/zen4:x86_64/amd/zen3:x86_64/amd/zen2:x86_64/generic

From 680e7b91836c33caeb1c2c493f0589d4b5a73219 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 17:28:59 +0100
Subject: [PATCH 008/203] adding zen4 checks

---
 .github/workflows/tests_archdetect.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 37338693c5..d1407637e0 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -13,6 +13,8 @@ jobs:
           - x86_64/intel/skylake_avx512/archspec-linux-6132
           - x86_64/amd/zen2/Azure-CentOS7-7V12
           - x86_64/amd/zen3/Azure-CentOS7-7V73X
+          - x86_64/amd/zen4/Azure-Alma8-9V33X
+          - x86_64/amd/zen4/Shinx-RHEL8-9654
           - ppc64le/power9le/unknown-power9le
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2

From 7070c047ebf57918dd0ae19c11ade011e99cefff Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 18:00:17 +0100
Subject: [PATCH 009/203] commenting out power to prevent conflict

---
 .github/workflows/tests_archdetect.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index d1407637e0..45e8dd2e60 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -15,10 +15,10 @@ jobs:
           - x86_64/amd/zen3/Azure-CentOS7-7V73X
           - x86_64/amd/zen4/Azure-Alma8-9V33X
           - x86_64/amd/zen4/Shinx-RHEL8-9654
-          - ppc64le/power9le/unknown-power9le
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2
           - aarch64/neoverse_v1/AWS-awslinux-graviton3
+          # - ppc64le/power9le/unknown-power9le
       fail-fast: false
     steps:
     - name: checkout

From ad70b6b0857f6e3508a73c4675795de30f6b40eb Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 19:27:14 +0100
Subject: [PATCH 010/203] commenting out power9 to prevent conflict

---
 .github/workflows/tests_archdetect.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 45e8dd2e60..68d25250ca 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -18,6 +18,8 @@ jobs:
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2
           - aarch64/neoverse_v1/AWS-awslinux-graviton3
+          # commented out since these targets are currently not supported in software.eessi.io repo
+          # (and some tests assume that the corresponding subdirectory in software layer is there)
           # - ppc64le/power9le/unknown-power9le
       fail-fast: false
     steps:

From fd3103e1f75157edffcf16023ef4fb6431c6b5eb Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 20:15:18 +0100
Subject: [PATCH 011/203] move to software.eessi.io

---
 .github/workflows/test_eessi.yml                  | 14 +++++++-------
 .github/workflows/test_eessi_container_script.yml | 12 ++++++------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
index 04195dd619..7c96b091d2 100644
--- a/.github/workflows/test_eessi.yml
+++ b/.github/workflows/test_eessi.yml
@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         EESSI_VERSION:
-        - 2021.12
+        - 2023.06
         EESSI_SOFTWARE_SUBDIR:
         - aarch64/generic
         - aarch64/graviton2
@@ -24,19 +24,19 @@ jobs:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
 
-        - name: Mount EESSI CernVM-FS pilot repository
+        - name: Mount EESSI CernVM-FS software repository
           uses: cvmfs-contrib/github-action-cvmfs@d4641d0d591c9a5c3be23835ced2fb648b44c04b # v3.1
           with:
               cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
               cvmfs_http_proxy: DIRECT
-              cvmfs_repositories: pilot.eessi-hpc.org
+              cvmfs_repositories: software.eessi.io
 
         - name: Test check_missing_installations.sh script
           run: |
-              source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
+              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               eb --version
-              export EESSI_PREFIX=/cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
@@ -45,10 +45,10 @@ jobs:
 
         - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
           run: |
-              source /cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}/init/bash
+              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
               module load EasyBuild
               eb --version
-              export EESSI_PREFIX=/cvmfs/pilot.eessi-hpc.org/versions/${{matrix.EESSI_VERSION}}
+              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
               export EESSI_OS_TYPE=linux
               export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
               env | grep ^EESSI | sort
diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index 929fb22cec..590aa4225b 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -90,15 +90,15 @@ jobs:
               elif [[ ${{matrix.SCRIPT_TEST}} == 'readwrite' ]]; then
                 outfile=out_readwrite.txt
                 fn="test_${RANDOM}.txt"
-                echo "touch /cvmfs/pilot.eessi-hpc.org/${fn}" > test_script.sh
+                echo "touch /cvmfs/software.eessi.io/${fn}" > test_script.sh
                 chmod u+x test_script.sh
                 export SINGULARITY_BIND="$PWD:/test"
                 ./eessi_container.sh --verbose --access rw --mode run /test/test_script.sh > ${outfile}
 
                 tmpdir=$(grep "\-\-resume" ${outfile} | sed "s/.*--resume \([^']*\).*/\1/g")
                 # note: must use '--access rw' again here, since touched file is in overlay upper dir
-                ./eessi_container.sh --verbose --resume ${tmpdir} --access rw --mode shell <<< "ls -l /cvmfs/pilot.eessi-hpc.org/${fn}" > ${outfile}
-                grep "/cvmfs/pilot.eessi-hpc.org/${fn}$" $outfile
+                ./eessi_container.sh --verbose --resume ${tmpdir} --access rw --mode shell <<< "ls -l /cvmfs/software.eessi.io/${fn}" > ${outfile}
+                grep "/cvmfs/software.eessi.io/${fn}$" $outfile
 
               # test use of --resume
               elif [[ ${{matrix.SCRIPT_TEST}} == 'resume' ]]; then
@@ -120,12 +120,12 @@ jobs:
               elif [[ ${{matrix.SCRIPT_TEST}} == 'save' ]]; then
                 outfile=out_save.txt
                 fn="test_${RANDOM}.txt"
-                test_cmd="touch /cvmfs/pilot.eessi-hpc.org/${fn}"
+                test_cmd="touch /cvmfs/software.eessi.io/${fn}"
                 ./eessi_container.sh --verbose --mode shell --access rw --save test-save.tar <<< "${test_cmd}" 2>&1 | tee ${outfile}
                 rm -f ${outfile}
 
-                ./eessi_container.sh --verbose --mode shell --access rw --resume test-save.tar <<< "ls -l /cvmfs/pilot.eessi-hpc.org/${fn}" > ${outfile}
-                grep "/cvmfs/pilot.eessi-hpc.org/${fn}$" $outfile
+                ./eessi_container.sh --verbose --mode shell --access rw --resume test-save.tar <<< "ls -l /cvmfs/software.eessi.io/${fn}" > ${outfile}
+                grep "/cvmfs/software.eessi.io/${fn}$" $outfile
 
                 tar tfv test-save.tar | grep "overlay-upper/${fn}"
 

From a13bce84ca477c9d866ad722993252aad924d5fd Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Wed, 10 Jan 2024 20:20:48 +0100
Subject: [PATCH 012/203] move from pilot to software

---
 .github/workflows/tests_readme.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/tests_readme.yml b/.github/workflows/tests_readme.yml
index 5c6d0318d4..034dae3780 100644
--- a/.github/workflows/tests_readme.yml
+++ b/.github/workflows/tests_readme.yml
@@ -24,7 +24,7 @@ jobs:
         - name: verify if README.md is consistent with EESSI_PILOT_VERSION from init/eessi_defaults
           run: |
             source init/eessi_defaults
-            grep "${EESSI_PILOT_VERSION}" README.md
+            grep "${EESSI_VERSION}" README.md
 
         - name: verify if README.md is consistent with EESSI_CVMFS_REPO from init/eessi_defaults
           run: |

From 473a5b52b960881f2b4371978279976b9a8bccae Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Thu, 11 Jan 2024 03:51:20 +0100
Subject: [PATCH 013/203] move EESSI action to v3

---
 .github/workflows/tests_archdetect.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index 68d25250ca..f09567d125 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -26,7 +26,8 @@ jobs:
     - name: checkout
       uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
     - name: Enable EESSI
-      uses: eessi/github-action-eessi@58b50fd2eead2162c2b9ac258d4fb60cc9f30503 # v2.0.13
+      #uses: eessi/github-action-eessi@58b50fd2eead2162c2b9ac258d4fb60cc9f30503 # v2.0.13
+      uses: eessi/github-action-eessi@v3
     - name: test eessi_archdetect.sh
       run: |
           export EESSI_MACHINE_TYPE=${{matrix.proc_cpuinfo}}

From 807d78471ad4104d0ff3f590dbc697d6cd2a3968 Mon Sep 17 00:00:00 2001
From: hugo meiland <hugo.meiland@microsoft.com>
Date: Mon, 15 Jan 2024 11:27:42 +0100
Subject: [PATCH 014/203] fix upstream merge

---
 .github/workflows/test_eessi.yml | 72 --------------------------------
 1 file changed, 72 deletions(-)
 delete mode 100644 .github/workflows/test_eessi.yml

diff --git a/.github/workflows/test_eessi.yml b/.github/workflows/test_eessi.yml
deleted file mode 100644
index 7c96b091d2..0000000000
--- a/.github/workflows/test_eessi.yml
+++ /dev/null
@@ -1,72 +0,0 @@
-# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
-name: Tests relying on having EESSI pilot repo mounted
-on: [push, pull_request, workflow_dispatch]
-permissions:
-  contents: read # to fetch code (actions/checkout)
-jobs:
-  eessi_pilot_repo:
-    runs-on: ubuntu-20.04
-    strategy:
-      fail-fast: false
-      matrix:
-        EESSI_VERSION:
-        - 2023.06
-        EESSI_SOFTWARE_SUBDIR:
-        - aarch64/generic
-        - aarch64/graviton2
-        - aarch64/graviton3
-        - x86_64/amd/zen2
-        - x86_64/amd/zen3
-        - x86_64/intel/haswell
-        - x86_64/intel/skylake_avx512
-        - x86_64/generic
-    steps:
-        - name: Check out software-layer repository
-          uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
-
-        - name: Mount EESSI CernVM-FS software repository
-          uses: cvmfs-contrib/github-action-cvmfs@d4641d0d591c9a5c3be23835ced2fb648b44c04b # v3.1
-          with:
-              cvmfs_config_package: https://github.com/EESSI/filesystem-layer/releases/download/latest/cvmfs-config-eessi_latest_all.deb
-              cvmfs_http_proxy: DIRECT
-              cvmfs_repositories: software.eessi.io
-
-        - name: Test check_missing_installations.sh script
-          run: |
-              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
-              module load EasyBuild
-              eb --version
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
-              export EESSI_OS_TYPE=linux
-              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
-              env | grep ^EESSI | sort
-              echo "just run check_missing_installations.sh (should use eessi-${{matrix.EESSI_VERSION}}.yml)"
-              ./check_missing_installations.sh
-
-        - name: Test check_missing_installations.sh with missing package (GCC/8.3.0)
-          run: |
-              source /cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}/init/bash
-              module load EasyBuild
-              eb --version
-              export EESSI_PREFIX=/cvmfs/software.eessi.io/versions/${{matrix.EESSI_VERSION}}
-              export EESSI_OS_TYPE=linux
-              export EESSI_SOFTWARE_SUBDIR=${{matrix.EESSI_SOFTWARE_SUBDIR}}
-              env | grep ^EESSI | sort
-              echo "modify eessi-${{matrix.EESSI_VERSION}}.yml by adding a missing package (GCC/8.3.0)"
-              echo "  GCC:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "    toolchains:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "      SYSTEM:" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              echo "        versions: '8.3.0'" >> eessi-${{matrix.EESSI_VERSION}}.yml
-              tail -n 4 eessi-${{matrix.EESSI_VERSION}}.yml
-              # note, check_missing_installations.sh exits 1 if a package was
-              # missing, which is intepreted as false (exit code based, not
-              # boolean logic), hence when the script exits 0 if no package was
-              # missing it is interpreted as true, thus the test did not capture
-              # the missing package
-              if ./check_missing_installations.sh; then
-                echo "did NOT capture missing package; test FAILED"
-                exit 1
-              else
-                echo "captured missing package; test PASSED"
-                exit 0
-              fi

From 743860fc06d5be09e9b15d62514f91ac2fb4aebc Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 13 Mar 2024 11:29:07 +0100
Subject: [PATCH 015/203] {2023.06}[foss/2023b] GROMACS 2024.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index e2d35276df..f906811a73 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -49,3 +49,6 @@ easyconfigs:
   - libspatialindex-1.9.3-GCCcore-13.2.0.eb:
       options:
         from-pr: 19922
+  - GROMACS-2024.1-foss-2023b.eb:
+      options:
+        from-pr: 20102

From 70d94a1361eaa02a8dea4c64495480f0a4cc6910 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Sat, 30 Mar 2024 22:58:48 +0100
Subject: [PATCH 016/203] add R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 3962f63bda..8a3e82d760 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,3 +11,4 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

From 3ccecf97e9008ddf98640d3a0ab970607c5b5779 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 12:58:22 +0200
Subject: [PATCH 017/203] Add possibility to ignore certain hooks on local
 modules. E.g. we don't want to be prevented from loading local CUDA modules
 because of the EESSI hook. See
 https://github.com/EESSI/software-layer/issues/523

---
 create_lmodsitepackage.py | 19 +++++++++++++++++--
 1 file changed, 17 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 29b2d39bd7..ffbe7a1531 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -19,6 +19,18 @@
     return content
 end
 
+local function from_eessi_prefix(t)
+    local eessi_prefix = os.getenv("EESSI_PREFIX")
+    -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
+    -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
+    if eessi_prefix == nil then
+        return False
+    else
+        -- Check if the full modulepath starts with the eessi_prefix
+        return t.fn:find( "^" .. eessi_prefix) ~= nil
+    end
+end
+
 local function load_site_specific_hooks()
     -- This function will be run after the EESSI hooks are registered
     -- It will load a local SitePackage.lua that is architecture independent (if it exists) from e.g.
@@ -152,10 +164,13 @@
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
-    eessi_cuda_enabled_load_hook(t)
+    -- Only apply CUDA hooks if the loaded module is in the EESSI prefix
+    -- This avoids getting an Lmod Error when trying to load a CUDA module from a local software stack
+    if from_eessi_prefix(t) then
+        eessi_cuda_enabled_load_hook(t)
+    end
 end
 
-
 hook.register("load", eessi_load_hook)
 
 -- Note that this needs to happen at the end, so that any EESSI specific hooks can be overwritten by the site

From bb20ab2078b25041011f242673a848b199aedb74 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 16:36:39 +0200
Subject: [PATCH 018/203] Also use hooks for site extensions in host_injections
 AND for user extensions in /home/casparl/eessi/...

---
 create_lmodsitepackage.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ffbe7a1531..f7d4d06bb9 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -20,14 +20,24 @@
 end
 
 local function from_eessi_prefix(t)
+    -- eessi_prefix is the prefix with official EESSI modules
+    -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
+    -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
+    -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
+    local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
+    -- eessi_prefix_user_home is the prefix with user-extensions (i.e. additional modules)
+    -- to the offocial EESSI modules, e.g. $HOME/eessi/versions/2023.06
+    local eessi_prefix_user_home = string.gsub(eessi_prefix, os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
     -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
     -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
     if eessi_prefix == nil then
         return False
     else
-        -- Check if the full modulepath starts with the eessi_prefix
-        return t.fn:find( "^" .. eessi_prefix) ~= nil
+        -- Check if the full modulepath starts with the eessi_prefix_*
+        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or
+        string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil or
+        string.find(t.fn, "^" .. eessi_prefix_user_home) ~= nil
     end
 end
 

From 838920bd332819b1e50706873ee53f2469cf3794 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Wed, 3 Apr 2024 16:38:24 +0200
Subject: [PATCH 019/203] Leave breadcrumb to notify that paths may need to be
 changed in the future

---
 create_lmodsitepackage.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index f7d4d06bb9..ce94a7e311 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -23,6 +23,10 @@
     -- eessi_prefix is the prefix with official EESSI modules
     -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
+
+    -- NOTE: exact paths for site and user extensions aren't final, so may need to be updated later.
+    -- See https://github.com/EESSI/software-layer/pull/371
+
     -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
     -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
     local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')

From 145706e751ea7a73202676894cd58be65bea97d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Apr 2024 11:53:36 +0200
Subject: [PATCH 020/203] add R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index ad3cfddfb6..2dadc5ab28 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -57,3 +57,4 @@ easyconfigs:
   - Highway-1.0.4-GCCcore-12.3.0.eb
   - ELPA-2023.05.001-foss-2023a.eb
   - libxc-6.2.2-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb

From cef7a277ac4092f8ff1256290ad6bb8b244c2443 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Apr 2024 13:03:35 +0200
Subject: [PATCH 021/203] add from-pr to bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index facd4230ab..60b9600589 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -67,4 +67,6 @@ easyconfigs:
   - MODFLOW-6.4.4-foss-2023a.eb:
       options:
         from-pr: 20142
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 19949

From 3745adee2c09aa73d44c7b693baca3ac4c96e70c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 Apr 2024 13:52:36 +0200
Subject: [PATCH 022/203] use pr 20316 for Bioconductor

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index d3ac5f1c5b..bfc408e045 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -73,4 +73,4 @@ easyconfigs:
         from-pr: 20238
   - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
       options:
-        from-pr: 19949
+        from-pr: 20316

From 03b708fe7af1fc1aa330bf17bdf3f25a601f093e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 Apr 2024 13:54:13 +0200
Subject: [PATCH 023/203] use PR  20316 for Bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2022b.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 8a3e82d760..da89e01a51 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,4 +11,6 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
-  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
+      options:
+        from-pr: 20316

From 1998a7cfe2904e1b8dacdba4d6eca1fe67eb6354 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 8 Apr 2024 15:16:08 +0200
Subject: [PATCH 024/203] add EB 4.9.1

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml             | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
new file mode 100644
index 0000000000..c5a08b5209
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - EasyBuild-4.9.1.eb:
+      options:
+        from-pr: 20299

From 1910871e228de824978f00b1d995879330745dec Mon Sep 17 00:00:00 2001
From: maxim-masterov <maxim.vadimovich@gmail.com>
Date: Tue, 9 Apr 2024 12:12:18 +0200
Subject: [PATCH 025/203] Add fix for permissions set on Lmod SitePackage

---
 create_lmodsitepackage.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 29b2d39bd7..38600cb471 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -4,6 +4,7 @@
 #
 import os
 import sys
+from stat import S_IREAD, S_IWRITE, S_IRGRP, S_IWGRP, S_IROTH
 
 DOT_LMOD = '.lmod'
 
@@ -180,6 +181,8 @@ def error(msg):
     os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True)
     with open(sitepackage_path, 'w') as fp:
         fp.write(hook_txt)
+    # Make sure that the created Lmod file has "read" permissions for the "other" UNIX group
+    os.chmod(sitepackage_path, S_IREAD|S_IWRITE|S_IRGRP|S_IWGRP|S_IROTH)
 
 except (IOError, OSError) as err:
     error("Failed to create %s: %s" % (sitepackage_path, err))

From 8f656a4dced151499045dd9c1c49dc6438fb7471 Mon Sep 17 00:00:00 2001
From: Maxim <maxim.vadimovich@gmail.com>
Date: Wed, 10 Apr 2024 16:19:37 +0200
Subject: [PATCH 026/203] Update create_lmodsitepackage.py

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 38600cb471..0761f2cdf1 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -181,7 +181,7 @@ def error(msg):
     os.makedirs(os.path.dirname(sitepackage_path), exist_ok=True)
     with open(sitepackage_path, 'w') as fp:
         fp.write(hook_txt)
-    # Make sure that the created Lmod file has "read" permissions for the "other" UNIX group
+    # Make sure that the created Lmod file has "read/write" for the user/group and "read" permissions for others
     os.chmod(sitepackage_path, S_IREAD|S_IWRITE|S_IRGRP|S_IWGRP|S_IROTH)
 
 except (IOError, OSError) as err:

From 1a396e03badc537ddf901257bba7efb1cbdc8281 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 12 Apr 2024 13:23:53 +0200
Subject: [PATCH 027/203] Ensure we use instructions introduced with ARM v8.2
 for Neoverse N1

---
 init/arch_specs/eessi_arch_arm.spec | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/init/arch_specs/eessi_arch_arm.spec b/init/arch_specs/eessi_arch_arm.spec
index b5c9275043..1400871f93 100755
--- a/init/arch_specs/eessi_arch_arm.spec
+++ b/init/arch_specs/eessi_arch_arm.spec
@@ -1,6 +1,6 @@
 # ARM CPU architecture specifications
 # Software path in EESSI 	| Vendor ID 	| List of defining CPU features
-"aarch64/neoverse_n1"	"ARM"		"asimd"		# Ampere Altra
-"aarch64/neoverse_n1"	""		"asimd"		# AWS Graviton2
-"aarch64/neoverse_v1"	"ARM"		"asimd svei8mm"
-"aarch64/neoverse_v1"	""		"asimd svei8mm"	# AWS Graviton3
+"aarch64/neoverse_n1"	"ARM"		"asimddp"		# Ampere Altra
+"aarch64/neoverse_n1"	""		"asimddp"		# AWS Graviton2
+"aarch64/neoverse_v1"	"ARM"		"asimddp svei8mm"
+"aarch64/neoverse_v1"	""		"asimddp svei8mm"	# AWS Graviton3

From cedcf73c5da8d51d47c8d8d209cab76222e82820 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 12 Apr 2024 16:19:43 +0200
Subject: [PATCH 028/203] Update eessi_arch_arm.spec

---
 init/arch_specs/eessi_arch_arm.spec | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/arch_specs/eessi_arch_arm.spec b/init/arch_specs/eessi_arch_arm.spec
index 1400871f93..8c1bc34d20 100755
--- a/init/arch_specs/eessi_arch_arm.spec
+++ b/init/arch_specs/eessi_arch_arm.spec
@@ -1,4 +1,4 @@
-# ARM CPU architecture specifications
+# ARM CPU architecture specifications (see https://gpages.juszkiewicz.com.pl/arm-socs-table/arm-socs.html for guidance)
 # Software path in EESSI 	| Vendor ID 	| List of defining CPU features
 "aarch64/neoverse_n1"	"ARM"		"asimddp"		# Ampere Altra
 "aarch64/neoverse_n1"	""		"asimddp"		# AWS Graviton2

From 04e04a308829b49f4b925d4420363739c728a58b Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@tcn1.local.snellius.surf.nl>
Date: Mon, 15 Apr 2024 11:33:08 +0200
Subject: [PATCH 029/203] Added ncdu

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml  | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
new file mode 100644
index 0000000000..3b51db3b11
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - ncdu-1.18-GCC-12.3.0.eb

From 8f81944b29dfb48edaf30b9466ce9edde4aa748f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 16 Apr 2024 09:04:47 +0200
Subject: [PATCH 030/203] make sure that software directory that corresponds to
 $EESSI_SOFTWARE_SUBDIR_OVERRIDE exists

---
 EESSI-install-software.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 567fed8e79..91effe4aba 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -143,6 +143,8 @@ if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
   echo ">> Determined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE via 'eessi_software_subdir.py $DETECTION_PARAMETERS' script"
 else
   echo ">> Picking up pre-defined \$EESSI_SOFTWARE_SUBDIR_OVERRIDE: ${EESSI_SOFTWARE_SUBDIR_OVERRIDE}"
+  # make sure directory exists (since it's expected by init/eessi_environment_variables when using archdetect)
+  mkdir -p ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
 # Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)

From 8331e4485a5734730b0929be69c3cd3c6beaa4b6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 16 Apr 2024 09:30:02 +0200
Subject: [PATCH 031/203] remove build_container.sh, as we now use
 eessi_container.sh

---
 build_container.sh | 69 ----------------------------------------------
 1 file changed, 69 deletions(-)
 delete mode 100755 build_container.sh

diff --git a/build_container.sh b/build_container.sh
deleted file mode 100755
index 23a9e665c9..0000000000
--- a/build_container.sh
+++ /dev/null
@@ -1,69 +0,0 @@
-#!/bin/bash
-
-base_dir=$(dirname $(realpath $0))
-
-BUILD_CONTAINER="docker://ghcr.io/eessi/build-node:debian11"
-
-if [ $# -lt 2 ]; then
-    echo "Usage: $0 <shell|run> <path for temporary directories>" >&2
-    exit 1
-fi
-SHELL_OR_RUN=$1
-EESSI_TMPDIR=$2
-shift 2
-
-if [ "$SHELL_OR_RUN" == "run" ] && [ $# -eq 0 ]; then
-    echo "ERROR: No command specified to run?!" >&2
-    exit 1
-fi
-
-# make sure specified temporary directory exists
-mkdir -p $EESSI_TMPDIR
-
-echo "Using $EESSI_TMPDIR as parent for temporary directories..."
-
-# create temporary directories
-mkdir -p $EESSI_TMPDIR/{home,overlay-upper,overlay-work}
-mkdir -p $EESSI_TMPDIR/{var-lib-cvmfs,var-run-cvmfs}
-# configure Singularity
-export SINGULARITY_CACHEDIR=$EESSI_TMPDIR/singularity_cache
-
-# take into account that $SINGULARITY_BIND may be defined already, to bind additional paths into the build container
-BIND_PATHS="$EESSI_TMPDIR/var-run-cvmfs:/var/run/cvmfs,$EESSI_TMPDIR/var-lib-cvmfs:/var/lib/cvmfs,$EESSI_TMPDIR"
-if [ -z $SINGULARITY_BIND ]; then
-    export SINGULARITY_BIND="$BIND_PATHS"
-else
-    export SINGULARITY_BIND="$SINGULARITY_BIND,$BIND_PATHS"
-fi
-
-# allow that SINGULARITY_HOME is defined before script is run
-if [ -z $SINGULARITY_HOME ]; then
-    export SINGULARITY_HOME="$EESSI_TMPDIR/home:/home/$USER"
-fi
-
-source ${base_dir}/init/eessi_defaults
-# strip "/cvmfs/" from default setting
-repo_name=${EESSI_CVMFS_REPO/\/cvmfs\//}
-
-# set environment variables for fuse mounts in Singularity container
-export EESSI_PILOT_READONLY="container:cvmfs2 ${repo_name} /cvmfs_ro/${repo_name}"
-export EESSI_PILOT_WRITABLE_OVERLAY="container:fuse-overlayfs -o lowerdir=/cvmfs_ro/${repo_name} -o upperdir=$EESSI_TMPDIR/overlay-upper -o workdir=$EESSI_TMPDIR/overlay-work ${EESSI_CVMFS_REPO}"
-
-# pass $EESSI_SOFTWARE_SUBDIR_OVERRIDE into build container (if set)
-if [ ! -z ${EESSI_SOFTWARE_SUBDIR_OVERRIDE} ]; then
-    export SINGULARITYENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
-    # also specify via $APPTAINERENV_* (future proof, cfr. https://apptainer.org/docs/user/latest/singularity_compatibility.html#singularity-environment-variable-compatibility)
-    export APPTAINERENV_EESSI_SOFTWARE_SUBDIR_OVERRIDE=${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
-fi
-
-if [ "$SHELL_OR_RUN" == "shell" ]; then
-    # start shell in Singularity container, with EESSI repository mounted with writable overlay
-    echo "Starting Singularity build container..."
-    singularity shell --fusemount "$EESSI_PILOT_READONLY" --fusemount "$EESSI_PILOT_WRITABLE_OVERLAY" $BUILD_CONTAINER
-elif [ "$SHELL_OR_RUN" == "run" ]; then
-    echo "Running '$@' in Singularity build container..."
-    singularity exec --fusemount "$EESSI_PILOT_READONLY" --fusemount "$EESSI_PILOT_WRITABLE_OVERLAY" $BUILD_CONTAINER "$@"
-else
-    echo "ERROR: Unknown action specified: $SHELL_OR_RUN (should be either 'shell' or 'run')" >&2
-    exit 1
-fi

From a7305456f10ca0289d1cbea8b212aa7cb4fb114a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 16 Apr 2024 09:32:23 +0200
Subject: [PATCH 032/203] replace build_container.sh by eessi_container.sh

---
 .github/workflows/tests_scripts.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 4944d9beaa..76d19d29fe 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -3,9 +3,9 @@ name: Tests for scripts
 on:
   push:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh
@@ -15,9 +15,9 @@ on:
 
   pull_request:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh

From 8593e595ee382a26c8f9621dd39ccb338e937259 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Thu, 18 Apr 2024 23:51:24 +0200
Subject: [PATCH 033/203] No hyphen any more so no need for lua escaping

---
 EESSI-extend-2023.06-easybuild.eb | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 8993c63cc3..ce55f619fb 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -69,8 +69,7 @@ if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
 elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then 
   easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
 else
-  -- Would have liked to use os.getenv("EESSI_CVMFS_REPO") here but the hypen needs to be escaped
-  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), "/cvmfs/pilot.eessi%-hpc.org", pathJoin(os.getenv("HOME"), "eessi"))
+  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
 end
 if (mode() == "load") then
   LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)

From 8e976c6a2c8fbef7751dbc3f0c434ac431db3c4d Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 00:58:16 +0200
Subject: [PATCH 034/203] Make the hooks part of the init dir

---
 EESSI-extend-2023.06-easybuild.eb | 17 +++--------------
 EESSI-install-software.sh         |  8 ++++++++
 2 files changed, 11 insertions(+), 14 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index ce55f619fb..6d71693db8 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -1,4 +1,4 @@
-easyblock = 'Binary'
+easyblock = 'Bundle'
 
 name = 'EESSI-extend'
 version = '2023.06'
@@ -22,13 +22,6 @@ description = """
 
 toolchain = SYSTEM
 
-source_urls = None
-sources = ['eb_hooks.py']
-checksums = ['8ae609f99b6953beae89aa1945913686c86c156509dbc55e2b6b8017b13fcf66']
-
-# Don't extend the PATH
-prepend_to_path = None
-
 # All the dependencies we filter in EESSI
 local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,M4,makeinfo,ncurses,util-linux,XZ,zlib"
 local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
@@ -45,12 +38,12 @@ modextravars = {
     'EASYBUILD_READ_ONLY_INSTALLDIR': '1',
     'EASYBUILD_MODULE_EXTENSIONS': '1',
     'EASYBUILD_EXPERIMENTAL': '1',
-    'EASYBUILD_HOOKS': '%(installdir)s/eb_hooks.py',
 }
 
 # Need a few other variables, but they are more dynamic
 # EASYBUILD_SYSROOT=${EPREFIX}
 # EASYBUILD_PREFIX=${WORKDIR}/easybuild
+# EASYBUILD_HOOKS=${EESSI_PREFIX}/init/easybuild/eb_hooks.py
 # EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
 # EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
 modluafooter = """
@@ -82,14 +75,10 @@ end
 setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
+setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "hooks.py"))
 if not ( isloaded("EasyBuild") ) then
     load("EasyBuild")
 end
 """
 
-sanity_check_paths = {
-    'files': ['eb_hooks.py'],
-    'dirs': ['']
-}
-
 moduleclass = 'devel'
diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 91effe4aba..9766c20aa1 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -264,6 +264,14 @@ fi
 
 ### add packages here
 
+# use PR patch file to determine if the EasyBuild hooks have changed
+changed_eb_hooks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eb_hooks.py$') 
+if [ -n "${changed_eb_hooks}" ]; then
+    # If the hooks have been changed we need to copy them over to the init directory
+    mkdir -p ${EESSI_PREFIX}/init/easybuild
+    cp eb_hooks.py ${EESSI_PREFIX}/init/easybuild
+fi
+
 echo ">> Creating/updating Lmod RC file..."
 export LMOD_CONFIG_DIR="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"

From dbe6d6bde6f7e6e498fe0e337836c4114d4bb0c3 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 01:00:43 +0200
Subject: [PATCH 035/203] Actually install the EESSI extension module

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3b51db3b11..b7d4370b84 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
+  - EESSI-extend-2023.06-easybuild.eb 

From 5ca2c4a25d702372f0993b57025a7f01459b21d9 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 09:52:39 +0200
Subject: [PATCH 036/203] Copy over hooks along with initi files

---
 EESSI-install-software.sh | 8 --------
 install_scripts.sh        | 6 ++++++
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 9766c20aa1..91effe4aba 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -264,14 +264,6 @@ fi
 
 ### add packages here
 
-# use PR patch file to determine if the EasyBuild hooks have changed
-changed_eb_hooks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^eb_hooks.py$') 
-if [ -n "${changed_eb_hooks}" ]; then
-    # If the hooks have been changed we need to copy them over to the init directory
-    mkdir -p ${EESSI_PREFIX}/init/easybuild
-    cp eb_hooks.py ${EESSI_PREFIX}/init/easybuild
-fi
-
 echo ">> Creating/updating Lmod RC file..."
 export LMOD_CONFIG_DIR="${EASYBUILD_INSTALLPATH}/.lmod"
 lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"
diff --git a/install_scripts.sh b/install_scripts.sh
index 508735975c..e6aecf4513 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -113,3 +113,9 @@ nvidia_files=(
     install_cuda_host_injections.sh link_nvidia_host_libraries.sh
 )
 copy_files_by_list ${TOPDIR}/scripts/gpu_support/nvidia ${INSTALL_PREFIX}/scripts/gpu_support/nvidia "${nvidia_files[@]}"
+
+# Copy over EasyBuild hooks file used for installations
+hook_files=(
+    eb_hooks.py
+)
+copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/easybuild "${hook_files[@]}"

From 148534a3922272b7f6f4f7a3e1b9d210b69ca933 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 09:58:10 +0200
Subject: [PATCH 037/203] Update install_scripts.sh

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index e6aecf4513..17f0b81008 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -118,4 +118,4 @@ copy_files_by_list ${TOPDIR}/scripts/gpu_support/nvidia ${INSTALL_PREFIX}/script
 hook_files=(
     eb_hooks.py
 )
-copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/easybuild "${hook_files[@]}"
+copy_files_by_list ${TOPDIR} ${INSTALL_PREFIX}/init/easybuild "${hook_files[@]}"

From dee801bbf1dc31c61a51a6e4b6dde702bf6337f8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:25:51 +0200
Subject: [PATCH 038/203] move bioconductor to 4.9.1 easystack

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
index 8a3e82d760..3962f63bda 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2022b.yml
@@ -11,4 +11,3 @@ easyconfigs:
   - R-4.2.2-foss-2022b.eb:
       options:
         from-pr: 20238
-  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

From cbad690f01b417a9a185685d20f7e160808242ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:26:05 +0200
Subject: [PATCH 039/203] add bioconductor

---
 .../2023.06/eessi-2023.06-eb-4.9.1-2022b.yml                 | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
new file mode 100644
index 0000000000..f80b99f187
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -0,0 +1,5 @@
+easyconfigs:
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
+      options:
+        from-pr: 20379
+

From b6a222639341313caca5bebb621590f8d0862373 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:30:08 +0200
Subject: [PATCH 040/203] move biocondutor to 4.9.1 stack, use pr 20379

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 ---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index bfc408e045..44952e2765 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,6 +71,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20316
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3b51db3b11..57cfc00297 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,5 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379

From 786e1e8189d75682c37150d2d7d58e465ec7e9ca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 10:31:08 +0200
Subject: [PATCH 041/203] remove blank line

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index f80b99f187..e547e45f2b 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -2,4 +2,3 @@ easyconfigs:
   - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
       options:
         from-pr: 20379
-

From d6336e181efb320a74b895e0baf73373e49875f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 11:50:15 +0200
Subject: [PATCH 042/203] move bioconductor back to 4.9.0 file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 +++
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 ---
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 44952e2765..23d64036f1 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,3 +71,6 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 57cfc00297..3b51db3b11 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,5 +1,2 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20379

From 339f358e46dd338649939c31042a0faf15f9e532 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 19 Apr 2024 13:59:23 +0200
Subject: [PATCH 043/203] add rebuild easystack for setuptools_scm fix

---
 ...move-setuptools_scm-from-hatchling-to-Python.yml | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
new file mode 100644
index 0000000000..56ea7a46a1
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -0,0 +1,13 @@
+# 2024-04-19
+# Move setuptools_scm extension from hatchling to Python by rebuilding
+# all affected modules with EasyBuild 4.9.1.
+# This solves an issue with pyarrow, which is part of the Arrow installation.
+# https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
+# https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
+easyconfigs:
+  - hatchling-1.18.0-GCCcore-12.3.0.eb
+  - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
+  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.3-GCCcore-12.3.0.eb
+  - Python-3.11.5-GCCcore-13.2.0.eb

From 4ad271e4891e9c4e1c533e1a04505f16e505bf0a Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 19 Apr 2024 19:30:27 +0200
Subject: [PATCH 044/203] Update EESSI-extend-2023.06-easybuild.eb

---
 EESSI-extend-2023.06-easybuild.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 6d71693db8..7acd0f0d36 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -75,7 +75,7 @@ end
 setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
-setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "hooks.py"))
+setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
 if not ( isloaded("EasyBuild") ) then
     load("EasyBuild")
 end

From db81fd36358c0430bfc6d3ae2784b7e0958d097a Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 07:05:40 +0200
Subject: [PATCH 045/203] zen4-only {2023.06}[system] EasyBuild v4.9.1

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml        | 4 ++++
 1 file changed, 4 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml
new file mode 100644
index 0000000000..c5a08b5209
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - EasyBuild-4.9.1.eb:
+      options:
+        from-pr: 20299

From 8cb9547b0c2b1b3bd1736b57d754fa9cad01516b Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 14:10:55 +0200
Subject: [PATCH 046/203] make sure lmod cfg files exists early in build
 environment

---
 EESSI-install-software.sh | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 91effe4aba..7f67b883f2 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -147,6 +147,24 @@ else
   mkdir -p ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
+# if we run the script for the first time, e.g., to start building for a new
+#   stack, we need to ensure certain files are present in
+#   ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+# - .lmod/lmodrc.lua
+# - .lmod/SitePackage.lua
+_eessi_software_path=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+_lmod_cfg_dir=${_eessi_software_path}/.lmod
+_lmod_rc_file=${_lmod_cfg_dir}/lmodrc.lua
+if [ ! -f ${_lmod_rc_file} ]; then
+    command -V python3
+    python3 ${TOPDIR}/create_lmodrc.py ${_eessi_software_path}
+fi
+_lmod_sitepackage_file=${_lmod_cfg_dir}/SitePackage.lua
+if [ ! -f ${_lmod_sitepackage_file} ]; then
+    command -V python3
+    python3 ${TOPDIR}/create_lmodrc.py ${_eessi_software_path}
+fi
+
 # Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
 # $EESSI_SILENT - don't print any messages
 # $EESSI_BASIC_ENV - give a basic set of environment variables

From bde1b728c6c39cfffcffbf0480323d5b7348346a Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:16:44 +0200
Subject: [PATCH 047/203] Allow for default site installations, and
 configurable project and/or user installations

---
 EESSI-extend-2023.06-easybuild.eb | 93 ++++++++++++++++++++++++++++---
 init/Magic_Castle/bash            |  2 +-
 init/bash                         |  2 -
 init/eessi_environment_variables  |  2 -
 4 files changed, 87 insertions(+), 12 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 7acd0f0d36..3f9b62a494 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -14,10 +14,26 @@ description = """
  personal workstations and cloud infrastructure.
 
  This module allows you to extend EESSI using the same configuration for
- EasyBuild as EESSI itself uses. The default installation is the users
- home directory, but this can be overridden for a site installation (by setting
- EESSI_SITE_INSTALL) or for a direct installation under CVMFS (by setting
- EESSI_CVMFS_INSTALL). 
+ EasyBuild as EESSI itself uses. A number of environment variables control the
+ behaviour of the module:
+ - EESSI_USER_INSTALL can be set to a location to install modules for use by
+   the user only. The location must already exist on the filesystem.
+ - EESSI_PROJECT_INSTALL can be set to a location to install modules for use by
+   a project. The location must already exist on the filesystem and you should
+   ensure that the location has the correct Linux group and the SGID permission
+   is set on that directory (`chmod g+s $EESSI_PROJECT_INSTALL`) so that all
+   members of the group have permission to read and write installations.
+ - EESSI_SITE_INSTALL is either defined or not and cannot be used with another
+   environment variable. A site installation is done in a defined location and
+   any installations there are (by default) world readable.
+ - EESSI_CVMFS_INSTALL is either defined or not and cannot be used with another
+   environment variable. A CVMFS installation targets a defined location which
+   will be ingested into CVMFS and is only useful for CVMFS administrators.
+ - If none of the environment variables above are defined, an EESSI_USER_INSTALL
+   is assumed with a value of $HOME/EESSI
+ If both EESSI_USER_INSTALL and EESSI_PROJECT_INSTALL are defined, both sets of
+ installations are exposed, but new installations are created as user
+ installations.
 """
 
 toolchain = SYSTEM
@@ -27,6 +43,7 @@ local_deps_to_filter = "Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,get
 local_arch_specific_deps_to_filter = {'aarch64': ',yasm', 'x86_64': ''}
 local_deps_to_filter += local_arch_specific_deps_to_filter[ARCH]
 
+# Set the universal EasyBuild variables
 modextravars = {
     'EASYBUILD_FILTER_DEPS': local_deps_to_filter,
     'EASYBUILD_IGNORE_OSDEPS': '1',
@@ -46,6 +63,12 @@ modextravars = {
 # EASYBUILD_HOOKS=${EESSI_PREFIX}/init/easybuild/eb_hooks.py
 # EASYBUILD_INSTALLPATH=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR}
 # EASYBUILD_SOURCEPATH=${WORKDIR}/easybuild/sources:${EESSI_SOURCEPATH}
+#
+# And also some optional ones based on the kind of installation
+# EASYBUILD_SET_GID_BIT
+# EASYBUILD_GROUP_WRITABLE_INSTALLDIR
+# EASYBUILD_UMASK
+# EASYBUILD_STICKY_BIT
 modluafooter = """
 if (mode() == "load") then
   -- Use a working directory for temporary build files
@@ -58,11 +81,48 @@ working_dir = os.getenv("WORKING_DIR") or pathJoin("/tmp", os.getenv("USER"))
 sysroot = os.getenv("EESSI_EPREFIX")
 -- Use an installation prefix that we _should_ have write access to
 if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
+  -- Make sure no other EESSI install environment variables are set
+  if (os.getenv("EESSI_SITE_INSTALL") ~= nil) or (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") then
+    LmodError("You cannot use EESSI_CVMFS_INSTALL in combination with any other EESSI_*_INSTALL environment variables")
+  end
+  eessi_cvmfs_install = true
   easybuild_installpath = os.getenv("EESSI_SOFTWARE_PATH")
-elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then 
+elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then
+  -- Make sure no other EESSI install environment variables are set
+  if (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") then
+    LmodError("You cannot use EESSI_SITE_INSTALL in combination with any other EESSI_*_INSTALL environment variables")
+  end
   easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')
 else
-  easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
+  -- Deal with user and project installs
+  project_install = os.getenv("EESSI_PROJECT_INSTALL")
+  project_modulepath = nil
+  if (project_install ~= nil) then
+    -- Check the folder exists
+    if not isDir(project_install) then
+      LmodError("The location of EESSI_PROJECT_INSTALL (" .. project_install .. ") does not exist or is not a folder")
+    end
+    LmodMessage("Configuring for use of EESSI_PROJECT_INSTALL under " .. project_install)
+    easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), project_install)
+    project_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
+  end
+  user_install = os.getenv("EESSI_USER_INSTALL")
+  user_modulepath = nil
+  if (project_install == nil) then
+    if (user_install ~= nil) then
+      user_install = pathJoin(os.getenv("HOME"), "eessi")
+    else
+      -- Check the folder exists
+      if not isDir(user_install) then
+        LmodError("The location of EESSI_USER_INSTALL (" .. user_install .. ") does not exist or is not a folder")
+      end
+    end
+  end
+  if (user_install ~= nil) then
+    LmodMessage("Configuring for use of EESSI_USER_INSTALL under " .. user_install)
+    easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), user_install)
+    user_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
+  end
 end
 if (mode() == "load") then
   LmodMessage("-- To create installations for EESSI, you _must_ have write permissions to " .. easybuild_installpath)
@@ -71,11 +131,30 @@ if (mode() == "load") then
     LmodMessage("-- You may wish to configure a sources directory for EasyBuild (for example, via setting the environment variable EASYBUILD_SOURCEPATH) to allow you to reuse existing sources for packages.")
   end
 end
--- Set the relevant environment variables for EasyBuild
+-- Set the relevant universal environment variables for EasyBuild
 setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
 setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
+
+-- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
+if (user_modulepath ~= nil) then
+  setenv ("EASYBUILD_SET_GID_BIT", "1")
+  setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
+  setenv ("EASYBUILD_UMASK", "002")
+  setenv ("EASYBUILD_STICKY_BIT", "0")
+  -- configure MODULEPATH
+  if (project_modulepath ~= nil) then
+    prepend_path("MODULEPATH", project_modulepath)
+  end
+  prepend_path("MODULEPATH", user_modulepath)
+elseif (project_modulepath ~= nil) then
+  setenv ("EASYBUILD_UMASK", "022")
+  setenv ("EASYBUILD_STICKY_BIT", "1")
+  -- configure MODULEPATH
+  prepend_path("MODULEPATH", project_modulepath)
+end
+-- Make aure EasyBuild itself is loaded
 if not ( isloaded("EasyBuild") ) then
     load("EasyBuild")
 end
diff --git a/init/Magic_Castle/bash b/init/Magic_Castle/bash
index e6c7ff294c..bf625e7e7b 100644
--- a/init/Magic_Castle/bash
+++ b/init/Magic_Castle/bash
@@ -10,7 +10,7 @@ source $(dirname "$BASH_SOURCE")/../eessi_environment_variables
 
 # Provide a clean MODULEPATH
 export MODULEPATH_ROOT=$EESSI_MODULEPATH
-export MODULEPATH=$EESSI_USER_MODULEPATH:$EESSI_SITE_MODULEPATH:$EESSI_MODULEPATH
+export MODULEPATH=$EESSI_SITE_MODULEPATH:$EESSI_MODULEPATH
 
 # Extensions are too many, let's not print them by default (requires Lmod 8.4.12)
 export LMOD_AVAIL_EXTENSIONS=no
diff --git a/init/bash b/init/bash
index 3c6aad47f1..565c37cc65 100644
--- a/init/bash
+++ b/init/bash
@@ -28,8 +28,6 @@ if [ $? -eq 0 ]; then
     module use $EESSI_MODULEPATH
     echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
     module use $EESSI_SITE_MODULEPATH
-    echo "Prepending user path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
-    module use $EESSI_USER_MODULEPATH
 
     #show_msg ""
     #show_msg "*** Known problems in the ${EESSI_VERSION} software stack ***"
diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 5ae2c5c3c6..dbf01cc9e4 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -91,8 +91,6 @@ if [ -d $EESSI_PREFIX ]; then
             show_msg "Using ${EESSI_MODULEPATH} as the directory to be added to MODULEPATH."
             export EESSI_SITE_MODULEPATH=${EESSI_MODULEPATH/versions/host_injections}
             show_msg "Using ${EESSI_SITE_MODULEPATH} as the site extension directory to be added to MODULEPATH."
-            export EESSI_USER_MODULEPATH=${EESSI_MODULEPATH/${EESSI_CVMFS_REPO}/${HOME}\/eessi}
-            show_msg "Using ${EESSI_USER_MODULEPATH} as the user extension directory to be added to MODULEPATH."
           else
             error "EESSI module path at $EESSI_MODULEPATH not found!"
             false

From da9f206f216c70b8559bdd002235a754125aba2d Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 14:18:58 +0200
Subject: [PATCH 048/203] use create_lmodsitepackage.py

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 7f67b883f2..13e94fb72d 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -162,7 +162,7 @@ fi
 _lmod_sitepackage_file=${_lmod_cfg_dir}/SitePackage.lua
 if [ ! -f ${_lmod_sitepackage_file} ]; then
     command -V python3
-    python3 ${TOPDIR}/create_lmodrc.py ${_eessi_software_path}
+    python3 ${TOPDIR}/create_lmodsitepackage.py ${_eessi_software_path}
 fi
 
 # Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)

From 82f58b24ae4cb2ada19c79ad6c8e7cef2727ed56 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:30:57 +0200
Subject: [PATCH 049/203] Fix conditions

---
 EESSI-extend-2023.06-easybuild.eb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 3f9b62a494..0f0b4bc9f9 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -82,14 +82,14 @@ sysroot = os.getenv("EESSI_EPREFIX")
 -- Use an installation prefix that we _should_ have write access to
 if (os.getenv("EESSI_CVMFS_INSTALL") ~= nil) then
   -- Make sure no other EESSI install environment variables are set
-  if (os.getenv("EESSI_SITE_INSTALL") ~= nil) or (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") then
+  if ((os.getenv("EESSI_SITE_INSTALL") ~= nil) or (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") ~= nil)) then
     LmodError("You cannot use EESSI_CVMFS_INSTALL in combination with any other EESSI_*_INSTALL environment variables")
   end
   eessi_cvmfs_install = true
   easybuild_installpath = os.getenv("EESSI_SOFTWARE_PATH")
 elseif (os.getenv("EESSI_SITE_INSTALL") ~= nil) then
   -- Make sure no other EESSI install environment variables are set
-  if (os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") then
+  if ((os.getenv("EESSI_PROJECT_INSTALL") ~= nil) or (os.getenv("EESSI_USER_INSTALL") ~= nil)) then
     LmodError("You cannot use EESSI_SITE_INSTALL in combination with any other EESSI_*_INSTALL environment variables")
   end
   easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), 'versions', 'host_injections')

From 4ebfc2057d08056a978743f0e63ce630e5912fef Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:35:32 +0200
Subject: [PATCH 050/203] Fix condition

---
 EESSI-extend-2023.06-easybuild.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 0f0b4bc9f9..900d584720 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -109,7 +109,7 @@ else
   user_install = os.getenv("EESSI_USER_INSTALL")
   user_modulepath = nil
   if (project_install == nil) then
-    if (user_install ~= nil) then
+    if (user_install == nil) then
       user_install = pathJoin(os.getenv("HOME"), "eessi")
     else
       -- Check the folder exists

From 5c5899b3230c64cb40f57e91fa3521b74d83bdd2 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:39:06 +0200
Subject: [PATCH 051/203] Messages only on module load

---
 EESSI-extend-2023.06-easybuild.eb | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 900d584720..303abe0410 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -102,7 +102,9 @@ else
     if not isDir(project_install) then
       LmodError("The location of EESSI_PROJECT_INSTALL (" .. project_install .. ") does not exist or is not a folder")
     end
-    LmodMessage("Configuring for use of EESSI_PROJECT_INSTALL under " .. project_install)
+    if (mode() == "load") then
+      LmodMessage("Configuring for use of EESSI_PROJECT_INSTALL under " .. project_install)
+    end
     easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), project_install)
     project_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
   end
@@ -119,7 +121,9 @@ else
     end
   end
   if (user_install ~= nil) then
-    LmodMessage("Configuring for use of EESSI_USER_INSTALL under " .. user_install)
+    if (mode() == "load") then
+      LmodMessage("Configuring for use of EESSI_USER_INSTALL under " .. user_install)
+    end
     easybuild_installpath = string.gsub(os.getenv("EESSI_SOFTWARE_PATH"), os.getenv("EESSI_CVMFS_REPO"), user_install)
     user_modulepath = pathJoin(easybuild_installpath, 'modules', 'all')
   end

From c4cbcd8b9b6212c830e371aa3013eee8977ff776 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 14:41:02 +0200
Subject: [PATCH 052/203] skip CUDA install if no EasyBuild module is found

---
 EESSI-install-software.sh | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 13e94fb72d..2d401e40ce 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -221,10 +221,21 @@ ${TOPDIR}/install_scripts.sh --prefix ${EESSI_PREFIX}
 # Hardcode this for now, see if it works
 # TODO: We should make a nice yaml and loop over all CUDA versions in that yaml to figure out what to install
 # Allow skipping CUDA SDK install in e.g. CI environments
+# The install_cuda... script uses EasyBuild. So, we need to check if we have EB
+# or skip this step.
+module_avail_out=$TMPDIR/ml.out
+module avail 2>&1 | grep EasyBuild &> ${module_avail_out}
+if [[ $? -eq 0 ]]; then
+    echo_green ">> Found an EasyBuild module"
+else
+    echo_yellow ">> No EasyBuild module found: skipping step to install CUDA (see output in ${module_avail_out})"
+    export skip_cuda_install=True
+fi
+if
 if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
     ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
 else
-    echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed"
+    echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed OR no EasyBuild module was found"
 fi
 
 # Install drivers in host_injections

From eeb5537e4b8889cbbf183ffd17e4743961357f3c Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 20 Apr 2024 14:45:17 +0200
Subject: [PATCH 053/203] remove extra if

---
 EESSI-install-software.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 2d401e40ce..8a5789c2b2 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -231,7 +231,7 @@ else
     echo_yellow ">> No EasyBuild module found: skipping step to install CUDA (see output in ${module_avail_out})"
     export skip_cuda_install=True
 fi
-if
+
 if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
     ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
 else

From 8122bbd6bd7f6c44f4db9c955dcbd0bc7d736ad4 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Sat, 20 Apr 2024 14:56:52 +0200
Subject: [PATCH 054/203] fix location of settings

---
 EESSI-extend-2023.06-easybuild.eb | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 303abe0410..ddf56648b9 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -143,18 +143,18 @@ setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuil
 
 -- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
 if (user_modulepath ~= nil) then
-  setenv ("EASYBUILD_SET_GID_BIT", "1")
-  setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
-  setenv ("EASYBUILD_UMASK", "002")
-  setenv ("EASYBUILD_STICKY_BIT", "0")
+  setenv ("EASYBUILD_UMASK", "022")
+  setenv ("EASYBUILD_STICKY_BIT", "1")
   -- configure MODULEPATH
   if (project_modulepath ~= nil) then
     prepend_path("MODULEPATH", project_modulepath)
   end
   prepend_path("MODULEPATH", user_modulepath)
 elseif (project_modulepath ~= nil) then
-  setenv ("EASYBUILD_UMASK", "022")
-  setenv ("EASYBUILD_STICKY_BIT", "1")
+  setenv ("EASYBUILD_SET_GID_BIT", "1")
+  setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
+  setenv ("EASYBUILD_UMASK", "002")
+  setenv ("EASYBUILD_STICKY_BIT", "0")
   -- configure MODULEPATH
   prepend_path("MODULEPATH", project_modulepath)
 end

From 4d465e9996b61bfb2f2643710bf944ee88bdd355 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Sun, 21 Apr 2024 17:47:40 +0200
Subject: [PATCH 055/203] Add SAMtools-1.18-GCC-12.3.0

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3b51db3b11..ec5fd3c638 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
+  - SAMtools-1.18-GCC-12.3.0.eb

From 04c6f0ee56bde553968da02f7daba36cbb363d78 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 22 Apr 2024 09:30:11 +0200
Subject: [PATCH 056/203] Always check for dir existence when using
 EESSI_USER_INSTALL

---
 EESSI-extend-2023.06-easybuild.eb | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index ddf56648b9..c06087a940 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -110,15 +110,14 @@ else
   end
   user_install = os.getenv("EESSI_USER_INSTALL")
   user_modulepath = nil
-  if (project_install == nil) then
-    if (user_install == nil) then
-      user_install = pathJoin(os.getenv("HOME"), "eessi")
-    else
-      -- Check the folder exists
-      if not isDir(user_install) then
-        LmodError("The location of EESSI_USER_INSTALL (" .. user_install .. ") does not exist or is not a folder")
-      end
+  if (user_install ~= nil) then
+    -- Check the folder exists
+    if not isDir(user_install) then
+      LmodError("The location of EESSI_USER_INSTALL (" .. user_install .. ") does not exist or is not a folder")
     end
+  elseif (user_install == nil) and (project_install == nil) then
+    -- No need to check for existence when we use a HOME subdir
+    user_install = pathJoin(os.getenv("HOME"), "eessi")
   end
   if (user_install ~= nil) then
     if (mode() == "load") then

From 8cd5d844e872fe58efcdbb49e38689e656f3f9a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 22 Apr 2024 16:39:45 +0200
Subject: [PATCH 057/203] attempt to fix the hatchling reinstallation issue

---
 EESSI-remove-software.sh | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 446a156cb8..d8a6dae63e 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -114,6 +114,11 @@ if [ $EUID -eq 0 ]; then
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     rm -rf ${app_dir}
                     rm -rf ${app_module}
+                    # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
+                    # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
+                    if [ ! -n "$(dirname ${app_dir})" ]; then
+                        rmdir "$(dirname ${app_dir})"
+                    fi
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From 76ecccf629f6b4dda1b65e4ee1f3f2d9d9b9457c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 22 Apr 2024 17:13:37 +0200
Subject: [PATCH 058/203] use right if condition for checking if dir is empty

---
 EESSI-remove-software.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index d8a6dae63e..f3c4f9e618 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -116,8 +116,9 @@ if [ $EUID -eq 0 ]; then
                     rm -rf ${app_module}
                     # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
                     # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
-                    if [ ! -n "$(dirname ${app_dir})" ]; then
-                        rmdir "$(dirname ${app_dir})"
+                    app_dir_parent=$(dirname "${app_dir}")
+                    if [ ! -n "$(ls -A ${app_dir_parent})" ]; then
+                        rmdir "${app_dir_parent}"
                     fi
                 done
             else

From 1642621d1b47b804f689280d7c797824d1662a2c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 14:24:46 +0200
Subject: [PATCH 059/203] undo parent dir removal, workaround didn't work

---
 EESSI-remove-software.sh | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index f3c4f9e618..446a156cb8 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -114,12 +114,6 @@ if [ $EUID -eq 0 ]; then
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     rm -rf ${app_dir}
                     rm -rf ${app_module}
-                    # if the parent dir of this application is now empty, remove it too to work around a weird issue with the overlay
-                    # see https://github.com/EESSI/software-layer/pull/546#issuecomment-2067018216
-                    app_dir_parent=$(dirname "${app_dir}")
-                    if [ ! -n "$(ls -A ${app_dir_parent})" ]; then
-                        rmdir "${app_dir_parent}"
-                    fi
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From a5bf9d3da294fad127aef0dc972af323a0488077 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 14:26:25 +0200
Subject: [PATCH 060/203] only rebuild 2023a easyconfigs

---
 ...eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index 56ea7a46a1..76dd37e870 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,13 +1,10 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# all affected modules with EasyBuild 4.9.1.
+# the affected modules in the 2023a toolchain with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
   - hatchling-1.18.0-GCCcore-12.3.0.eb
-  - hatchling-1.18.0-GCCcore-13.2.0.eb
   - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
-  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
   - Python-3.11.3-GCCcore-12.3.0.eb
-  - Python-3.11.5-GCCcore-13.2.0.eb

From c4af218d2c7dd604f10cea7454d1f672b00498ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 15:04:02 +0200
Subject: [PATCH 061/203] only try 2023b versions

---
 ...4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index 76dd37e870..f3484a3486 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,10 +1,10 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# the affected modules in the 2023a toolchain with EasyBuild 4.9.1.
+# the affected modules in the 2023b toolchain with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
-  - hatchling-1.18.0-GCCcore-12.3.0.eb
-  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
-  - Python-3.11.3-GCCcore-12.3.0.eb
+  - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.5-GCCcore-13.2.0.eb

From 33cb74f5e2f4f63cd286e0d1b71818ccb1eca1a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 15:33:15 +0200
Subject: [PATCH 062/203] try adding write permissions instead of removing

---
 EESSI-remove-software.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 446a156cb8..1a488dcb67 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -112,8 +112,9 @@ if [ $EUID -eq 0 ]; then
                     app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
-                    rm -rf ${app_dir}
-                    rm -rf ${app_module}
+                    #rm -rf ${app_dir}
+                    #rm -rf ${app_module}
+                    chmod -R u+w ${app_dir} ${app_module}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From 1e92daf31bca8a879b2888cefc5156c76774f7ec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 26 Apr 2024 16:12:21 +0200
Subject: [PATCH 063/203] do remove the module to make sure it gets rebuilt

---
 EESSI-remove-software.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 1a488dcb67..9d82dd8aa6 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -113,8 +113,8 @@ if [ $EUID -eq 0 ]; then
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
                     #rm -rf ${app_dir}
-                    #rm -rf ${app_module}
-                    chmod -R u+w ${app_dir} ${app_module}
+                    rm -rf ${app_module}
+                    chmod -R u+w ${app_dir}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From d0229ccb3adb03eac5cdddde76858b00d20832bf Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Mon, 29 Apr 2024 14:40:50 +0200
Subject: [PATCH 064/203] Update create_lmodsitepackage.py

---
 create_lmodsitepackage.py | 22 +++++++++-------------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ce94a7e311..862902d80e 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -24,24 +24,20 @@
     -- e.g. /cvmfs/software.eessi.io/versions/2023.06
     local eessi_prefix = os.getenv("EESSI_PREFIX")
 
-    -- NOTE: exact paths for site and user extensions aren't final, so may need to be updated later.
-    -- See https://github.com/EESSI/software-layer/pull/371
-
-    -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
-    -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
-    local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
-    -- eessi_prefix_user_home is the prefix with user-extensions (i.e. additional modules)
-    -- to the offocial EESSI modules, e.g. $HOME/eessi/versions/2023.06
-    local eessi_prefix_user_home = string.gsub(eessi_prefix, os.getenv("EESSI_CVMFS_REPO"), pathJoin(os.getenv("HOME"), "eessi"))
     -- If EESSI_PREFIX wasn't defined, we cannot check if this module was from the EESSI environment
     -- In that case, we assume it isn't, otherwise EESSI_PREFIX would (probably) have been set
     if eessi_prefix == nil then
         return False
     else
-        -- Check if the full modulepath starts with the eessi_prefix_*
-        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or
-        string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil or
-        string.find(t.fn, "^" .. eessi_prefix_user_home) ~= nil
+        -- NOTE: exact paths for site so may need to be updated later.
+        -- See https://github.com/EESSI/software-layer/pull/371
+
+        -- eessi_prefix_host_injections is the prefix with site-extensions (i.e. additional modules)
+        -- to the official EESSI modules, e.g. /cvmfs/software.eessi.io/host_injections/2023.06
+        local eessi_prefix_host_injections = string.gsub(eessi_prefix, 'versions', 'host_injections')
+        
+       -- Check if the full modulepath starts with the eessi_prefix_*
+        return string.find(t.fn, "^" .. eessi_prefix) ~= nil or string.find(t.fn, "^" .. eessi_prefix_host_injections) ~= nil
     end
 end
 

From b6371d0e2766720a8fbccdb2ed322b5858dc834f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Apr 2024 11:06:30 +0200
Subject: [PATCH 065/203] use easyconfig PR for GROMACS 2024.1 that uses
 backported patch to fix problems with tests

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 3 ---
 .../2023.06/eessi-2023.06-eb-4.9.1-2023b.yml                  | 4 ++++
 2 files changed, 4 insertions(+), 3 deletions(-)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index d45ebfb9ba..86c5106c85 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -57,6 +57,3 @@ easyconfigs:
   - Qt5-5.15.13-GCCcore-13.2.0.eb:
       options:
         from-pr: 20201
-  - GROMACS-2024.1-foss-2023b.eb:
-      options:
-        from-pr: 20102
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
new file mode 100644
index 0000000000..1392fa2f5a
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -0,0 +1,4 @@
+easyconfigs:
+  - GROMACS-2024.1-foss-2023b.eb:
+      options:
+        from-pr: 20439

From b94fa6262a2845a03d58a9095b5da4fb84b8e710 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 15:13:53 +0200
Subject: [PATCH 066/203] restore easystack, rebuild all required versions

---
 ...eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
index f3484a3486..56ea7a46a1 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240419-eb-4.9.1-move-setuptools_scm-from-hatchling-to-Python.yml
@@ -1,10 +1,13 @@
 # 2024-04-19
 # Move setuptools_scm extension from hatchling to Python by rebuilding
-# the affected modules in the 2023b toolchain with EasyBuild 4.9.1.
+# all affected modules with EasyBuild 4.9.1.
 # This solves an issue with pyarrow, which is part of the Arrow installation.
 # https://github.com/easybuilders/easybuild-easyconfigs/pull/19777
 # https://github.com/easybuilders/easybuild-easyconfigs/issues/19849
 easyconfigs:
+  - hatchling-1.18.0-GCCcore-12.3.0.eb
   - hatchling-1.18.0-GCCcore-13.2.0.eb
+  - Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb
   - Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb
+  - Python-3.11.3-GCCcore-12.3.0.eb
   - Python-3.11.5-GCCcore-13.2.0.eb

From 66724f282e405579021811813721aaf79dc35a75 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 15:14:50 +0200
Subject: [PATCH 067/203] undo changes

---
 EESSI-remove-software.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/EESSI-remove-software.sh b/EESSI-remove-software.sh
index 9d82dd8aa6..446a156cb8 100755
--- a/EESSI-remove-software.sh
+++ b/EESSI-remove-software.sh
@@ -112,9 +112,8 @@ if [ $EUID -eq 0 ]; then
                     app_dir=${EASYBUILD_INSTALLPATH}/software/${app}
                     app_module=${EASYBUILD_INSTALLPATH}/modules/all/${app}.lua
                     echo_yellow "Removing ${app_dir} and ${app_module}..."
-                    #rm -rf ${app_dir}
+                    rm -rf ${app_dir}
                     rm -rf ${app_module}
-                    chmod -R u+w ${app_dir}
                 done
             else
                 fatal_error "Easystack file ${easystack_file} not found!"

From 01c49de45a802aafdc5d0bcf7cd577c0213cfac0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 30 Apr 2024 20:54:28 +0200
Subject: [PATCH 068/203] avoid building GROMACS 2024.1 with SVE on Neoverse
 V1, stick to Neon for now (cfr.
 https://gitlab.com/gromacs/gromacs/-/issues/5057)

---
 eb_hooks.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index 20b5f76cfc..f02c8db48c 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -335,6 +335,21 @@ def pre_configure_hook(self, *args, **kwargs):
         PRE_CONFIGURE_HOOKS[self.name](self, *args, **kwargs)
 
 
+def pre_configure_hook_gromacs(self, *args, **kwargs):
+    """
+    Pre-configure hook for GROMACS:
+    - avoid building with SVE instructions on Neoverse V1 as workaround for failing tests,
+      see https://gitlab.com/gromacs/gromacs/-/issues/5057 + https://gitlab.com/eessi/support/-/issues/47
+    """
+    if self.name == 'GROMACS':
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if LooseVersion(self.version) <= LooseVersion('2024.1') and cpu_target == CPU_TARGET_NEOVERSE_V1:
+            self.cfg.update('configopts', '-DGMX_SIMD=ARM_NEON_ASIMD')
+            print_msg("Avoiding use of SVE instructions for GROMACS %s by using ARM_NEON_ASIMD as GMX_SIMD value", self.version)
+    else:
+        raise EasyBuildError("GROMACS-specific hook triggered for non-GROMACS easyconfig?!")
+
+
 def pre_configure_hook_openblas_optarch_generic(self, *args, **kwargs):
     """
     Pre-configure hook for OpenBLAS: add DYNAMIC_ARCH=1 to build/test/install options when using --optarch=GENERIC
@@ -665,6 +680,7 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
+    'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,

From ac82cc840bfbdae0638438fb85f9a5004e020f2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 30 Apr 2024 21:21:32 +0200
Subject: [PATCH 069/203] move bioconductor to eb 4.9.1 file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml | 3 ---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 23d64036f1..44952e2765 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -71,6 +71,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
-      options:
-        from-pr: 20379
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index ec5fd3c638..e65747e4a5 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,3 +1,6 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
   - SAMtools-1.18-GCC-12.3.0.eb
+  - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
+      options:
+        from-pr: 20379

From 3eee364b47b4cae85aa675d020a7bd7a362b47f0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 1 May 2024 11:11:41 +0200
Subject: [PATCH 070/203] register known issue for GROMACS 2024.1 on
 neoverse_v1

---
 eessi-2023.06-known-issues.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml
index 011cb2dc08..2d1256354f 100644
--- a/eessi-2023.06-known-issues.yml
+++ b/eessi-2023.06-known-issues.yml
@@ -19,6 +19,9 @@
   - FFTW.MPI-3.3.10-gompi-2023b:
       - issue: https://github.com/EESSI/software-layer/issues/325
       - info: "Flaky FFTW tests, random failures"
+  - GROMACS-2024.1-foss-2023b:
+      - issue: https://github.com/EESSI/software-layer/issues/557
+      - info: "SVE disabled due to known bug which causes test failures"
   - Highway-1.0.3-GCCcore-12.2.0.eb:
     - issue: https://github.com/EESSI/software-layer/issues/469
     - info: "failing SVE test due to wrong expected value"

From fe0c7c534db6ce8d369aafaa84b4d0afaf7b3cc2 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Wed, 1 May 2024 17:14:47 +0200
Subject: [PATCH 071/203] Add Lmod hook for ESPReSso

---
 create_lmodsitepackage.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 0761f2cdf1..ef17448f0c 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+z#!/usr/bin/env python3
 #
 # Create SitePackage.lua configuration file for Lmod.
 #
@@ -150,10 +150,24 @@
     end
 end
 
+local function eessi_espresso_deprecated_warning(t)
+    local frameStk  = require("FrameStk"):singleton()
+    local mt        = frameStk:mt()
+    local simpleName = string.match(t.modFullName, "(.-)/")
+    local version = string.match(t.modFullName, "%d.%d.%d")
+    if simpleName == 'ESPResSo' and version == '4.2.1'
+        local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
+        advice = advice .. 'For details see https://github.com/espressomd/espresso/issues/4856\\n'
+        advice = advice .. 'Use version 4.2.1 at your own risk!\\nn'
+        LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
+        end
+end
+
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
     eessi_cuda_enabled_load_hook(t)
+    eessi_espresso_deprecated_warning(t)
 end
 
 

From 8f253276033d83d08ea770c1dd8ef946d6675d63 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Mon, 6 May 2024 09:36:04 +0200
Subject: [PATCH 072/203] Fix typo

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ef17448f0c..61b40c4252 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -1,4 +1,4 @@
-z#!/usr/bin/env python3
+#!/usr/bin/env python3
 #
 # Create SitePackage.lua configuration file for Lmod.
 #

From a9e8ae8192e916b3b6bcbfa6c47206a748d362b8 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 6 May 2024 16:06:22 +0200
Subject: [PATCH 073/203] Match name stub of files to CUDA allow list to ship

---
 .../2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml | 8 ++++++++
 eb_hooks.py                                               | 4 ++--
 2 files changed, 10 insertions(+), 2 deletions(-)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
new file mode 100644
index 0000000000..2a9daf7ba6
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
@@ -0,0 +1,8 @@
+# 2024.05.06
+# Original matching of files we could ship was not done correctly. We were
+# matching the basename for files (e.g., libcudart.so from libcudart.so.12)
+# rather than the name stub (libcudart)
+easyconfigs:
+  - CUDA-12.1.1.eb:
+      options:
+        accept-eula-for: CUDA
diff --git a/eb_hooks.py b/eb_hooks.py
index f02c8db48c..8b0a11b0ed 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -612,8 +612,8 @@ def post_sanitycheck_cuda(self, *args, **kwargs):
                 full_path = os.path.join(dir_path, filename)
                 # we only really care about real files, i.e. not symlinks
                 if not os.path.islink(full_path):
-                    # check if the current file is part of the allowlist
-                    basename = os.path.splitext(filename)[0]
+                    # check if the current file name stub is part of the allowlist
+                    basename = filename.split('.')[0]
                     if basename in allowlist:
                         self.log.debug("%s is found in allowlist, so keeping it: %s", basename, full_path)
                     else:

From 28e5e9c52005cb46855e7fe965cd41997e9c48d6 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Mon, 6 May 2024 18:49:34 +0200
Subject: [PATCH 074/203] Update
 2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml

---
 .../2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml        | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
index 2a9daf7ba6..058ab75e80 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/2024.05.06-eb-4.9.1-CUDA-12.1.1-ship-full-runtime.yml
@@ -2,6 +2,7 @@
 # Original matching of files we could ship was not done correctly. We were
 # matching the basename for files (e.g., libcudart.so from libcudart.so.12)
 # rather than the name stub (libcudart)
+# See https://github.com/EESSI/software-layer/pull/559
 easyconfigs:
   - CUDA-12.1.1.eb:
       options:

From cc91f3411df6010ff29247a94bfe9356e70cf342 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <trz42@users.noreply.github.com>
Date: Tue, 7 May 2024 10:50:48 +0200
Subject: [PATCH 075/203] fix tiny typo

---
 EESSI-extend-2023.06-easybuild.eb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index c06087a940..e6e540bf45 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -157,7 +157,7 @@ elseif (project_modulepath ~= nil) then
   -- configure MODULEPATH
   prepend_path("MODULEPATH", project_modulepath)
 end
--- Make aure EasyBuild itself is loaded
+-- Make sure EasyBuild itself is loaded
 if not ( isloaded("EasyBuild") ) then
     load("EasyBuild")
 end

From 38a0581480ac284c2802e5e63a0541fae31f786a Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 7 May 2024 10:55:28 +0200
Subject: [PATCH 076/203] use eessi.io/docs and system easystack file

---
 EESSI-extend-2023.06-easybuild.eb                               | 2 +-
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml               | 1 +
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml  | 1 -
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index e6e540bf45..241cde264b 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -5,7 +5,7 @@ version = '2023.06'
 # May have different ways to extend EESSI in future (manually, other tools,...)
 versionsuffix = '-easybuild'
 
-homepage = 'https://eessi.github.io/docs/'
+homepage = 'https://eessi.io/docs/'
 
 description = """
  The goal of the European Environment for Scientific Software Installations
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index c5a08b5209..46ac979719 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - EasyBuild-4.9.1.eb:
       options:
         from-pr: 20299
+  - EESSI-extend-2023.06-easybuild.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index b7d4370b84..3b51db3b11 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,3 +1,2 @@
 easyconfigs:
   - ncdu-1.18-GCC-12.3.0.eb
-  - EESSI-extend-2023.06-easybuild.eb 

From 0ff23347d31156ed4501f49f1a7f187f51257ecf Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Tue, 7 May 2024 12:05:38 +0200
Subject: [PATCH 077/203] Update EESSI-extend-2023.06-easybuild.eb

---
 EESSI-extend-2023.06-easybuild.eb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 241cde264b..76e96766f9 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -139,9 +139,11 @@ setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
 setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
+setenv ("EASYBUILD_UMASK", "002")
 
 -- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
 if (user_modulepath ~= nil) then
+  -- Use a more restrictive umask for this case
   setenv ("EASYBUILD_UMASK", "022")
   setenv ("EASYBUILD_STICKY_BIT", "1")
   -- configure MODULEPATH
@@ -152,7 +154,6 @@ if (user_modulepath ~= nil) then
 elseif (project_modulepath ~= nil) then
   setenv ("EASYBUILD_SET_GID_BIT", "1")
   setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
-  setenv ("EASYBUILD_UMASK", "002")
   setenv ("EASYBUILD_STICKY_BIT", "0")
   -- configure MODULEPATH
   prepend_path("MODULEPATH", project_modulepath)

From 6682c7d36d54641aeb6a5cd9eeaf2cd981ef89d7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Tue, 7 May 2024 13:32:25 +0200
Subject: [PATCH 078/203] move OSU-Micro-Benchmarks 2023b to 2023b easystack

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 -
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 44952e2765..8f5608d881 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -35,7 +35,6 @@ easyconfigs:
         from-pr: 19996
   - dask-2023.9.2-foss-2023a.eb
   - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb
-  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
   - JupyterNotebook-7.0.2-GCCcore-12.3.0.eb
   - ImageMagick-7.1.1-15-GCCcore-12.3.0.eb:
       options:
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 86c5106c85..15c02951d7 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -57,3 +57,4 @@ easyconfigs:
   - Qt5-5.15.13-GCCcore-13.2.0.eb:
       options:
         from-pr: 20201
+  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb

From 298159e516db7c696b12ca57bf51a5328588ebf9 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 7 May 2024 14:27:24 +0200
Subject: [PATCH 079/203] bumping scorecard-action version to 2.3.1

---
 .github/workflows/scorecards.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
index dc18fd584a..7eff557094 100644
--- a/.github/workflows/scorecards.yml
+++ b/.github/workflows/scorecards.yml
@@ -40,7 +40,7 @@ jobs:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@99c53751e09b9529366343771cc321ec74e9bd3d # v2.0.6
+        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
         with:
           results_file: results.sarif
           results_format: sarif

From 462adc5cdd5c3f2255f0275e45a7f6a82da584bf Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 May 2024 15:28:38 +0200
Subject: [PATCH 080/203] {2023.06,zen4} foss/2023a

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml               | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
new file mode 100644
index 0000000000..c821df1afb
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - foss-2023a.eb

From 06f88dbbc5f90654fb1d48c888a9575cb768be59 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 May 2024 18:15:55 +0200
Subject: [PATCH 081/203] stick to x86_64/amd/zen3 when AMD Genoa (Zen4) is
 detected, until optimized software installations are available for Zen4

---
 init/eessi_environment_variables | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 5450b2bfb4..e7f8f2faaa 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -48,6 +48,14 @@ if [ -d $EESSI_PREFIX ]; then
     fi
     if [ ! -z $EESSI_SOFTWARE_SUBDIR ]; then
 
+        # use x86_64/amd/zen3 for now when AMD Genoa (Zen4) CPU is detected,
+        # since optimized software installations for Zen4 are a work-in-progress,
+        # see https://gitlab.com/eessi/support/-/issues/37
+        if [[ "${EESSI_SOFTWARE_SUBDIR}" == "x86_64/amd/zen4" ]]; then
+            export EESSI_SOFTWARE_SUBDIR="x86_64/amd/zen3"
+            echo -e "\e[33mSticking to ${EESSI_SOFTWARE_SUBDIR} for now, since optimized installations for AMD Genoa (Zen4) are a work in progress, see https://gitlab.com/eessi/support/-/issues/37 for more information\e[0m"
+        fi
+
         show_msg "Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory."
         export EESSI_SOFTWARE_PATH=$EESSI_PREFIX/software/$EESSI_OS_TYPE/$EESSI_SOFTWARE_SUBDIR
 

From 8cce17c83ba3230774a56de285de3fe369792595 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 May 2024 19:19:54 +0200
Subject: [PATCH 082/203] relax check for existence of software overlay dir in
 script to create tarball to deploy

---
 create_tarball.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 2d77acfc43..0a7669f73f 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -28,7 +28,7 @@ fi
 
 overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
 
-software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}/software/${os}/${cpu_arch_subdir}"
+software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then
     echo "Software directory overlay ${software_dir_overlay} does not exist?!" >&2
     exit 3

From 39dddf641af1d59498076154c77c9de500451d9d Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 7 May 2024 19:29:25 +0200
Subject: [PATCH 083/203] Update init/bash

Co-authored-by: Kenneth Hoste <kenneth.hoste@ugent.be>
---
 init/bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/bash b/init/bash
index 565c37cc65..655260841d 100644
--- a/init/bash
+++ b/init/bash
@@ -26,7 +26,7 @@ if [ $? -eq 0 ]; then
     # prepend location of modules for EESSI software stack to $MODULEPATH
     show_msg "Prepending $EESSI_MODULEPATH to \$MODULEPATH..."
     module use $EESSI_MODULEPATH
-    echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..." >> $output
+    echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..."
     module use $EESSI_SITE_MODULEPATH
 
     #show_msg ""

From 500b1de874a93e523ec308721f85a5824b8260e1 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Tue, 7 May 2024 19:32:03 +0200
Subject: [PATCH 084/203] Update init/bash
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Thomas Röblitz <trz42@users.noreply.github.com>
---
 init/bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/bash b/init/bash
index 655260841d..93471e075e 100644
--- a/init/bash
+++ b/init/bash
@@ -26,7 +26,7 @@ if [ $? -eq 0 ]; then
     # prepend location of modules for EESSI software stack to $MODULEPATH
     show_msg "Prepending $EESSI_MODULEPATH to \$MODULEPATH..."
     module use $EESSI_MODULEPATH
-    echo "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..."
+    show_msg "Prepending site path $EESSI_SITE_MODULEPATH to \$MODULEPATH..."
     module use $EESSI_SITE_MODULEPATH
 
     #show_msg ""

From 999cbd359528edf4feedd822859b9e2d0f922d9b Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 7 May 2024 19:45:16 +0200
Subject: [PATCH 085/203] relax check or tarball is not created unless also
 software was built

---
 create_tarball.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 2d77acfc43..0a7669f73f 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -28,7 +28,7 @@ fi
 
 overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
 
-software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}/software/${os}/${cpu_arch_subdir}"
+software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then
     echo "Software directory overlay ${software_dir_overlay} does not exist?!" >&2
     exit 3

From 78b4e13a230b0b95cb4f41df013bf016c9b286b6 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 7 May 2024 15:30:44 +0200
Subject: [PATCH 086/203] {2023.06,zen4} foss/2023b

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml               | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
new file mode 100644
index 0000000000..75dc4e6602
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - foss-2023b.eb

From ac3e74795c735eb99acf93e0fe9c024d6d81291a Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 11:16:49 +0200
Subject: [PATCH 087/203] Only correct the Zen4 software subdirectory if it has
 not been overridden

---
 init/eessi_environment_variables | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 71e70ee071..78851a9c95 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -52,8 +52,10 @@ if [ -d $EESSI_PREFIX ]; then
         # since optimized software installations for Zen4 are a work-in-progress,
         # see https://gitlab.com/eessi/support/-/issues/37
         if [[ "${EESSI_SOFTWARE_SUBDIR}" == "x86_64/amd/zen4" ]]; then
-            export EESSI_SOFTWARE_SUBDIR="x86_64/amd/zen3"
-            echo -e "\e[33mSticking to ${EESSI_SOFTWARE_SUBDIR} for now, since optimized installations for AMD Genoa (Zen4) are a work in progress, see https://gitlab.com/eessi/support/-/issues/37 for more information\e[0m"
+            if [ -z $EESSI_SOFTWARE_SUBDIR_OVERRIDE ]; then
+                export EESSI_SOFTWARE_SUBDIR="x86_64/amd/zen3"
+                echo -e "\e[33mSticking to ${EESSI_SOFTWARE_SUBDIR} for now, since optimized installations for AMD Genoa (Zen4) are a work in progress, see https://gitlab.com/eessi/support/-/issues/37 for more information\e[0m"
+            fi
         fi
 
         show_msg "Using ${EESSI_SOFTWARE_SUBDIR} as software subdirectory."

From d043d867a3dccce1b978ee2531923e970b6e6176 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 12:10:19 +0200
Subject: [PATCH 088/203] Add `psm2` to filtered dependencies for `2023.06`

`PSM2` was introduced as a dependency of `libfabric` in https://github.com/easybuilders/easybuild-easyconfigs/pull/20501.

We already have PSM2 in the compat layer, so we can filter this dependency out, but longer term we probably actually want it since it should be built with accelerator support.
---
 configure_easybuild | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/configure_easybuild b/configure_easybuild
index c67b879cf3..60e3744603 100644
--- a/configure_easybuild
+++ b/configure_easybuild
@@ -32,6 +32,12 @@ if [[ "$EESSI_CPU_FAMILY" == "aarch64" ]]; then
     DEPS_TO_FILTER="${DEPS_TO_FILTER},Yasm"
 fi
 
+# Version 23.06 of EESSI ships PSM2 in the compat layer, so we can filter this out while retaining support for OFA fabric
+# (longer term this is probably not the right move as PSM2 should be configured with accelerator support, hence the restricted version)
+if [[ "$EESSI_VERSION" == "2023.06" ]]; then
+    DEPS_TO_FILTER="${DEPS_TO_FILTER},psm2"
+fi
+
 export EASYBUILD_FILTER_DEPS=$DEPS_TO_FILTER
 
 export EASYBUILD_MODULE_EXTENSIONS=1

From ec2e8bdf04456b85bf9dae3a46ea132acba90df3 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 12:14:20 +0200
Subject: [PATCH 089/203] Update configure_easybuild

---
 configure_easybuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/configure_easybuild b/configure_easybuild
index 60e3744603..ed3e651a4c 100644
--- a/configure_easybuild
+++ b/configure_easybuild
@@ -35,7 +35,7 @@ fi
 # Version 23.06 of EESSI ships PSM2 in the compat layer, so we can filter this out while retaining support for OFA fabric
 # (longer term this is probably not the right move as PSM2 should be configured with accelerator support, hence the restricted version)
 if [[ "$EESSI_VERSION" == "2023.06" ]]; then
-    DEPS_TO_FILTER="${DEPS_TO_FILTER},psm2"
+    DEPS_TO_FILTER="${DEPS_TO_FILTER},PSM2"
 fi
 
 export EASYBUILD_FILTER_DEPS=$DEPS_TO_FILTER

From 3cdb7b2653336dd707b65197bf578f4012a6b0ff Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 12:43:43 +0200
Subject: [PATCH 090/203] Add a rebuild of GROMACS

---
 ...240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml | 11 +++++++++++
 1 file changed, 11 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
new file mode 100644
index 0000000000..e767c63f6e
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
@@ -0,0 +1,11 @@
+# 2024.05.15
+# Originally shipped version forgot to bump the gmxapi version and source
+# tarball, it was still using an older version from the 2023.3 tarball. Looking
+# at https://gitlab.com/gromacs/gromacs/-/blob/v2024.1/python_packaging/gmxapi/src/gmxapi/version.py?ref_type=tags#L68,
+# the 2024.1 release includes gmxapi 0.5.0.
+#
+# See https://github.com/easybuilders/easybuild-easyconfigs/pull/20522
+easyconfigs:
+  - GROMACS-2024.1-foss-2023b.eb:
+      options:
+        from-pr: 20522

From fb329a4bfe535cffc8d70958fc65fa0072180416 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 12:57:36 +0200
Subject: [PATCH 091/203] Also add new dependency on scikit-build-core

---
 .../20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml     | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
index e767c63f6e..4eca76fd66 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
@@ -4,8 +4,13 @@
 # at https://gitlab.com/gromacs/gromacs/-/blob/v2024.1/python_packaging/gmxapi/src/gmxapi/version.py?ref_type=tags#L68,
 # the 2024.1 release includes gmxapi 0.5.0.
 #
+# This also introduced a new build dependency on scikit-build-core for GROMACS
+#
 # See https://github.com/easybuilders/easybuild-easyconfigs/pull/20522
 easyconfigs:
+  - scikit-build-core-0.9.3-GCCcore-13.2.0.eb:
+      options:
+        from-pr: 20526
   - GROMACS-2024.1-foss-2023b.eb:
       options:
         from-pr: 20522

From 792ea3ebdbf011665f3b673ecd974b93e961f8c1 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 15:01:57 +0200
Subject: [PATCH 092/203] Use from-commit for merged PRs

---
 .../20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
index 4eca76fd66..93d87bbcf3 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
@@ -10,7 +10,7 @@
 easyconfigs:
   - scikit-build-core-0.9.3-GCCcore-13.2.0.eb:
       options:
-        from-pr: 20526
+        from-commit: 61d07bff09afe63cfe1ae35dc58a0c8be01eed62
   - GROMACS-2024.1-foss-2023b.eb:
       options:
-        from-pr: 20522
+        from-commit: a0a467a88506c765a93a96b20d7a8fcb01d46b24

From 6cf63359d04a7662ae3aa021763765bf01d5f8c7 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 16:06:35 +0200
Subject: [PATCH 093/203] Allow EESSI-extend as a loaded module when using
 EasyBuild

---
 EESSI-extend-2023.06-easybuild.eb | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 76e96766f9..42defbacc8 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -139,12 +139,17 @@ setenv ("EASYBUILD_SYSROOT", sysroot)
 setenv ("EASYBUILD_PREFIX", pathJoin(working_dir, "easybuild"))
 setenv ("EASYBUILD_INSTALLPATH", easybuild_installpath)
 setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuild", "eb_hooks.py"))
-setenv ("EASYBUILD_UMASK", "002")
+
+-- Make sure to use the general umask that allows a global read
+setenv ("EASYBUILD_UMASK", "022")
+
+-- All this module to be loaded when running EasyBuild
+setenv ("EASYBUILD_ALLOW_LOADED_MODULES", "EasyBuild,EESSI-extend")
 
 -- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
 if (user_modulepath ~= nil) then
   -- Use a more restrictive umask for this case
-  setenv ("EASYBUILD_UMASK", "022")
+  setenv ("EASYBUILD_UMASK", "077")
   setenv ("EASYBUILD_STICKY_BIT", "1")
   -- configure MODULEPATH
   if (project_modulepath ~= nil) then
@@ -155,6 +160,7 @@ elseif (project_modulepath ~= nil) then
   setenv ("EASYBUILD_SET_GID_BIT", "1")
   setenv ("EASYBUILD_GROUP_WRITABLE_INSTALLDIR", "1")
   setenv ("EASYBUILD_STICKY_BIT", "0")
+  setenv ("EASYBUILD_UMASK", "002")
   -- configure MODULEPATH
   prepend_path("MODULEPATH", project_modulepath)
 end

From fbdb8461fca7dbb28add02b128877d5b59bb24fc Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 16:11:17 +0200
Subject: [PATCH 094/203] Rebuild the module

---
 .../20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml         | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
new file mode 100644
index 0000000000..5cf2bd6b9d
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
@@ -0,0 +1,5 @@
+# 2024.05.15
+# The module is an EasyBuil created module and therefore needs to be an allowed
+# module when running EasyBuild
+easyconfigs:
+  - EESSI-extend-2023.06-easybuild.eb 

From 375bf370137a33b748ed649625e532d836a962d5 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 16:17:53 +0200
Subject: [PATCH 095/203] Update
 20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml

Issues seen when trying to use `from-commit` in https://github.com/EESSI/software-layer/pull/577
---
 .../20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml    | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
index 93d87bbcf3..eacfad7079 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240515-eb-4.9.1-GROMACS-correct-gmxapi-version.yml
@@ -10,7 +10,9 @@
 easyconfigs:
   - scikit-build-core-0.9.3-GCCcore-13.2.0.eb:
       options:
-        from-commit: 61d07bff09afe63cfe1ae35dc58a0c8be01eed62
+        # from-commit: 61d07bff09afe63cfe1ae35dc58a0c8be01eed62
+        from-pr: 20526
   - GROMACS-2024.1-foss-2023b.eb:
       options:
-        from-commit: a0a467a88506c765a93a96b20d7a8fcb01d46b24
+        # from-commit: a0a467a88506c765a93a96b20d7a8fcb01d46b24
+        from-pr: 20522

From 2b30e1f2cca0a60b1dbf9ee0680aa48ba3f260da Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Wed, 15 May 2024 17:09:18 +0200
Subject: [PATCH 096/203] Allow overriding the Lmod GPU driver check

---
 EESSI-install-software.sh | 3 +++
 create_lmodsitepackage.py | 9 ++++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 8a5789c2b2..40f0ed8c3d 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -243,6 +243,9 @@ fi
 #       if not, an error is produced, and the bot flags the whole build as failed (even when not installing GPU software)
 # ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
 
+# Don't run the Lmod GPU driver check when doing builds (may not have a GPU, and it's not relevant for vanilla builds anyway)
+export EESSI_OVERRIDE_GPU_CHECK=1 
+
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 
 if [ -z "${changed_easystacks}" ]; then
diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 47aa20e51e..816302f7fc 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -131,8 +131,9 @@
     end
     -- when loading CUDA enabled modules check if the necessary driver libraries are accessible to the EESSI linker,
     -- otherwise, refuse to load the requested module and print error message
-    local haveGpu = mt:haveProperty(simpleName,"arch","gpu")
-    if haveGpu then
+    local checkGpu = mt:haveProperty(simpleName,"arch","gpu")
+    local overrideGpuCheck = os.getenv("EESSI_OVERRIDE_GPU_CHECK")
+    if checkGpu and (overrideGpuCheck == nil) then
         local arch = os.getenv("EESSI_CPU_FAMILY") or ""
         local cudaVersionFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/cuda_version.txt"
         local cudaDriverFile = "/cvmfs/software.eessi.io/host_injections/nvidia/" .. arch .. "/latest/libcuda.so"
@@ -141,7 +142,9 @@
         if not (cudaDriverExists or singularityCudaExists)  then
             local advice = "which relies on the CUDA runtime environment and driver libraries. "
             advice = advice .. "In order to be able to use the module, you will need "
-            advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system.\\n"
+            advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system. You can "
+            advice = advice .. "override this check by setting the environment variable EESSI_OVERRIDE_GPU_CHECK but "
+            advice = advice .. "the loaded application will not be able to execute on your system.\\n"
             advice = advice .. refer_to_docs
             LmodError("\\nYou requested to load ", simpleName, " ", advice)
         else

From 705030d6aca132df57e5432aa6ada663f04d682d Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 16 May 2024 12:48:25 +0200
Subject: [PATCH 097/203] use directory of called script as base dir for other
 scripts

---
 bot/inspect.sh | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/bot/inspect.sh b/bot/inspect.sh
index 9d1fa87e1f..f0589cd827 100755
--- a/bot/inspect.sh
+++ b/bot/inspect.sh
@@ -27,6 +27,8 @@
 # stop as soon as something fails
 set -e
 
+SCRIPT_DIR=$(dirname $(realpath $BASH_SOURCE))
+
 display_help() {
   echo "usage: $0 [OPTIONS]"
   echo "  -h | --help            -  display this usage information"
@@ -81,8 +83,8 @@ done
 set -- "${POSITIONAL_ARGS[@]}"
 
 # source utils.sh and cfg_files.sh
-source scripts/utils.sh
-source scripts/cfg_files.sh
+source ${SCRIPT_DIR}/../scripts/utils.sh
+source ${SCRIPT_DIR}/../scripts/cfg_files.sh
 
 if [[ -z ${resume_tgz} ]]; then
     echo_red "path to tarball for resuming build job is missing"
@@ -432,14 +434,14 @@ echo "Executing command to start interactive session to inspect build job:"
 # These initializations are combined into a single script that is executed when
 # the shell in startprefix is started. We set the env variable BASH_ENV here.
 if [[ -z ${run_in_prefix} ]]; then
-    echo "./eessi_container.sh ${CMDLINE_ARGS[@]}"
+    echo "${SCRIPT_DIR}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
     echo "                     -- ${EESSI_COMPAT_LAYER_DIR}/startprefix"
-    ./eessi_container.sh "${CMDLINE_ARGS[@]}" \
+    ${SCRIPT_DIR}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
                      -- ${EESSI_COMPAT_LAYER_DIR}/startprefix
 else
-    echo "./eessi_container.sh ${CMDLINE_ARGS[@]}"
+    echo "${SCRIPT_DIR}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
     echo "                     -- ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< ${run_in_prefix}"
-    ./eessi_container.sh "${CMDLINE_ARGS[@]}" \
+    ${SCRIPT_DIR}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
                      -- ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< ${run_in_prefix}
 fi
 

From 082722eb6cb9028567f2b5af3bbb1c12d9fc5c15 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 16 May 2024 17:17:01 +0200
Subject: [PATCH 098/203] use single variable for directory containing script;
 use lowercase var name

---
 bot/inspect.sh | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/bot/inspect.sh b/bot/inspect.sh
index f0589cd827..533968bffc 100755
--- a/bot/inspect.sh
+++ b/bot/inspect.sh
@@ -27,7 +27,9 @@
 # stop as soon as something fails
 set -e
 
-SCRIPT_DIR=$(dirname $(realpath $BASH_SOURCE))
+# script_dir is the directory that contains THIS (inspect.sh) script, usually
+# stored in the directory '.../bot'
+script_dir=$(dirname $(realpath $BASH_SOURCE))
 
 display_help() {
   echo "usage: $0 [OPTIONS]"
@@ -83,8 +85,8 @@ done
 set -- "${POSITIONAL_ARGS[@]}"
 
 # source utils.sh and cfg_files.sh
-source ${SCRIPT_DIR}/../scripts/utils.sh
-source ${SCRIPT_DIR}/../scripts/cfg_files.sh
+source ${script_dir}/../scripts/utils.sh
+source ${script_dir}/../scripts/cfg_files.sh
 
 if [[ -z ${resume_tgz} ]]; then
     echo_red "path to tarball for resuming build job is missing"
@@ -257,10 +259,8 @@ CMDLINE_ARGS+=("--storage" "${JOB_STORAGE}")
 
 # make sure some environment settings are available inside the shell started via
 # startprefix
-base_dir=$(dirname $(realpath $0))
-# base_dir of inspect.sh script is '.../bot', 'init' dir is at the same level
 # TODO better use script from tarball???
-source ${base_dir}/../init/eessi_defaults
+source ${script_dir}/../init/eessi_defaults
 
 if [ -z $EESSI_VERSION ]; then
     echo "ERROR: \$EESSI_VERSION must be set!" >&2
@@ -434,14 +434,14 @@ echo "Executing command to start interactive session to inspect build job:"
 # These initializations are combined into a single script that is executed when
 # the shell in startprefix is started. We set the env variable BASH_ENV here.
 if [[ -z ${run_in_prefix} ]]; then
-    echo "${SCRIPT_DIR}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
+    echo "${script_dir}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
     echo "                     -- ${EESSI_COMPAT_LAYER_DIR}/startprefix"
-    ${SCRIPT_DIR}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
+    ${script_dir}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
                      -- ${EESSI_COMPAT_LAYER_DIR}/startprefix
 else
-    echo "${SCRIPT_DIR}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
+    echo "${script_dir}/../eessi_container.sh ${CMDLINE_ARGS[@]}"
     echo "                     -- ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< ${run_in_prefix}"
-    ${SCRIPT_DIR}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
+    ${script_dir}/../eessi_container.sh "${CMDLINE_ARGS[@]}" \
                      -- ${EESSI_COMPAT_LAYER_DIR}/startprefix <<< ${run_in_prefix}
 fi
 

From 9fd84f95e19477a75d781cbf1590fd0068ee7587 Mon Sep 17 00:00:00 2001
From: Neves-P <p.m.santos.neves@rug.nl>
Date: Fri, 17 May 2024 20:15:44 +0200
Subject: [PATCH 099/203] Fix syntax errors

---
 create_lmodsitepackage.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 61b40c4252..4817f14181 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -155,12 +155,12 @@
     local mt        = frameStk:mt()
     local simpleName = string.match(t.modFullName, "(.-)/")
     local version = string.match(t.modFullName, "%d.%d.%d")
-    if simpleName == 'ESPResSo' and version == '4.2.1'
+    if simpleName == 'ESPResSo' and version == '4.2.1' then
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
         advice = advice .. 'For details see https://github.com/espressomd/espresso/issues/4856\\n'
         advice = advice .. 'Use version 4.2.1 at your own risk!\\nn'
         LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
-        end
+    end
 end
 
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod

From 9d8dbb9e105b8c325a267cb3e7f1504dccc82d94 Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 14:09:04 +0000
Subject: [PATCH 100/203] add (empty) RISC-V spec file

---
 init/arch_specs/eessi_arch_riscv.spec | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 init/arch_specs/eessi_arch_riscv.spec

diff --git a/init/arch_specs/eessi_arch_riscv.spec b/init/arch_specs/eessi_arch_riscv.spec
new file mode 100644
index 0000000000..430dd2e72d
--- /dev/null
+++ b/init/arch_specs/eessi_arch_riscv.spec
@@ -0,0 +1 @@
+# Software path in EESSI 	| Vendor ID 	| List of defining CPU features

From 19d14eeb913fedd61604e1fc44675dbcc2a11799 Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 14:09:35 +0000
Subject: [PATCH 101/203] add initial riscv64 support

---
 init/eessi_archdetect.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/init/eessi_archdetect.sh b/init/eessi_archdetect.sh
index 58b79b0f2a..e89bc75e13 100755
--- a/init/eessi_archdetect.sh
+++ b/init/eessi_archdetect.sh
@@ -85,6 +85,7 @@ cpupath(){
         "x86_64") local spec_file="eessi_arch_x86.spec";;
         "aarch64") local spec_file="eessi_arch_arm.spec";;
         "ppc64le") local spec_file="eessi_arch_ppc.spec";;
+        "riscv64") local spec_file="eessi_arch_riscv.spec";;
         *) log "ERROR" "cpupath: Unsupported CPU architecture $machine_type"
     esac
     # spec files are located in a subfolder with this script

From 02683fb5325fc7c599e4bd847a927a4447894e0c Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 14:09:56 +0000
Subject: [PATCH 102/203] use different defaults for RISC-V

---
 init/eessi_defaults | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/init/eessi_defaults b/init/eessi_defaults
index d1779a36ae..c1ce82d1ce 100644
--- a/init/eessi_defaults
+++ b/init/eessi_defaults
@@ -8,8 +8,20 @@
 # license: GPLv2
 #
 
-export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/software.eessi.io}"
-export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=2023.06}"
+# use different defaults for RISC-V, as we want to redirect to the riscv.eessi.io repo
+if [[ $(uname -m) == "riscv64" ]]; then
+    export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/riscv.eessi.io}"
+    export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=20240402}"
+    if [[ ! -v EESSI_SILENT ]]; then
+        echo "RISC-V architecture detected, but there is no RISC-V support yet in the production repository."
+        echo "Automatically switching to version ${EESSI_VERSION} of the RISC-V development repository ${EESSI_CVMFS_REPO}."
+        echo "For more details about this repository, see https://www.eessi.io/docs/repositories/riscv.eessi.io/."
+        echo ""
+    fi
+else
+    export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/software.eessi.io}"
+    export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=2023.06}"
+fi
 # use archdetect by default, unless otherwise specified
 export EESSI_USE_ARCHDETECT="${EESSI_USE_ARCHDETECT:=1}"
 export EESSI_USE_ARCHSPEC="${EESSI_USE_ARCHSPEC:=0}"

From 243620e734d1514d9104c85d8c0b835007c9dfd7 Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 14:10:23 +0000
Subject: [PATCH 103/203] update comment about CPU families: add RISC-V, remove
 POWER

---
 init/minimal_eessi_env | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/init/minimal_eessi_env b/init/minimal_eessi_env
index 5b3562068d..03b337ccf7 100644
--- a/init/minimal_eessi_env
+++ b/init/minimal_eessi_env
@@ -16,7 +16,7 @@ else
     export EESSI_OS_TYPE='macos'
 fi
 
-# aarch64 (Arm 64-bit), ppc64le (POWER 64-bit), x86_64 (x86 64-bit)
+# aarch64 (Arm 64-bit), riscv64 (RISC-V 64-bit), x86_64 (x86 64-bit)
 export EESSI_CPU_FAMILY=$(uname -m)
 
 # set $EPREFIX since that is basically a standard in Gentoo Prefix

From 84036fa5a262712ccde2bd0bdb9ee5b701e87e20 Mon Sep 17 00:00:00 2001
From: Bob Droge <b.e.droge@rug.nl>
Date: Tue, 21 May 2024 21:06:19 +0000
Subject: [PATCH 104/203] also install RISC-V spec file

---
 install_scripts.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/install_scripts.sh b/install_scripts.sh
index 17f0b81008..ab06e47997 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -92,7 +92,7 @@ copy_files_by_list ${TOPDIR}/init ${INSTALL_PREFIX}/init "${init_files[@]}"
 
 # Copy for the init/arch_specs directory
 arch_specs_files=(
-   eessi_arch_arm.spec eessi_arch_ppc.spec eessi_arch_x86.spec
+   eessi_arch_arm.spec eessi_arch_ppc.spec eessi_arch_riscv.spec eessi_arch_x86.spec
 )
 copy_files_by_list ${TOPDIR}/init/arch_specs ${INSTALL_PREFIX}/init/arch_specs "${arch_specs_files[@]}"
 

From 9a185ea42e8d96282f43fc9a90652347da9afb28 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Wed, 22 May 2024 17:51:15 +0200
Subject: [PATCH 105/203] Add ESPResSo v.4.2.2 to foss/2023a 4.9.1 stack

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index e65747e4a5..2fdc40e284 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -4,3 +4,6 @@ easyconfigs:
   - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
       options:
         from-pr: 20379
+  - ESPResSo-4.2.2-foss-2023a.eb:
+      options:
+        from-pr: 20595

From 20ccd475f61f664fd55cc17b857c750f0821ad19 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Thu, 23 May 2024 14:14:18 +0200
Subject: [PATCH 106/203] Advice refers to release notes, not single issue

ESPResSo Lmod warning <= v4.2.1 points users to v4.2.2 release notes instead of only one of the bugs fixed
---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index e0d7b31f9e..84b18d499b 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -179,7 +179,7 @@
     local version = string.match(t.modFullName, "%d.%d.%d")
     if simpleName == 'ESPResSo' and version == '4.2.1' then
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
-        advice = advice .. 'For details see https://github.com/espressomd/espresso/issues/4856\\n'
+        advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
         advice = advice .. 'Use version 4.2.1 at your own risk!\\nn'
         LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
     end

From 7f328675deec19f88969eee91945f44617f68ab6 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 23 May 2024 15:51:36 +0200
Subject: [PATCH 107/203] Use EESSI_OVERRIDE_GPU_CHECK everywhere

---
 eessi_container.sh | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 7d00d1400c..a95a2c87c9 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -464,10 +464,9 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
         [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
         if [[ "${NVIDIA_MODE}" == "install" ]] ; then
-            # We need to "trick" our LMOD_RC file to allow us to load CUDA modules even without a CUDA driver
-            # (this works because we build within a container and the LMOD_RC recognises that)
-            touch ${EESSI_TMPDIR}/libcuda.so
-            export SINGULARITY_CONTAINLIBS="${EESSI_TMPDIR}/libcuda.so"
+            # No GPU so we need to "trick" Lmod to allow us to load CUDA modules even without a CUDA driver
+            # (this variable means EESSI_OVERRIDE_GPU_CHECK=1 will be set inside the container)
+            export SINGULARITYENV_EESSI_OVERRIDE_GPU_CHECK=1
         fi
     fi
 fi

From df4ac260e209e9ccc2578562845ceb2a328dbbb0 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Thu, 23 May 2024 16:05:27 +0200
Subject: [PATCH 108/203] Restrict overridding the GPU driver check to when we
 know it is valid

---
 EESSI-install-software.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 40f0ed8c3d..8a5789c2b2 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -243,9 +243,6 @@ fi
 #       if not, an error is produced, and the bot flags the whole build as failed (even when not installing GPU software)
 # ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
 
-# Don't run the Lmod GPU driver check when doing builds (may not have a GPU, and it's not relevant for vanilla builds anyway)
-export EESSI_OVERRIDE_GPU_CHECK=1 
-
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 
 if [ -z "${changed_easystacks}" ]; then

From bee4b001322a0d22c79642b5b1427f2c397a9f3b Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 24 May 2024 10:47:45 +0200
Subject: [PATCH 109/203] Make sure EESSI_OVERRIDE_GPU_CHECK is still set when
 in prefix shell

---
 run_in_compat_layer_env.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/run_in_compat_layer_env.sh b/run_in_compat_layer_env.sh
index f57c4d0749..b8e9cf979b 100755
--- a/run_in_compat_layer_env.sh
+++ b/run_in_compat_layer_env.sh
@@ -26,6 +26,9 @@ fi
 if [ ! -z ${EESSI_VERSION_OVERRIDE} ]; then
     INPUT="export EESSI_VERSION_OVERRIDE=${EESSI_VERSION_OVERRIDE}; ${INPUT}"
 fi
+if [ ! -z ${EESSI_OVERRIDE_GPU_CHECK} ]; then
+    INPUT="export EESSI_OVERRIDE_GPU_CHECK=${EESSI_OVERRIDE_GPU_CHECK}; ${INPUT}"
+fi
 if [ ! -z ${http_proxy} ]; then
     INPUT="export http_proxy=${http_proxy}; ${INPUT}"
 fi

From f788ca3ab94ab384ee2e4a98e5b76e2a9317102f Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Fri, 24 May 2024 11:18:04 +0200
Subject: [PATCH 110/203] Only install NVIDIA drivers if nvidia-smi command
 exists

---
 EESSI-install-software.sh | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 8a5789c2b2..7d358e205a 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -17,6 +17,11 @@ display_help() {
   echo "  --skip-cuda-install    -  disable installing a full CUDA SDK in the host_injections prefix (e.g. in CI)"
 }
 
+# Function to check if a command exists
+function command_exists() {
+    command -v "$1" >/dev/null 2>&1
+}
+
 function copy_build_log() {
     # copy specified build log to specified directory, with some context added
     build_log=${1}
@@ -238,10 +243,11 @@ else
     echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed OR no EasyBuild module was found"
 fi
 
-# Install drivers in host_injections
-# TODO: this is commented out for now, because the script assumes that nvidia-smi is available and works;
-#       if not, an error is produced, and the bot flags the whole build as failed (even when not installing GPU software)
-# ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
+# Install NVIDIA drivers in host_injections (if they exist)
+if command_exists "nvidia-smi"; then
+    echo "Command 'nvidia-smi' found. Installing NVIDIA drivers for use in prefix shell..."
+    ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
+fi
 
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 

From f974c34a85b3fb322906b974b7fcf084fa6398df Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Mon, 27 May 2024 09:49:10 +0200
Subject: [PATCH 111/203] Fix typo in create_lmodsitepackage.py ESPReSso
 warning

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 84b18d499b..31c040718d 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -180,7 +180,7 @@
     if simpleName == 'ESPResSo' and version == '4.2.1' then
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
         advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
-        advice = advice .. 'Use version 4.2.1 at your own risk!\\nn'
+        advice = advice .. 'Use version 4.2.1 at your own risk!\\n'
         LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
     end
 end

From 39c8abac220d428dc60f0fcf016dbcf6e0a2d049 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Mon, 27 May 2024 09:59:09 +0200
Subject: [PATCH 112/203] ESPReSso -> ESPResSo

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 31c040718d..bca2970e39 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -181,7 +181,7 @@
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
         advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
         advice = advice .. 'Use version 4.2.1 at your own risk!\\n'
-        LmodWarning("\\nESPReSso v4.2.1 has known issues and has been deprecated. ", advice)
+        LmodWarning("\\nESPResSo v4.2.1 has known issues and has been deprecated. ", advice)
     end
 end
 

From b15fc3d58c270ad3e28727f30e92c78744cbeee9 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Mon, 27 May 2024 10:54:00 +0200
Subject: [PATCH 113/203] Update bot build script to support whether GPU is
 available or not

---
 bot/build.sh     | 10 +++++++++-
 scripts/utils.sh |  5 +++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/bot/build.sh b/bot/build.sh
index dcc61c19d4..c9a362fdca 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -223,7 +223,15 @@ mkdir -p ${TARBALL_TMP_BUILD_STEP_DIR}
 BUILD_STEP_ARGS+=("--save" "${TARBALL_TMP_BUILD_STEP_DIR}")
 BUILD_STEP_ARGS+=("--storage" "${STORAGE}")
 # add options required to handle NVIDIA support
-BUILD_STEP_ARGS+=("--nvidia" "all")
+if command_exists "nvidia-smi"; then
+    echo "Command 'nvidia-smi' found, using available GPU"
+    BUILD_STEP_ARGS+=("--nvidia" "all")
+else
+    echo "No 'nvidia-smi' found, no available GPU but allowing overriding this check"
+    BUILD_STEP_ARGS+=("--nvidia" "install")
+fi
+# Retain location for host injections so we don't reinstall CUDA
+# (Always need to run the driver installation as available driver may change)
 if [[ ! -z ${SHARED_FS_PATH} ]]; then
     BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections")
 fi
diff --git a/scripts/utils.sh b/scripts/utils.sh
index b2be3f6221..962decd20e 100644
--- a/scripts/utils.sh
+++ b/scripts/utils.sh
@@ -78,6 +78,11 @@ function create_directory_structure() {
   return $return_code
 }
 
+# Function to check if a command exists
+function command_exists() {
+    command -v "$1" >/dev/null 2>&1
+}
+
 function get_path_for_tool {
     tool_name=$1
     tool_envvar_name=$2

From bb4b3c1b17e9eb6ca588a64690445a505353c1c9 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Tue, 28 May 2024 20:31:11 +0200
Subject: [PATCH 114/203] {2023.06}[gfbf/2023a] ipympl v0.9.3

---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023a.yml           | 10 +++++++---
 .../2023.06/eessi-2023.06-eb-4.9.1-2023a.yml           |  8 ++++++++
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 8f5608d881..4b58cb6106 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -48,9 +48,13 @@ easyconfigs:
   - PyOpenGL-3.1.7-GCCcore-12.3.0.eb:
       options:
         from-pr: 20007
-  - ipympl-0.9.3-foss-2023a.eb:
-      options:
-        from-pr: 20126
+  # removed by https://github.com/easybuilders/easybuild-easyconfigs/pull/20586
+  # adding ipympl-0.9.3-gfbf-2023a.eb as a replacement in
+  # easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+  # comment the below out here or CI will fail
+  # - ipympl-0.9.3-foss-2023a.eb:
+  #    options:
+  #      from-pr: 20126
   - OpenJPEG-2.5.0-GCCcore-12.3.0.eb
   - OpenFOAM-10-foss-2023a.eb
   - Highway-1.0.4-GCCcore-12.3.0.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index e65747e4a5..32b388854d 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -4,3 +4,11 @@ easyconfigs:
   - R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb:
       options:
         from-pr: 20379
+  # replacement for ipympl-0.9.3-foss-2023a.eb which has been built via
+  # easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml and was
+  # later removed in https://github.com/easybuilders/easybuild-easyconfigs/pull/20586
+  # below we use the replacement ec file which is provided by
+  # https://github.com/easybuilders/easybuild-easyconfigs/pull/18852
+  - ipympl-0.9.3-gfbf-2023a.eb:
+     options:
+       from-pr: 18852

From 9a036d8c9059c4eda163279322dda915e601b7e3 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Wed, 29 May 2024 06:34:05 +0200
Subject: [PATCH 115/203] {2023.06}[foss/2023a] GATK v4.5.0.0

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 8238b379f9..3e5c09090e 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -15,3 +15,4 @@ easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb:
       options:
         from-pr: 20595
+  - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb

From 7c48321761b291bb68046722f628360837a134e0 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Fri, 31 May 2024 11:52:11 +0200
Subject: [PATCH 116/203] Print message, not warning

On ESPResSo version 4.2.1 message, don't use `LmodWarning` but use `LmodMessage` instead
---
 create_lmodsitepackage.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index ed98d1f0f0..f159f186eb 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -175,16 +175,18 @@
     end
 end
 
-local function eessi_espresso_deprecated_warning(t)
+local function eessi_espresso_deprecated_message(t)
     local frameStk  = require("FrameStk"):singleton()
     local mt        = frameStk:mt()
     local simpleName = string.match(t.modFullName, "(.-)/")
     local version = string.match(t.modFullName, "%d.%d.%d")
     if simpleName == 'ESPResSo' and version == '4.2.1' then
+    -- Print a message on loading ESPreSso v <= 4.2.1 recommending using v 4.2.2 and above.
+    -- A message and not a warning as the exit code would break CI runs otherwise.
         local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
         advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
         advice = advice .. 'Use version 4.2.1 at your own risk!\\n'
-        LmodWarning("\\nESPResSo v4.2.1 has known issues and has been deprecated. ", advice)
+        LmodMessage("\\nESPResSo v4.2.1 has known issues and has been deprecated. ", advice)
     end
 end
 

From 76babe873669777a79a30e6abc33517873fa31a3 Mon Sep 17 00:00:00 2001
From: Pedro Santos Neves <10762799+Neves-P@users.noreply.github.com>
Date: Fri, 31 May 2024 13:57:20 +0200
Subject: [PATCH 117/203] Correctly use `eessi_espresso_deprecated_message()`

---
 create_lmodsitepackage.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index f159f186eb..7e55bce2a5 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -193,7 +193,7 @@
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
-    eessi_espresso_deprecated_warning(t)
+    eessi_espresso_deprecated_message(t)
     -- Only apply CUDA hooks if the loaded module is in the EESSI prefix
     -- This avoids getting an Lmod Error when trying to load a CUDA module from a local software stack
     if from_eessi_prefix(t) then

From 22578c43328a6e6257b5023e0cac52d21c5f637b Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 3 Jun 2024 09:43:04 +0000
Subject: [PATCH 118/203] {2023.06}[foss/2022b] ParaView v5.11.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index e547e45f2b..d023fbbaf1 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
       options:
         from-pr: 20379
+  - ParaView-5.11.1-foss-2022b.eb

From c77c2676ce98260b88fc9b23130f82cf693168f3 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 4 Jun 2024 06:37:24 +0000
Subject: [PATCH 119/203] {2023.06}[foss/2023a] WhatsHap v2.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 3e5c09090e..49a7191121 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -16,3 +16,4 @@ easyconfigs:
       options:
         from-pr: 20595
   - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
+  - WhatsHap-2.2-foss-2023a.eb

From 3d3019db4be7ecda681ae862ab33962cc1d61e37 Mon Sep 17 00:00:00 2001
From: Alan O'Cais <alan.ocais@cecam.org>
Date: Tue, 4 Jun 2024 10:48:27 +0200
Subject: [PATCH 120/203] Update scorecards to latest version

---
 .github/workflows/scorecards.yml | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/scorecards.yml b/.github/workflows/scorecards.yml
index 7eff557094..5b482763f2 100644
--- a/.github/workflows/scorecards.yml
+++ b/.github/workflows/scorecards.yml
@@ -4,24 +4,20 @@
 
 name: Scorecards supply-chain security
 on:
-  # For Branch-Protection check. Only the default branch is supported. See
-  # https://github.com/ossf/scorecard/blob/main/docs/checks.md#branch-protection
-  branch_protection_rule:
   # To guarantee Maintained check is occasionally updated. See
   # https://github.com/ossf/scorecard/blob/main/docs/checks.md#maintained
   schedule:
     - cron: '25 15 * * 3'
   push:
-    branches: [ "main" ]
-  pull_request:
-    branches:    
-      - main
+    branches:
+      - '2023.06-software.eessi.io'
 
 # Declare default permissions as read only.
 permissions: read-all
 
 jobs:
   analysis:
+    if: github.repository_owner == 'EESSI'   # Prevent running on forks
     name: Scorecards analysis
     runs-on: ubuntu-latest
     permissions:
@@ -35,12 +31,12 @@ jobs:
 
     steps:
       - name: "Checkout code"
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
         with:
           persist-credentials: false
 
       - name: "Run analysis"
-        uses: ossf/scorecard-action@0864cf19026789058feabb7e87baa5f140aac736 # v2.3.1
+        uses: ossf/scorecard-action@dc50aa9510b46c811795eb24b2f1ba02a914e534 # v2.3.3
         with:
           results_file: results.sarif
           results_format: sarif
@@ -62,7 +58,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@3cea5372237819ed00197afe530f5a7ea3e805c8 # v3.1.0
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
         with:
           name: SARIF file
           path: results.sarif
@@ -70,6 +66,6 @@ jobs:
 
       # Upload the results to GitHub's code scanning dashboard.
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@807578363a7869ca324a79039e6db9c843e0e100 # v2.1.27
+        uses: github/codeql-action/upload-sarif@9fdb3e49720b44c48891d036bb502feb25684276 # v3.25.6
         with:
           sarif_file: results.sarif

From a111b6db76a816e030b40d9d4e60e93686f80709 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Jun 2024 07:53:55 +0200
Subject: [PATCH 121/203] {2023.06,2023b,zen4} SciPy-bundle v2023.11

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
index 75dc4e6602..bc736c4056 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - foss-2023b.eb
+  - SciPy-bundle-2023.11-gfbf-2023b.eb

From fe809a5228a05c699169fd1280de89ce15a753b8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 6 Jun 2024 07:54:28 +0200
Subject: [PATCH 122/203] {2023.06,2023b,zen4} SciPy-bundle v2023.07

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
index c821df1afb..b3afe2b368 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - foss-2023a.eb
+  - SciPy-bundle-2023.07-gfbf-2023a.eb

From fa2fd59c37432395ac45dceffdd99c8a4ea08948 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Thu, 6 Jun 2024 06:36:30 +0000
Subject: [PATCH 123/203] {2023.06}[gfbf/2022b] ASE v3.22.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index d023fbbaf1..385f33b5cb 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -3,3 +3,4 @@ easyconfigs:
       options:
         from-pr: 20379
   - ParaView-5.11.1-foss-2022b.eb
+  - ASE-3.22.1-gfbf-2022b.eb

From 08e09ca1655348b7e08e11a4cca710522509f291 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 7 Jun 2024 06:14:03 +0000
Subject: [PATCH 124/203] {2023.06}[foss/2023b] NLTK v3.8.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
index 1392fa2f5a..b06cb2788e 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - GROMACS-2024.1-foss-2023b.eb:
       options:
         from-pr: 20439
+  - NLTK-3.8.1-foss-2023b.eb

From 9b3f02da7e8c1279cf20cb9a37356b7c430e32f7 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 7 Jun 2024 08:07:14 +0000
Subject: [PATCH 125/203] {2023.06}[foss/2022b] SEPP v4.5.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index 385f33b5cb..57c985b020 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -4,3 +4,4 @@ easyconfigs:
         from-pr: 20379
   - ParaView-5.11.1-foss-2022b.eb
   - ASE-3.22.1-gfbf-2022b.eb
+  - SEPP-4.5.1-foss-2022b.eb

From 46d9018f40db4ca174f60746102335ba87ad53b5 Mon Sep 17 00:00:00 2001
From: ocaisa <alan.ocais@cecam.org>
Date: Fri, 7 Jun 2024 12:03:50 +0200
Subject: [PATCH 126/203] Apply suggestions from code review
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 EESSI-extend-2023.06-easybuild.eb                               | 2 +-
 .../rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/EESSI-extend-2023.06-easybuild.eb b/EESSI-extend-2023.06-easybuild.eb
index 42defbacc8..b525ee462d 100644
--- a/EESSI-extend-2023.06-easybuild.eb
+++ b/EESSI-extend-2023.06-easybuild.eb
@@ -143,7 +143,7 @@ setenv ("EASYBUILD_HOOKS", pathJoin(os.getenv("EESSI_PREFIX"), "init", "easybuil
 -- Make sure to use the general umask that allows a global read
 setenv ("EASYBUILD_UMASK", "022")
 
--- All this module to be loaded when running EasyBuild
+-- Allow this module to be loaded when running EasyBuild
 setenv ("EASYBUILD_ALLOW_LOADED_MODULES", "EasyBuild,EESSI-extend")
 
 -- Set all related environment variables if we have project or user installations (including extending MODULEPATH)
diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
index 5cf2bd6b9d..93c4950fc8 100644
--- a/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
@@ -1,5 +1,5 @@
 # 2024.05.15
-# The module is an EasyBuil created module and therefore needs to be an allowed
+# The module is an EasyBuild created module and therefore needs to be an allowed
 # module when running EasyBuild
 easyconfigs:
   - EESSI-extend-2023.06-easybuild.eb 

From 51118efbea0730b820493ff27dab231f256fb53f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 7 Jun 2024 12:08:09 +0200
Subject: [PATCH 127/203] remove double hyphen in filename

---
 ...loaded.yml => 20240506-eb-4.9.1-EESSI-extend-allow-loaded.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename easystacks/software.eessi.io/2023.06/rebuilds/{20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml => 20240506-eb-4.9.1-EESSI-extend-allow-loaded.yml} (100%)

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240506-eb-4.9.1-EESSI-extend-allow-loaded.yml
similarity index 100%
rename from easystacks/software.eessi.io/2023.06/rebuilds/20240506--eb-4.9.1-EESSI-extend-allow-loaded.yml
rename to easystacks/software.eessi.io/2023.06/rebuilds/20240506-eb-4.9.1-EESSI-extend-allow-loaded.yml

From 3bdfff7a7fe360b066a971a0c29f67414470c12f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 8 Jun 2024 14:33:46 +0200
Subject: [PATCH 128/203] {2023.06,zen4}[foss/2023a] ESPResSo 4.2.1

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
index b3afe2b368..a529746676 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -1,3 +1,4 @@
 easyconfigs:
   - foss-2023a.eb
   - SciPy-bundle-2023.07-gfbf-2023a.eb
+  - ESPResSo-4.2.1-foss-2023a.eb

From 0b715d73f2fb7c157a28953de233cf71703b6136 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 10 Jun 2024 05:52:26 +0000
Subject: [PATCH 129/203] {2023.06}[gompi/2023a] BLAST+ v2.14.1

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 49a7191121..f53ad9235c 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -17,3 +17,6 @@ easyconfigs:
         from-pr: 20595
   - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
   - WhatsHap-2.2-foss-2023a.eb
+  - BLAST+-2.14.1-gompi-2023a.eb:
+      options:     
+        from-pr: 20751

From c7a2e6e348e99a2ac7ca170c4c2d7b1eddc46a94 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int5.local.snellius.surf.nl>
Date: Mon, 10 Jun 2024 11:06:39 +0200
Subject: [PATCH 130/203] Change smile for failed test runs

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index f045b9500a..3b16e5c415 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -101,7 +101,7 @@ elif [[ ${ERROR} -eq 1 ]]; then
     reason="EESSI test suite was not run, test step itself failed to execute."
     status="FAILURE"
 else
-    summary=":grin: FAILURE"
+    summary=":cry: FAILURE"
     reason="Failed for unknown reason"
     status="FAILURE"
 fi

From ad17f4384c1e9500c9c34aa71ae6b0d51e3c446e Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Mon, 10 Jun 2024 11:43:55 +0200
Subject: [PATCH 131/203] Fix emoticon

---
 bot/check-test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/check-test.sh b/bot/check-test.sh
index f045b9500a..3b16e5c415 100755
--- a/bot/check-test.sh
+++ b/bot/check-test.sh
@@ -101,7 +101,7 @@ elif [[ ${ERROR} -eq 1 ]]; then
     reason="EESSI test suite was not run, test step itself failed to execute."
     status="FAILURE"
 else
-    summary=":grin: FAILURE"
+    summary=":cry: FAILURE"
     reason="Failed for unknown reason"
     status="FAILURE"
 fi

From 596c70299d3f73098f0e6b711e5b246ffd54766e Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Mon, 10 Jun 2024 15:24:13 +0200
Subject: [PATCH 132/203] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index f53ad9235c..be3b9c1bbf 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -19,4 +19,4 @@ easyconfigs:
   - WhatsHap-2.2-foss-2023a.eb
   - BLAST+-2.14.1-gompi-2023a.eb:
       options:     
-        from-pr: 20751
+        from-pr: 20784

From f288436f8193c70e87485bce1e3866915525720a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 10 Jun 2024 20:42:07 +0200
Subject: [PATCH 133/203] add Valgrind

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 1 +
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml   | 1 +
 3 files changed, 3 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index 57c985b020..1805c581c3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -5,3 +5,4 @@ easyconfigs:
   - ParaView-5.11.1-foss-2022b.eb
   - ASE-3.22.1-gfbf-2022b.eb
   - SEPP-4.5.1-foss-2022b.eb
+  - Valgrind-3.21.0-gompi-2022b.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 49a7191121..db9a6d7e36 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -17,3 +17,4 @@ easyconfigs:
         from-pr: 20595
   - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
   - WhatsHap-2.2-foss-2023a.eb
+  - Valgrind-3.21.0-gompi-2023a.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
index b06cb2788e..c071f220cf 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -3,3 +3,4 @@ easyconfigs:
       options:
         from-pr: 20439
   - NLTK-3.8.1-foss-2023b.eb
+  - Valgrind-3.23.0-gompi-2023b.eb

From c9287ed954484034e94fed5a8b6292d8c135bb1f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Mon, 10 Jun 2024 20:44:35 +0200
Subject: [PATCH 134/203] add --from-pr to Valgrind

---
 .../2023.06/eessi-2023.06-eb-4.9.1-2023b.yml                  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
index c071f220cf..888bddace3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -3,4 +3,6 @@ easyconfigs:
       options:
         from-pr: 20439
   - NLTK-3.8.1-foss-2023b.eb
-  - Valgrind-3.23.0-gompi-2023b.eb
+  - Valgrind-3.23.0-gompi-2023b.eb:
+      options:
+        from-pr: 20792

From c4af3895e61781cba2dbb3d5982e024d95a15d77 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 11 Jun 2024 09:19:04 +0000
Subject: [PATCH 135/203] {2023.06}[foss/2023a] OrthoFinder v2.5.5

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index be3b9c1bbf..1d74452e45 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -20,3 +20,4 @@ easyconfigs:
   - BLAST+-2.14.1-gompi-2023a.eb:
       options:     
         from-pr: 20784
+  - OrthoFinder-2.5.5-foss-2023a.eb

From 525b23e9af30453137617ce27f456279151bc1e7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 10:26:49 +0200
Subject: [PATCH 136/203] add easystack for EB 4.9.2 and install it

---
 .../2023.06/eessi-2023.06-eb-4.9.2-001-system.yml            | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
new file mode 100644
index 0000000000..cd87626494
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
@@ -0,0 +1,5 @@
+easyconfigs:
+  - EasyBuild-4.9.2.eb:
+      options:
+        from-pr: 20801
+        include-easyblocks-from-pr: 3358

From 460da691db015a88e00a0df8548f3f0721b0c6ad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 13:03:30 +0200
Subject: [PATCH 137/203] add EB 4.9.2

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml             | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index 46ac979719..8f96cf9450 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -3,3 +3,7 @@ easyconfigs:
       options:
         from-pr: 20299
   - EESSI-extend-2023.06-easybuild.eb
+  - EasyBuild-4.9.2.eb:
+      options:
+        from-pr: 20801
+        include-easyblocks-from-pr: 3358

From 911737d2bea6cea92c09262bcfa605e18ba553eb Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 14:05:46 +0200
Subject: [PATCH 138/203] Add template field for mem per node

---
 reframe_config_bot.py.tmpl | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/reframe_config_bot.py.tmpl b/reframe_config_bot.py.tmpl
index 0cc3e9f530..607373767a 100644
--- a/reframe_config_bot.py.tmpl
+++ b/reframe_config_bot.py.tmpl
@@ -34,6 +34,11 @@ site_configuration = {
                             'options': ['--mem={size}'],
                         }
                     ],
+                    'extras': {
+                        # Make sure to round down, otherwise a job might ask for more mem than is available
+                        # per node
+                        'mem_per_node': __MEM_PER_NODE__,
+                    },
                     'max_jobs': 1
                     }
                 ]

From e10b227d3299a0945edd5ecede13b9784c4fd748 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 14:14:36 +0200
Subject: [PATCH 139/203] Get memory limit for cgroup of current job / UID and
 put this into the ReFrame config file

---
 test_suite.sh | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 95eb9daa2a..5c157f7a47 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -135,7 +135,7 @@ export RFM_PREFIX=$PWD/reframe_runs
 echo "Configured reframe with the following environment variables:"
 env | grep "RFM_"
 
-# Inject correct CPU properties into the ReFrame config file
+# Inject correct CPU/memory properties into the ReFrame config file
 cpuinfo=$(lscpu)
 if [[ "${cpuinfo}" =~ CPU\(s\):[^0-9]*([0-9]+) ]]; then
     cpu_count=${BASH_REMATCH[1]}
@@ -157,11 +157,19 @@ if [[ "${cpuinfo}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
 else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
+cgroup_mem_bytes=$(cat /sys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
+if [[ $? -eq 0 ]]
+    # Convert to MiB
+    cgroup_mem_mib=$((cgroup_mem_bytes/(1024*1024)))
+else
+    fatal_error "Failed to get the memory limit in bytes from the current cgroup"
+fi
 cp ${RFM_CONFIG_FILE_TEMPLATE} ${RFM_CONFIG_FILES}
 sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
+sed -i "s/__MEM_PER_NODE__/${cgroup_mem_mib/g" $RFM_CONFIG_FILES
 
 # Workaround for https://github.com/EESSI/software-layer/pull/467#issuecomment-1973341966
 export PSM3_DEVICES='self,shm'  # this is enough, since we only run single node for now

From 644eddcb66a46871cdfe93ef54ca70954169f548 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 14:16:02 +0200
Subject: [PATCH 140/203] Missing bracket

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 5c157f7a47..2d072d3d95 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -169,7 +169,7 @@ sed -i "s/__NUM_CPUS__/${cpu_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_SOCKETS__/${socket_count}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_CORE__/${threads_per_core}/g" $RFM_CONFIG_FILES
 sed -i "s/__NUM_CPUS_PER_SOCKET__/${cores_per_socket}/g" $RFM_CONFIG_FILES
-sed -i "s/__MEM_PER_NODE__/${cgroup_mem_mib/g" $RFM_CONFIG_FILES
+sed -i "s/__MEM_PER_NODE__/${cgroup_mem_mib}/g" $RFM_CONFIG_FILES
 
 # Workaround for https://github.com/EESSI/software-layer/pull/467#issuecomment-1973341966
 export PSM3_DEVICES='self,shm'  # this is enough, since we only run single node for now

From bcba10e3553806f4f1dda6d27412f4756464f13c Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 14:16:48 +0200
Subject: [PATCH 141/203] Fix if-else syntax

---
 test_suite.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test_suite.sh b/test_suite.sh
index 2d072d3d95..46b43ee78a 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -158,7 +158,7 @@ else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
 cgroup_mem_bytes=$(cat /sys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
-if [[ $? -eq 0 ]]
+if [[ $? -eq 0 ]]; then
     # Convert to MiB
     cgroup_mem_mib=$((cgroup_mem_bytes/(1024*1024)))
 else

From 70c1b146789d3d0c4d92f0a368ab078c724b898a Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 15:18:17 +0200
Subject: [PATCH 142/203] Make sure we bind-mount /sys/fs/cgroup into the
 container, so that we can use it to determine available memory for
 dynamically configuring ReFrame in the test step

---
 bot/test.sh        |  3 ++
 eessi_container.sh | 78 ++++++++++++++++++++++++++--------------------
 test_suite.sh      |  2 +-
 3 files changed, 48 insertions(+), 35 deletions(-)

diff --git a/bot/test.sh b/bot/test.sh
index 4984340e6e..b3f6acf0ea 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -204,6 +204,9 @@ if [[ -z ${RESUME_DIR} ]]; then
 else
   TEST_STEP_ARGS+=("--resume" "${RESUME_DIR}")
 fi
+# Bind mount /sys/fs/cgroup so that we can determine the amount of memory available in our cgroup for
+# Reframe configuration
+TEST_STEP_ARGS+=("--extra-bind-paths /sys/fs/cgroup:/hostsys/fs/cgroup:ro")
 
 # prepare arguments to test_suite.sh (specific to test step)
 declare -a TEST_SUITE_ARGS=()
diff --git a/eessi_container.sh b/eessi_container.sh
index a95a2c87c9..eac8e74c83 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -70,40 +70,43 @@ export EESSI_REPOS_CFG_FILE="${EESSI_REPOS_CFG_DIR}/repos.cfg"
 display_help() {
   echo "usage: $0 [OPTIONS] [[--] SCRIPT or COMMAND]"
   echo " OPTIONS:"
-  echo "  -a | --access {ro,rw}  - ro (read-only), rw (read & write) [default: ro]"
-  echo "  -c | --container IMG   - image file or URL defining the container to use"
-  echo "                           [default: docker://ghcr.io/eessi/build-node:debian11]"
-  echo "  -f | --fakeroot        - run the container with --fakeroot [default: false]"
-  echo "  -g | --storage DIR     - directory space on host machine (used for"
-  echo "                           temporary data) [default: 1. TMPDIR, 2. /tmp]"
-  echo "  -h | --help            - display this usage information [default: false]"
-  echo "  -i | --host-injections - directory to link to for host_injections "
-  echo "                           [default: /..storage../opt-eessi]"
-  echo "  -l | --list-repos      - list available repository identifiers [default: false]"
-  echo "  -m | --mode MODE       - with MODE==shell (launch interactive shell) or"
-  echo "                           MODE==run (run a script or command) [default: shell]"
-  echo "  -n | --nvidia MODE     - configure the container to work with NVIDIA GPUs,"
-  echo "                           MODE==install for a CUDA installation, MODE==run to"
-  echo "                           attach a GPU, MODE==all for both [default: false]"
-  echo "  -r | --repository CFG  - configuration file or identifier defining the"
-  echo "                           repository to use [default: EESSI via"
-  echo "                           default container, see --container]"
-  echo "  -u | --resume DIR/TGZ  - resume a previous run from a directory or tarball,"
-  echo "                           where DIR points to a previously used tmp directory"
-  echo "                           (check for output 'Using DIR as tmp ...' of a previous"
-  echo "                           run) and TGZ is the path to a tarball which is"
-  echo "                           unpacked the tmp dir stored on the local storage space"
-  echo "                           (see option --storage above) [default: not set]"
-  echo "  -s | --save DIR/TGZ    - save contents of tmp directory to a tarball in"
-  echo "                           directory DIR or provided with the fixed full path TGZ"
-  echo "                           when a directory is provided, the format of the"
-  echo "                           tarball's name will be {REPO_ID}-{TIMESTAMP}.tgz"
-  echo "                           [default: not set]"
-  echo "  -v | --verbose         - display more information [default: false]"
-  echo "  -x | --http-proxy URL  - provides URL for the env variable http_proxy"
-  echo "                           [default: not set]; uses env var \$http_proxy if set"
-  echo "  -y | --https-proxy URL - provides URL for the env variable https_proxy"
-  echo "                           [default: not set]; uses env var \$https_proxy if set"
+  echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
+  echo "  -c | --container IMG    - image file or URL defining the container to use"
+  echo "                            [default: docker://ghcr.io/eessi/build-node:debian11]"
+  echo "  -f | --fakeroot         - run the container with --fakeroot [default: false]"
+  echo "  -g | --storage DIR      - directory space on host machine (used for"
+  echo "                            temporary data) [default: 1. TMPDIR, 2. /tmp]"
+  echo "  -h | --help             - display this usage information [default: false]"
+  echo "  -i | --host-injections  - directory to link to for host_injections "
+  echo "                            [default: /..storage../opt-eessi]"
+  echo "  -l | --list-repos       - list available repository identifiers [default: false]"
+  echo "  -m | --mode MODE        - with MODE==shell (launch interactive shell) or"
+  echo "                            MODE==run (run a script or command) [default: shell]"
+  echo "  -n | --nvidia MODE      - configure the container to work with NVIDIA GPUs,"
+  echo "                            MODE==install for a CUDA installation, MODE==run to"
+  echo "                            attach a GPU, MODE==all for both [default: false]"
+  echo "  -r | --repository CFG   - configuration file or identifier defining the"
+  echo "                            repository to use [default: EESSI via"
+  echo "                            default container, see --container]"
+  echo "  -u | --resume DIR/TGZ   - resume a previous run from a directory or tarball,"
+  echo "                            where DIR points to a previously used tmp directory"
+  echo "                            (check for output 'Using DIR as tmp ...' of a previous"
+  echo "                            run) and TGZ is the path to a tarball which is"
+  echo "                            unpacked the tmp dir stored on the local storage space"
+  echo "                            (see option --storage above) [default: not set]"
+  echo "  -s | --save DIR/TGZ     - save contents of tmp directory to a tarball in"
+  echo "                            directory DIR or provided with the fixed full path TGZ"
+  echo "                            when a directory is provided, the format of the"
+  echo "                            tarball's name will be {REPO_ID}-{TIMESTAMP}.tgz"
+  echo "                            [default: not set]"
+  echo "  -v | --verbose          - display more information [default: false]"
+  echo "  -x | --http-proxy URL   - provides URL for the env variable http_proxy"
+  echo "                            [default: not set]; uses env var \$http_proxy if set"
+  echo "  -y | --https-proxy URL  - provides URL for the env variable https_proxy"
+  echo "                            [default: not set]; uses env var \$https_proxy if set"
+  echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
+  echo "                            To specify multiple bind paths, seperate by comma."
+  echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
   echo
   echo " If value for --mode is 'run', the SCRIPT/COMMAND provided is executed. If"
   echo " arguments to the script/command start with '-' or '--', use the flag terminator"
@@ -197,6 +200,10 @@ while [[ $# -gt 0 ]]; do
       export https_proxy=${HTTPS_PROXY}
       shift 2
       ;;
+    -b|--extra-bind-paths)
+      EXTRA_BIND_PATHS="$2"
+      shift 2
+      ;;
     --)
       shift
       POSITIONAL_ARGS+=("$@") # save positional args
@@ -439,6 +446,9 @@ fi
 BIND_PATHS="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
 # provide a '/tmp' inside the container
 BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
+if [[ ! -z ${EXTRA_BIND_PATHS} ]]; then
+    BIND_PATHS="${BIND_PATHS},${EXTRA_BIND_PATHS}"
+fi
 
 [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
 
diff --git a/test_suite.sh b/test_suite.sh
index 46b43ee78a..6e73fbd87c 100755
--- a/test_suite.sh
+++ b/test_suite.sh
@@ -157,7 +157,7 @@ if [[ "${cpuinfo}" =~ (Core\(s\) per socket:[^0-9]*([0-9]+)) ]]; then
 else
     fatal_error "Failed to get the number of cores per socket for the current test hardware with lscpu."
 fi
-cgroup_mem_bytes=$(cat /sys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
+cgroup_mem_bytes=$(cat /hostsys/fs/cgroup/memory/slurm/uid_${UID}/job_${SLURM_JOB_ID}/memory.limit_in_bytes)
 if [[ $? -eq 0 ]]; then
     # Convert to MiB
     cgroup_mem_mib=$((cgroup_mem_bytes/(1024*1024)))

From 5bfd7c1c0898ee268530295f794438cd1fd29836 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com>
Date: Thu, 13 Jun 2024 16:45:32 +0200
Subject: [PATCH 143/203] Update eessi_container.sh
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 eessi_container.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index eac8e74c83..55b0aa4c63 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -71,6 +71,9 @@ display_help() {
   echo "usage: $0 [OPTIONS] [[--] SCRIPT or COMMAND]"
   echo " OPTIONS:"
   echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
+  echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
+  echo "                            To specify multiple bind paths, seperate by comma."
+  echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
   echo "  -c | --container IMG    - image file or URL defining the container to use"
   echo "                            [default: docker://ghcr.io/eessi/build-node:debian11]"
   echo "  -f | --fakeroot         - run the container with --fakeroot [default: false]"
@@ -104,9 +107,6 @@ display_help() {
   echo "                            [default: not set]; uses env var \$http_proxy if set"
   echo "  -y | --https-proxy URL  - provides URL for the env variable https_proxy"
   echo "                            [default: not set]; uses env var \$https_proxy if set"
-  echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
-  echo "                            To specify multiple bind paths, seperate by comma."
-  echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
   echo
   echo " If value for --mode is 'run', the SCRIPT/COMMAND provided is executed. If"
   echo " arguments to the script/command start with '-' or '--', use the flag terminator"

From a7fca5155a4e9c145d73c416c85e4c1e6f2c2c12 Mon Sep 17 00:00:00 2001
From: Caspar van Leeuwen <casparl@int4.local.snellius.surf.nl>
Date: Thu, 13 Jun 2024 16:46:33 +0200
Subject: [PATCH 144/203] Sort alphabetically

---
 eessi_container.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index eac8e74c83..aa5df50af6 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -137,6 +137,10 @@ while [[ $# -gt 0 ]]; do
       ACCESS="$2"
       shift 2
       ;;
+    -b|--extra-bind-paths)
+      EXTRA_BIND_PATHS="$2"
+      shift 2
+      ;;
     -c|--container)
       CONTAINER="$2"
       shift 2
@@ -200,10 +204,6 @@ while [[ $# -gt 0 ]]; do
       export https_proxy=${HTTPS_PROXY}
       shift 2
       ;;
-    -b|--extra-bind-paths)
-      EXTRA_BIND_PATHS="$2"
-      shift 2
-      ;;
     --)
       shift
       POSITIONAL_ARGS+=("$@") # save positional args

From 13366e7c3f3c1aa59192f70e8a26e451611a15d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 16:48:42 +0200
Subject: [PATCH 145/203] fix typo

---
 eessi_container.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 891b793f9d..fb14e2118f 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -72,7 +72,7 @@ display_help() {
   echo " OPTIONS:"
   echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
   echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
-  echo "                            To specify multiple bind paths, seperate by comma."
+  echo "                            To specify multiple bind paths, separate by comma."
   echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
   echo "  -c | --container IMG    - image file or URL defining the container to use"
   echo "                            [default: docker://ghcr.io/eessi/build-node:debian11]"

From 63c1abfb8d03fbceb23914d3143abef68dd23bdf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 16:55:06 +0200
Subject: [PATCH 146/203] remove EB 4.9.2 from 4.9.1 easystack

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml             | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index 8f96cf9450..46ac979719 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -3,7 +3,3 @@ easyconfigs:
       options:
         from-pr: 20299
   - EESSI-extend-2023.06-easybuild.eb
-  - EasyBuild-4.9.2.eb:
-      options:
-        from-pr: 20801
-        include-easyblocks-from-pr: 3358

From 7f6cb8d740ef9761cabd65eb221d9cdc52a84f63 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 17:04:18 +0200
Subject: [PATCH 147/203] remove include-easyblocks-from-pr for EB 4.9.2

---
 .../2023.06/eessi-2023.06-eb-4.9.2-001-system.yml                | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
index cd87626494..a90f565412 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
@@ -2,4 +2,3 @@ easyconfigs:
   - EasyBuild-4.9.2.eb:
       options:
         from-pr: 20801
-        include-easyblocks-from-pr: 3358

From 1d56c7239aec4a4521f1114c482b95b7b1f8f2c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 17:21:47 +0200
Subject: [PATCH 148/203] use separate quotes for option and argument

---
 bot/test.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bot/test.sh b/bot/test.sh
index b3f6acf0ea..04bff346cd 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -206,7 +206,7 @@ else
 fi
 # Bind mount /sys/fs/cgroup so that we can determine the amount of memory available in our cgroup for
 # Reframe configuration
-TEST_STEP_ARGS+=("--extra-bind-paths /sys/fs/cgroup:/hostsys/fs/cgroup:ro")
+TEST_STEP_ARGS+=("--extra-bind-paths" "/sys/fs/cgroup:/hostsys/fs/cgroup:ro")
 
 # prepare arguments to test_suite.sh (specific to test step)
 declare -a TEST_SUITE_ARGS=()

From 158f0eb96d2027a51bb8d5ad8ae347405790c8d4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 20:17:44 +0200
Subject: [PATCH 149/203] add EB 4.9.2

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml             | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index 46ac979719..9e6f4ddb1a 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -3,3 +3,7 @@ easyconfigs:
       options:
         from-pr: 20299
   - EESSI-extend-2023.06-easybuild.eb
+easyconfigs:
+  - EasyBuild-4.9.2.eb:
+      options:
+        from-pr: 20818

From 4c5cc45627041da2526ad9d9f8ca11b8be10580e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 20:19:45 +0200
Subject: [PATCH 150/203] remove 4.9.2 easystack

---
 .../2023.06/eessi-2023.06-eb-4.9.2-001-system.yml             | 4 ----
 1 file changed, 4 deletions(-)
 delete mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
deleted file mode 100644
index a90f565412..0000000000
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-001-system.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-easyconfigs:
-  - EasyBuild-4.9.2.eb:
-      options:
-        from-pr: 20801

From 8581d3f53f5dde36c46152faecb7de2d88521236 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 13 Jun 2024 22:27:29 +0200
Subject: [PATCH 151/203] Remove line

---
 .../2023.06/eessi-2023.06-eb-4.9.1-001-system.yml                | 1 -
 1 file changed, 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
index 9e6f4ddb1a..866766a36b 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.1-001-system.yml
@@ -3,7 +3,6 @@ easyconfigs:
       options:
         from-pr: 20299
   - EESSI-extend-2023.06-easybuild.eb
-easyconfigs:
   - EasyBuild-4.9.2.eb:
       options:
         from-pr: 20818

From 39cf7a0395e67e341808f96dbea812576bef5eb1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 13:24:55 +0200
Subject: [PATCH 152/203] {2023.06,zen4}[foss/2023a] ESPResSo 4.2.2

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml               | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
new file mode 100644
index 0000000000..f148a7fdf9
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - ESPResSo-4.2.2-foss-2023a.eb

From eb363eddaccdde1d70a622d77123d480e6b226c9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 15:49:49 +0200
Subject: [PATCH 153/203] {2023.06,zen4}[foss/2023a] TensorFlow 2.13.0

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
index f148a7fdf9..f2f4c9d1f5 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb
+  - TensorFlow-2.13.0-foss-2023a.eb

From c810b4e3cf420b4c9f0285211da7f83a5a8e8f7b Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 21:47:31 +0200
Subject: [PATCH 154/203] {2023.06,zen4}[foss/2023a] R 4.3.2

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
index f2f4c9d1f5..09f525364f 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,3 +1,4 @@
 easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb
   - TensorFlow-2.13.0-foss-2023a.eb
+  - R-4.3.2-gfbf-2023a.eb

From c92f941875f91696e305232fdca1e4d13bd2b091 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 14 Jun 2024 23:22:14 +0200
Subject: [PATCH 155/203] {2023.06,zen4}[foss/2023b] GROMACS 2024.1

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml               | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
new file mode 100644
index 0000000000..af2c3bfca6
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - GROMACS-2024.1-foss-2023b.eb

From ce370806de21ad95fd6825dcad24262bc8d28ec5 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 15 Jun 2024 09:35:29 +0200
Subject: [PATCH 156/203] {2023.06,zen4} add missing installations with
 foss/2023b

---
 .../zen4/eessi-2023.06-eb-4.9.2-2023b.yml        | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
index af2c3bfca6..30a6745ccc 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,2 +1,18 @@
 easyconfigs:
   - GROMACS-2024.1-foss-2023b.eb
+  - netCDF-4.9.2-gompi-2023b.eb
+  - matplotlib-3.8.2-gfbf-2023b.eb
+  - DP3-6.0-foss-2023b.eb
+  - WSClean-3.4-foss-2023b.eb
+  - CDO-2.2.2-gompi-2023b.eb
+  - python-casacore-3.5.2-foss-2023b.eb
+  - libspatialindex-1.9.3-GCCcore-13.2.0.eb
+  - LittleCMS-2.15-GCCcore-13.2.0.eb
+  - giflib-5.2.1-GCCcore-13.2.0.eb
+  - OpenJPEG-2.5.0-GCCcore-13.2.0.eb
+  - libwebp-1.3.2-GCCcore-13.2.0.eb
+  - Wayland-1.22.0-GCCcore-13.2.0.eb
+  - Qt5-5.15.13-GCCcore-13.2.0.eb
+  - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
+  - NLTK-3.8.1-foss-2023b.eb
+  - Valgrind-3.23.0-gompi-2023b.eb

From 1183ae9cc174af34792363048f18cd7086c4666c Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 17 Jun 2024 11:33:11 +0000
Subject: [PATCH 157/203] {2023.06}[GCCcore/13.2.0] IPython v8.17.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml  | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
new file mode 100644
index 0000000000..c23b5b001d
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - IPython-8.17.2-GCCcore-13.2.0.eb

From e8c2d0636e087d4e565d5d5993d2894fa21da6b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Mon, 17 Jun 2024 15:10:28 +0200
Subject: [PATCH 158/203] first steps to support multiple CVMFS repositories

---
 eessi_container.sh | 99 +++++++++++++++++++++++++++++++++++-----------
 1 file changed, 77 insertions(+), 22 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index fb14e2118f..9b1ab69a3b 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -48,7 +48,11 @@ HTTPS_PROXY_ERROR_EXITCODE=$((${ANY_ERROR_EXITCODE} << 10))
 RUN_SCRIPT_MISSING_EXITCODE=$((${ANY_ERROR_EXITCODE} << 11))
 NVIDIA_MODE_UNKNOWN_EXITCODE=$((${ANY_ERROR_EXITCODE} << 12))
 
+# we use an associative array for storing sets of settings per CVMFS repository
+declare -A cvmfs_repo_settings
+
 # CernVM-FS settings
+# TODO may need to put them into repository specific map
 CVMFS_VAR_LIB="var-lib-cvmfs"
 CVMFS_VAR_RUN="var-run-cvmfs"
 
@@ -89,8 +93,9 @@ display_help() {
   echo "                            MODE==install for a CUDA installation, MODE==run to"
   echo "                            attach a GPU, MODE==all for both [default: false]"
   echo "  -r | --repository CFG   - configuration file or identifier defining the"
-  echo "                            repository to use [default: EESSI via"
-  echo "                            default container, see --container]"
+  echo "                            repository to use; can be given multiple times"
+  echo "                            [default: software.eessi.io via CVMFS config available"
+  echo "                            via default container, see --container]"
   echo "  -u | --resume DIR/TGZ   - resume a previous run from a directory or tarball,"
   echo "                            where DIR points to a previously used tmp directory"
   echo "                            (check for output 'Using DIR as tmp ...' of a previous"
@@ -123,7 +128,7 @@ STORAGE=
 LIST_REPOS=0
 MODE="shell"
 SETUP_NVIDIA=0
-REPOSITORY="EESSI"
+REPOSITORIES=()
 RESUME=
 SAVE=
 HTTP_PROXY=${http_proxy:-}
@@ -179,7 +184,7 @@ while [[ $# -gt 0 ]]; do
       shift 2
       ;;
     -r|--repository)
-      REPOSITORY="$2"
+      REPOSITORIES+=("$2")
       shift 2
       ;;
     -s|--save)
@@ -221,22 +226,50 @@ done
 
 set -- "${POSITIONAL_ARGS[@]}"
 
+# define a list of CVMFS repositories that are accessible via the
+# CVMFS config repository which is always mounted
+declare -A eessi_cvmfs_repos=(["dev.eessi.io"]="extra", ["riscv.eessi.io"]="extra", ["software.eessi.io"]="default")
+eessi_default_cvmfs_repo="software.eessi.io"
+
+# if REPOSITORIES is empty add default repository given above
+if [[ ${#REPOSITORIES[@]} -eq 0 ]]; then
+    REPOSITORIES+=(${eessi_default_cvmfs_repo})
+fi
+
+# define a list of CVMFS repositories that are accessible via the
+# configuration file provided via $EESSI_REPOS_CFG_FILE
+declare -A cfg_cvmfs_repos=()
+if [[ -r ${EESSI_REPOS_CFG_FILE} ]]; then
+    cfg_load ${EESSI_REPOS_CFG_FILE}
+    sections=$(cfg_sections)
+    while IFS= read -r repo_id
+    do
+        cfg_cvmfs_repos[${repo_id}]=${EESSI_REPOS_CFG_FILE}
+    done <<< "${sections}"
+fi
+
 if [[ ${LIST_REPOS} -eq 1 ]]; then
-    echo "Listing available repositories with format 'name [source]':"
-    echo "    EESSI [default]"
-    if [[ -r ${EESSI_REPOS_CFG_FILE} ]]; then
-        cfg_load ${EESSI_REPOS_CFG_FILE}
-        sections=$(cfg_sections)
-        while IFS= read -r repo_id
-        do
-            echo "    ${repo_id} [${EESSI_REPOS_CFG_FILE}]"
-        done <<< "${sections}"
-    fi
+    echo "Listing available repositories with format 'name [source[, 'default']]'."
+    echo "Note, without argument '--repository' the one labeled 'default' will be mounted."
+    for cvmfs_repo in "${!eessi_cvmfs_repos[@]}"
+    do
+        if [[ ${eessi_cvmfs_repos[${cvmfs_repo}]} == "default" ]] ; then
+            default_label=", default"
+        else
+            default_label=""
+	fi
+        echo "    ${cvmfs_repo} [CVMFS config repo${default_label}]"
+    done
+    for cfg_repo in "${!cfg_cvmfs_repos[@]}"
+    do
+        echo "    ${cfg_repo} [${cfg_cvmfs_repos[$cfg_repo]}]"
+    done
     exit 0
 fi
 
 # 1. check if argument values are valid
 # (arg -a|--access) check if ACCESS is supported
+# TODO use the value as global setting, suffix to --repository can specify an access mode per repository
 if [[ "${ACCESS}" != "ro" && "${ACCESS}" != "rw" ]]; then
     fatal_error "unknown access method '${ACCESS}'" "${ACCESS_UNKNOWN_EXITCODE}"
 fi
@@ -260,10 +293,16 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
     fi
 fi
 
-# TODO (arg -r|--repository) check if repository is known
+# TODO (arg -r|--repository) check if all explicitly listed repositories are known
 # REPOSITORY_ERROR_EXITCODE
-if [[ ! -z "${REPOSITORY}" && "${REPOSITORY}" != "EESSI" && ! -r ${EESSI_REPOS_CFG_FILE} ]]; then
-    fatal_error "arg '--repository ${REPOSITORY}' requires a cfg file at '${EESSI_REPOS_CFG_FILE}'" "${REPOSITORY_ERROR_EXITCODE}"
+if [[ ${#REPOSITORIES[@]} -ne 0 ]] ; then
+    # iterate over entries in REPOSITORIES and check if they are known
+    for cvmfs_repo in "${REPOSITORIES[@]}"
+    do
+        if [[ ! -n "${eessi_cvmfs_repos[${cvmfs_repo}]}" && ! -n ${cfg_cvmfs_repos[${cvmfs_repo}]} ]]; then
+            fatal_error "The repository '${cvmfs_repo}' is not an EESSI CVMFS repository or it is not known how to mount it (could be due to a typo or missing configuration). Run '$0 -l' to obtain a list of available repositories." "${REPOSITORY_ERROR_EXITCODE}"
+        fi
+    done
 fi
 
 # TODO (arg -u|--resume) check if it exists, if user has read permission,
@@ -337,22 +376,36 @@ if [[ ! -z ${RESUME} && -f ${RESUME} ]]; then
 fi
 
 # 3. set up common vars and directories
+# TODO change to be able to support multiple CVMFS repositories
 #    directory structure should be:
 #      ${EESSI_HOST_STORAGE}
 #      |-singularity_cache
-#      |-${CVMFS_VAR_LIB}
-#      |-${CVMFS_VAR_RUN}
-#      |-overlay-upper
-#      |-overlay-work
 #      |-home
 #      |-repos_cfg
-#      |-opt-eessi (unless otherwise specificed for host_injections)
+#      |-CVMFS_REPO_1
+#      |   |-repo_settings (name, access_mode, host_injections)
+#      |   |-${CVMFS_VAR_LIB}
+#      |   |-${CVMFS_VAR_RUN}
+#      |   |-overlay-upper
+#      |   |-overlay-work
+#      |   |-opt-eessi (unless otherwise specificed for host_injections)
+#      |-CVMFS_REPO_n
+#          |-repo_settings (name, access_mode, host_injections)
+#          |-${CVMFS_VAR_LIB}
+#          |-${CVMFS_VAR_RUN}
+#          |-overlay-upper
+#          |-overlay-work
+#          |-opt-eessi (unless otherwise specificed for host_injections)
 
 # tmp dir for EESSI
 EESSI_TMPDIR=${EESSI_HOST_STORAGE}
 mkdir -p ${EESSI_TMPDIR}
 [[ ${VERBOSE} -eq 1 ]] && echo "EESSI_TMPDIR=${EESSI_TMPDIR}"
 
+# TODO make this specific to repository
+# TODO move this code to when we already know which repositories we want to access
+#      actually we should know this already here, but we should rather move this to
+#      where repository args are being processed
 # Set host_injections directory and ensure it is a writable directory (if user provided)
 if [ -z ${USER_HOST_INJECTIONS+x} ]; then
     # Not set, so use our default
@@ -486,6 +539,8 @@ if [[ ${FAKEROOT} -eq 1 ]]; then
   ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
 fi
 
+exit 0; # CONTINUE HERE
+# TODO iterate over repositories in array REPOSITORIES
 # set up repository config (always create directory repos_cfg and populate it with info when
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg

From 4057496eabede14e228fe08d2fec670870411a1b Mon Sep 17 00:00:00 2001
From: julianmorillo <julianmorillo@users.noreply.github.com>
Date: Tue, 18 Jun 2024 12:00:19 +0200
Subject: [PATCH 159/203] Update eessi-2023.06-eb-4.9.2-2023b.yml including DLB

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index c23b5b001d..38bfa81142 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - IPython-8.17.2-GCCcore-13.2.0.eb
+  - dlb-3.4-gompi-2023b.eb

From c7a1ca2fbbb736b3eea2242c7143aaa3be063fca Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Tue, 18 Jun 2024 15:05:17 +0200
Subject: [PATCH 160/203] further changes to support multiple repositories

---
 eessi_container.sh | 248 +++++++++++++++++++++++++++------------------
 1 file changed, 148 insertions(+), 100 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 9b1ab69a3b..d561d37792 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -228,16 +228,14 @@ set -- "${POSITIONAL_ARGS[@]}"
 
 # define a list of CVMFS repositories that are accessible via the
 # CVMFS config repository which is always mounted
+# TODO instead of hard-coding the 'extra' and 'default' repositories here one
+#      could have another script in the GitHub and/or CVMFS repository which
+#      provides this "configuration"
 declare -A eessi_cvmfs_repos=(["dev.eessi.io"]="extra", ["riscv.eessi.io"]="extra", ["software.eessi.io"]="default")
-eessi_default_cvmfs_repo="software.eessi.io"
-
-# if REPOSITORIES is empty add default repository given above
-if [[ ${#REPOSITORIES[@]} -eq 0 ]]; then
-    REPOSITORIES+=(${eessi_default_cvmfs_repo})
-fi
+eessi_default_cvmfs_repo="software.eessi.io,access=${ACCESS}"
 
 # define a list of CVMFS repositories that are accessible via the
-# configuration file provided via $EESSI_REPOS_CFG_FILE
+#   configuration file provided via $EESSI_REPOS_CFG_FILE
 declare -A cfg_cvmfs_repos=()
 if [[ -r ${EESSI_REPOS_CFG_FILE} ]]; then
     cfg_load ${EESSI_REPOS_CFG_FILE}
@@ -267,6 +265,11 @@ if [[ ${LIST_REPOS} -eq 1 ]]; then
     exit 0
 fi
 
+# if REPOSITORIES is empty add default repository given above
+if [[ ${#REPOSITORIES[@]} -eq 0 ]]; then
+    REPOSITORIES+=(${eessi_default_cvmfs_repo})
+fi
+
 # 1. check if argument values are valid
 # (arg -a|--access) check if ACCESS is supported
 # TODO use the value as global setting, suffix to --repository can specify an access mode per repository
@@ -295,15 +298,45 @@ fi
 
 # TODO (arg -r|--repository) check if all explicitly listed repositories are known
 # REPOSITORY_ERROR_EXITCODE
-if [[ ${#REPOSITORIES[@]} -ne 0 ]] ; then
-    # iterate over entries in REPOSITORIES and check if they are known
-    for cvmfs_repo in "${REPOSITORIES[@]}"
-    do
-        if [[ ! -n "${eessi_cvmfs_repos[${cvmfs_repo}]}" && ! -n ${cfg_cvmfs_repos[${cvmfs_repo}]} ]]; then
-            fatal_error "The repository '${cvmfs_repo}' is not an EESSI CVMFS repository or it is not known how to mount it (could be due to a typo or missing configuration). Run '$0 -l' to obtain a list of available repositories." "${REPOSITORY_ERROR_EXITCODE}"
+# iterate over entries in REPOSITORIES and check if they are known
+for cvmfs_repo in "${REPOSITORIES[@]}"
+do
+    # split into name and access mode if ',access=' in $cvmfs_repo
+    if [[ ${cvmfs_repo} == *",access="* ]] ; then
+        cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
+    else
+        cvmfs_repo_name="${cvmfs_repo}"
+    fi
+    if [[ ! -n "${eessi_cvmfs_repos[${cvmfs_repo_name}]}" && ! -n ${cfg_cvmfs_repos[${cvmfs_repo_name}]} ]]; then
+        fatal_error "The repository '${cvmfs_repo_name}' is not an EESSI CVMFS repository or it is not known how to mount it (could be due to a typo or missing configuration). Run '$0 -l' to obtain a list of available repositories." "${REPOSITORY_ERROR_EXITCODE}"
+    fi
+done
+
+# make sure each repository is only listed once
+declare -A listed_repos=()
+for cvmfs_repo in "${REPOSITORIES[@]}"
+do
+    cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode
+    echo "checking for duplicates: '${cvmfs_repo}' and '${cvmfs_repo_name}'"
+    # if cvmfs_repo_name is not in eessi_cvmfs_repos, assume it's in cfg_cvmfs_repos
+    #   and obtain actual repo_name from config
+    cfg_repo_id=''
+    if [[ ! -n "${eessi_cvmfs_repos[${cvmfs_repo_name}]}" ]] ; then
+        [[ ${VERBOSE} -eq 1 ]] && echo "repo '${cvmfs_repo_name}' is not an EESSI CVMFS repository..."
+        # cvmfs_repo_name is actually a repository ID, use that to obtain
+	#   the actual name from the EESSI_REPOS_CFG_FILE
+        cfg_repo_id=${cvmfs_repo_name}
+        cvmfs_repo_name=$(cfg_get_value ${cfg_repo_id} "repo_name")
+    fi
+    if [[ -n "${listed_repos[${cvmfs_repo_name}]}" ]] ; then
+        via_cfg=""
+        if [[ -n "${cfg_repo_id}" ]] ; then
+            via_cfg=" (via repository ID '${cfg_repo_id}')"
         fi
-    done
-fi
+        fatal_error "CVMFS repository '${cvmfs_repo_name}'${via_cfg} listed multiple times"
+    fi
+    listed_repos+=([${cvmfs_repo_name}]=true)
+done
 
 # TODO (arg -u|--resume) check if it exists, if user has read permission,
 #      if it contains data from a previous run
@@ -382,17 +415,15 @@ fi
 #      |-singularity_cache
 #      |-home
 #      |-repos_cfg
+#      |-${CVMFS_VAR_LIB}
+#      |-${CVMFS_VAR_RUN}
 #      |-CVMFS_REPO_1
 #      |   |-repo_settings (name, access_mode, host_injections)
-#      |   |-${CVMFS_VAR_LIB}
-#      |   |-${CVMFS_VAR_RUN}
 #      |   |-overlay-upper
 #      |   |-overlay-work
 #      |   |-opt-eessi (unless otherwise specificed for host_injections)
 #      |-CVMFS_REPO_n
 #          |-repo_settings (name, access_mode, host_injections)
-#          |-${CVMFS_VAR_LIB}
-#          |-${CVMFS_VAR_RUN}
 #          |-overlay-upper
 #          |-overlay-work
 #          |-opt-eessi (unless otherwise specificed for host_injections)
@@ -402,7 +433,7 @@ EESSI_TMPDIR=${EESSI_HOST_STORAGE}
 mkdir -p ${EESSI_TMPDIR}
 [[ ${VERBOSE} -eq 1 ]] && echo "EESSI_TMPDIR=${EESSI_TMPDIR}"
 
-# TODO make this specific to repository
+# TODO make this specific to repository?
 # TODO move this code to when we already know which repositories we want to access
 #      actually we should know this already here, but we should rather move this to
 #      where repository args are being processed
@@ -481,6 +512,7 @@ fi
 [[ ${VERBOSE} -eq 1 ]] && echo "CONTAINER=${CONTAINER}"
 
 # set env vars and create directories for CernVM-FS
+# TODO need to use separate values for separate repos?
 EESSI_CVMFS_VAR_LIB=${EESSI_TMPDIR}/${CVMFS_VAR_LIB}
 EESSI_CVMFS_VAR_RUN=${EESSI_TMPDIR}/${CVMFS_VAR_RUN}
 mkdir -p ${EESSI_CVMFS_VAR_LIB}
@@ -539,92 +571,106 @@ if [[ ${FAKEROOT} -eq 1 ]]; then
   ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
 fi
 
-exit 0; # CONTINUE HERE
 # TODO iterate over repositories in array REPOSITORIES
 # set up repository config (always create directory repos_cfg and populate it with info when
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg
-if [[ "${REPOSITORY}" == "EESSI" ]]; then
-  # need to source defaults as late as possible (see other sourcing below)
-  source ${TOPDIR}/init/eessi_defaults
-
-  # strip "/cvmfs/" from default setting
-  repo_name=${EESSI_CVMFS_REPO/\/cvmfs\//}
-else
-  # TODO implement more flexible specification of repo cfgs
-  #      REPOSITORY => repo-id OR repo-cfg-file (with a single section) OR
-  #                    repo-cfg-file:repo-id (repo-id defined in repo-cfg-file)
-  #
-  # for now, assuming repo-id is defined in config file pointed to
-  #   EESSI_REPOS_CFG_FILE, which is to be copied into the working directory
-  #   (could also become part of the software layer to define multiple
-  #    standard EESSI repositories)
-  cfg_load ${EESSI_REPOS_CFG_FILE}
-
-  # copy repos.cfg to job directory --> makes it easier to inspect the job
-  cp -a ${EESSI_REPOS_CFG_FILE} ${EESSI_TMPDIR}/repos_cfg/.
-
-  # cfg file should include: repo_name, repo_version, config_bundle,
-  #   map { local_filepath -> container_filepath }
-  #
-  # repo_name_domain is the domain part of the repo_name, e.g.,
-  #   eessi.io for software.eessi.io
-  #
-  # where config bundle includes the files (-> target location in container)
-  # - default.local -> /etc/cvmfs/default.local
-  #   contains CVMFS settings, e.g., CVMFS_HTTP_PROXY, CVMFS_QUOTA_LIMIT, ...
-  # - ${repo_name_domain}.conf -> /etc/cvmfs/domain.d/${repo_name_domain}.conf
-  #   contains CVMFS settings, e.g., CVMFS_SERVER_URL (Stratum 1s),
-  #   CVMFS_KEYS_DIR, CVMFS_USE_GEOAPI, ...
-  # - ${repo_name_domain}/ -> /etc/cvmfs/keys/${repo_name_domain}
-  #   a directory that contains the public key to access the repository, key
-  #   itself then doesn't need to be BIND mounted
-  # - ${repo_name_domain}/${repo_name}.pub
-  #   (-> /etc/cvmfs/keys/${repo_name_domain}/${repo_name}.pub
-  #   the public key to access the repository, key itself is BIND mounted
-  #   via directory ${repo_name_domain}
-  repo_name=$(cfg_get_value ${REPOSITORY} "repo_name")
-  # derive domain part from repo_name (everything after first '.')
-  repo_name_domain=${repo_name#*.}
-  repo_version=$(cfg_get_value ${REPOSITORY} "repo_version")
-  config_bundle=$(cfg_get_value ${REPOSITORY} "config_bundle")
-  config_map=$(cfg_get_value ${REPOSITORY} "config_map")
-
-  # convert config_map into associative array cfg_file_map
-  cfg_init_file_map "${config_map}"
-  [[ ${VERBOSE} -eq 1 ]] && cfg_print_map
-
-  # use information to set up dir ${EESSI_TMPDIR}/repos_cfg,
-  #     define BIND mounts and override repo name and version
-  # check if config_bundle exists, if so, unpack it into ${EESSI_TMPDIR}/repos_cfg
-  # if config_bundle is relative path (no '/' at start) prepend it with
-  # EESSI_REPOS_CFG_DIR
-  config_bundle_path=
-  if [[ ! "${config_bundle}" =~ ^/ ]]; then
-      config_bundle_path=${EESSI_REPOS_CFG_DIR}/${config_bundle}
-  else
-      config_bundle_path=${config_bundle}
-  fi
+[[ ${VERBOSE} -eq 1 ]] && echo
+[[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS before processing REPOSITORIES\n  BIND_PATHS=${BIND_PATHS}"
+[[ ${VERBOSE} -eq 1 ]] && echo
+for cvmfs_repo in "${REPOSITORIES[@]}"
+do
+    echo "process CVMFS repo spec '${cvmfs_repo}'"
+    # split into name and access mode if ',access=' in $cvmfs_repo
+    if [[ ${cvmfs_repo} == *",access="* ]] ; then
+        cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
+        cvmfs_repo_access=${cvmfs_repo/*,access=/} # remove repo name part
+    else
+        cvmfs_repo_name="${cvmfs_repo}"
+        cvmfs_repo_access="${ACCESS}" # use globally defined access mode
+    fi
+    # if cvmfs_repo_name is in cfg_cvmfs_repos, it is a "repository ID" and was
+    #   derived from information in EESSI_REPOS_CFG_FILE, namely the section
+    #   names in that .ini-type file
+    # in the if-block below, we'll use cfg_repo_id to refer to that ID
+    # we need to process/provide the config from EESSI_REPOS_CFG_FILE, such
+    #   that the necessary information for accessing a CVMFS repository is made
+    #   available inside the container
+    if [[ -n "${cfg_cvmfs_repos[${cvmfs_repo_name}]}" ]] ; then
+	cfg_repo_id=${cvmfs_repo_name}
+
+	# obtain CVMFS repository name from section for the given ID
+        cfg_repo_name=$(cfg_get_value ${cfg_repo_id} "repo_name")
+	# derive domain part from (cfg_)repo_name (everything after first '.')
+        repo_name_domain=${repo_name#*.}
+
+        # cfg_cvmfs_repos is populated through reading the file pointed to by
+        #   EESSI_REPOS_CFG_FILE. We need to copy that file and data it needs
+        #   into the job's working directory.
+
+        # copy repos.cfg to job directory --> makes it easier to inspect the job
+        cp -a ${EESSI_REPOS_CFG_FILE} ${EESSI_TMPDIR}/repos_cfg/.
+
+	# cfg file should include sections (one per CVMFS repository to be mounted)
+	#   with each section containing the settings:
+	#   - repo_name,
+	#   - repo_version,
+	#   - config_bundle, and
+	#   - a map { filepath_in_bundle -> container_filepath }
+        #
+	# The config_bundle includes the files which are mapped ('->') to a target
+	# location in container:
+        # - default.local -> /etc/cvmfs/default.local
+        #   contains CVMFS settings, e.g., CVMFS_HTTP_PROXY, CVMFS_QUOTA_LIMIT, ...
+        # - ${repo_name_domain}.conf -> /etc/cvmfs/domain.d/${repo_name_domain}.conf
+        #   contains CVMFS settings, e.g., CVMFS_SERVER_URL (Stratum 1s),
+        #   CVMFS_KEYS_DIR, CVMFS_USE_GEOAPI, ...
+        # - ${repo_name_domain}/ -> /etc/cvmfs/keys/${repo_name_domain}
+        #   a directory that contains the public key to access the repository, key
+        #   itself then doesn't need to be BIND mounted
+        # - ${repo_name_domain}/${cfg_repo_name}.pub
+        #   (-> /etc/cvmfs/keys/${repo_name_domain}/${cfg_repo_name}.pub
+        #   the public key to access the repository, key itself is BIND mounted
+        #   via directory ${repo_name_domain}
+        cfg_repo_version=$(cfg_get_value ${cfg_repo_id} "repo_version")
+        cfg_config_bundle=$(cfg_get_value ${cfg_repo_id} "config_bundle")
+        cfg_config_map=$(cfg_get_value ${cfg_repo_id} "config_map")
+
+        # convert cfg_config_map into associative array cfg_file_map
+        cfg_init_file_map "${cfg_config_map}"
+        [[ ${VERBOSE} -eq 1 ]] && cfg_print_map
+
+        # use information to set up dir ${EESSI_TMPDIR}/repos_cfg and define
+        #   BIND mounts
+        # check if config_bundle exists, if so, unpack it into
+	#   ${EESSI_TMPDIR}/repos_cfg; if it doesn't, exit with an error
+        # if config_bundle is relative path (no '/' at start) prepend it with
+        #   EESSI_REPOS_CFG_DIR
+        config_bundle_path=
+        if [[ ! "${cfg_config_bundle}" =~ ^/ ]]; then
+            config_bundle_path=${EESSI_REPOS_CFG_DIR}/${cfg_config_bundle}
+        else
+            config_bundle_path=${cfg_config_bundle}
+        fi
 
-  if [[ ! -r ${config_bundle_path} ]]; then
-    fatal_error "config bundle '${config_bundle_path}' is not readable" ${REPOSITORY_ERROR_EXITCODE}
-  fi
+        if [[ ! -r ${config_bundle_path} ]]; then
+            fatal_error "config bundle '${config_bundle_path}' is not readable" ${REPOSITORY_ERROR_EXITCODE}
+        fi
 
-  # only unpack config_bundle if we're not resuming from a previous run
-  if [[ -z ${RESUME} ]]; then
-    tar xf ${config_bundle_path} -C ${EESSI_TMPDIR}/repos_cfg
-  fi
+        # only unpack cfg_config_bundle if we're not resuming from a previous run
+        if [[ -z ${RESUME} ]]; then
+            tar xf ${config_bundle_path} -C ${EESSI_TMPDIR}/repos_cfg
+        fi
 
-  for src in "${!cfg_file_map[@]}"
-  do
-    target=${cfg_file_map[${src}]}
-    BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
-  done
-  export EESSI_VERSION_OVERRIDE=${repo_version}
-  export EESSI_CVMFS_REPO_OVERRIDE="/cvmfs/${repo_name}"
-  # need to source defaults as late as possible (after *_OVERRIDEs)
-  source ${TOPDIR}/init/eessi_defaults
-fi
+        for src in "${!cfg_file_map[@]}"
+        do
+            target=${cfg_file_map[${src}]}
+            BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
+        done
+    fi
+    [[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS after processing '${cvmfs_repo}'\n  BIND_PATHS=${BIND_PATHS}"
+    [[ ${VERBOSE} -eq 1 ]] && echo
+done
 
 # if http_proxy is not empty, we assume that the machine accesses internet
 # via a proxy. then we need to add CVMFS_HTTP_PROXY to
@@ -650,14 +696,16 @@ if [[ ! -z ${http_proxy} ]]; then
         export BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/default.local:/etc/cvmfs/default.local"
     fi
 fi
+exit 0; # CONTINUE HERE
 
 # 4. set up vars and dirs specific to a scenario
 
 declare -a EESSI_FUSE_MOUNTS=()
 
-# always mount cvmfs-config repo (to get access to software.eessi.io)
+# always mount cvmfs-config repo (to get access to EESSI repositories such as software.eessi.io)
 EESSI_FUSE_MOUNTS+=("--fusemount" "container:cvmfs2 cvmfs-config.cern.ch /cvmfs/cvmfs-config.cern.ch")
 
+# TODO iterate over REPOSITORIES and either use repository-specific access mode or global setting (possibly a global default)
 if [[ "${ACCESS}" == "ro" ]]; then
   export EESSI_READONLY="container:cvmfs2 ${repo_name} /cvmfs/${repo_name}"
 

From 934059a731f55d5a11cc10b6e3719abf65b1d478 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Wed, 19 Jun 2024 15:21:27 +0200
Subject: [PATCH 161/203] configure multiple fusemounts

---
 eessi_container.sh | 123 +++++++++++++++++++++++++++------------------
 1 file changed, 74 insertions(+), 49 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index d561d37792..c549d04d8c 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -52,7 +52,6 @@ NVIDIA_MODE_UNKNOWN_EXITCODE=$((${ANY_ERROR_EXITCODE} << 12))
 declare -A cvmfs_repo_settings
 
 # CernVM-FS settings
-# TODO may need to put them into repository specific map
 CVMFS_VAR_LIB="var-lib-cvmfs"
 CVMFS_VAR_RUN="var-run-cvmfs"
 
@@ -272,7 +271,7 @@ fi
 
 # 1. check if argument values are valid
 # (arg -a|--access) check if ACCESS is supported
-# TODO use the value as global setting, suffix to --repository can specify an access mode per repository
+# use the value as global setting, suffix to --repository can specify an access mode per repository
 if [[ "${ACCESS}" != "ro" && "${ACCESS}" != "rw" ]]; then
     fatal_error "unknown access method '${ACCESS}'" "${ACCESS_UNKNOWN_EXITCODE}"
 fi
@@ -317,7 +316,7 @@ declare -A listed_repos=()
 for cvmfs_repo in "${REPOSITORIES[@]}"
 do
     cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode
-    echo "checking for duplicates: '${cvmfs_repo}' and '${cvmfs_repo_name}'"
+    [[ ${VERBOSE} -eq 1 ]] && echo "checking for duplicates: '${cvmfs_repo}' and '${cvmfs_repo_name}'"
     # if cvmfs_repo_name is not in eessi_cvmfs_repos, assume it's in cfg_cvmfs_repos
     #   and obtain actual repo_name from config
     cfg_repo_id=''
@@ -409,7 +408,6 @@ if [[ ! -z ${RESUME} && -f ${RESUME} ]]; then
 fi
 
 # 3. set up common vars and directories
-# TODO change to be able to support multiple CVMFS repositories
 #    directory structure should be:
 #      ${EESSI_HOST_STORAGE}
 #      |-singularity_cache
@@ -528,14 +526,18 @@ fi
 [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_HOME=${SINGULARITY_HOME}"
 
 # define paths to add to SINGULARITY_BIND (added later when all BIND mounts are defined)
-BIND_PATHS="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
+if [[ -z ${SINGULARITY_BIND} ]] ; then
+    SINGULARITY_BIND="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
+else
+    SINGULARITY_BIND="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi,${SINGULARITY_BIND}"
+fi
 # provide a '/tmp' inside the container
-BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
+SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
 if [[ ! -z ${EXTRA_BIND_PATHS} ]]; then
-    BIND_PATHS="${BIND_PATHS},${EXTRA_BIND_PATHS}"
+    SINGULARITY_BIND="${SINGULARITY_BIND},${EXTRA_BIND_PATHS}"
 fi
 
-[[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
+[[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
 
 declare -a ADDITIONAL_CONTAINER_OPTIONS=()
 
@@ -556,8 +558,8 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         EESSI_USR_LOCAL_CUDA=${EESSI_TMPDIR}/usr-local-cuda
         mkdir -p ${EESSI_VAR_LOG}
         mkdir -p ${EESSI_USR_LOCAL_CUDA}
-        BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
-        [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
+        SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
+        [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
         if [[ "${NVIDIA_MODE}" == "install" ]] ; then
             # No GPU so we need to "trick" Lmod to allow us to load CUDA modules even without a CUDA driver
             # (this variable means EESSI_OVERRIDE_GPU_CHECK=1 will be set inside the container)
@@ -571,16 +573,16 @@ if [[ ${FAKEROOT} -eq 1 ]]; then
   ADDITIONAL_CONTAINER_OPTIONS+=("--fakeroot")
 fi
 
-# TODO iterate over repositories in array REPOSITORIES
 # set up repository config (always create directory repos_cfg and populate it with info when
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg
 [[ ${VERBOSE} -eq 1 ]] && echo
-[[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS before processing REPOSITORIES\n  BIND_PATHS=${BIND_PATHS}"
+[[ ${VERBOSE} -eq 1 ]] && echo -e "SINGULARITY_BIND before processing REPOSITORIES\n  SINGULARITY_BIND=${SINGULARITY_BIND}"
 [[ ${VERBOSE} -eq 1 ]] && echo
+# iterate over repositories in array REPOSITORIES
 for cvmfs_repo in "${REPOSITORIES[@]}"
 do
-    echo "process CVMFS repo spec '${cvmfs_repo}'"
+    [[ ${VERBOSE} -eq 1 ]] && echo "process CVMFS repo spec '${cvmfs_repo}'"
     # split into name and access mode if ',access=' in $cvmfs_repo
     if [[ ${cvmfs_repo} == *",access="* ]] ; then
         cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
@@ -665,17 +667,21 @@ do
         for src in "${!cfg_file_map[@]}"
         do
             target=${cfg_file_map[${src}]}
-            BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
+            # if target is alreay BIND mounted, exit with an error
+            if [[ ${SINGULARITY_BIND} =~ "${target}" ]]; then
+                fatal_error "target '${target}' is already listed in paths to bind mount into the container ('${SINGULARITY_BIND}')" ${REPOSITORY_ERROR_EXITCODE}
+            fi
+            export SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
         done
     fi
-    [[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS after processing '${cvmfs_repo}'\n  BIND_PATHS=${BIND_PATHS}"
+    [[ ${VERBOSE} -eq 1 ]] && echo -e "SINGULARITY_BIND after processing '${cvmfs_repo}'\n  SINGULARITY_BIND=${SINGULARITY_BIND}"
     [[ ${VERBOSE} -eq 1 ]] && echo
 done
 
 # if http_proxy is not empty, we assume that the machine accesses internet
 # via a proxy. then we need to add CVMFS_HTTP_PROXY to
-# ${EESSI_TMPDIR}/repos_cfg/default.local on host (and possibly add a BIND
-# MOUNT if it was not yet in BIND_PATHS)
+# ${EESSI_TMPDIR}/repos_cfg/default.local on the host (and possibly add a BIND
+# MOUNT if it was not yet in SINGULARITY_BIND)
 if [[ ! -z ${http_proxy} ]]; then
     # TODO tolerate other formats for proxy URLs, for now assume format is
     # http://SOME_HOSTNAME:SOME_PORT/
@@ -691,12 +697,14 @@ if [[ ! -z ${http_proxy} ]]; then
     [[ ${VERBOSE} -eq 1 ]] && echo "contents of default.local"
     [[ ${VERBOSE} -eq 1 ]] && cat ${EESSI_TMPDIR}/repos_cfg/default.local
 
-    # if default.local is not BIND mounted into container, add it to BIND_PATHS
-    if [[ ! ${BIND_PATHS} =~ "${EESSI_TMPDIR}/repos_cfg/default.local:/etc/cvmfs/default.local" ]]; then
-        export BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/default.local:/etc/cvmfs/default.local"
+    # if default.local is not BIND mounted into container, add it to SINGULARITY_BIND
+    src=${EESSI_TMPDIR}/repos_cfg/default.local
+    target=/etc/cvmfs/default.local
+    if [[ ${SINGULARITY_BIND} =~ "${target}" ]]; then
+        fatal_error "BIND target in '${src}:${target}' is already in paths to be bind mounted into the container ('${SINGULARITY_BIND}')" ${REPOSITORY_ERROR_EXITCODE}
     fi
+    export SINGULARITY_BIND="${SINGULARITY_BIND},${src}:${target}"
 fi
-exit 0; # CONTINUE HERE
 
 # 4. set up vars and dirs specific to a scenario
 
@@ -705,42 +713,59 @@ declare -a EESSI_FUSE_MOUNTS=()
 # always mount cvmfs-config repo (to get access to EESSI repositories such as software.eessi.io)
 EESSI_FUSE_MOUNTS+=("--fusemount" "container:cvmfs2 cvmfs-config.cern.ch /cvmfs/cvmfs-config.cern.ch")
 
-# TODO iterate over REPOSITORIES and either use repository-specific access mode or global setting (possibly a global default)
-if [[ "${ACCESS}" == "ro" ]]; then
-  export EESSI_READONLY="container:cvmfs2 ${repo_name} /cvmfs/${repo_name}"
-
-  EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
-  export EESSI_FUSE_MOUNTS
-fi
+# iterate over REPOSITORIES and either use repository-specific access mode or global setting (possibly a global default)
+for cvmfs_repo in "${REPOSITORIES[@]}"
+do
+    [[ ${VERBOSE} -eq 1 ]] && echo "add fusemount options for CVMFS repo '${cvmfs_repo}'"
+    # split into name and access mode if ',access=' in $cvmfs_repo
+    if [[ ${cvmfs_repo} == *",access="* ]] ; then
+        cvmfs_repo_name=${cvmfs_repo/,access=*/} # remove access mode specification
+        cvmfs_repo_access=${cvmfs_repo/*,access=/} # remove repo name part
+    else
+        cvmfs_repo_name="${cvmfs_repo}"
+        cvmfs_repo_access="${ACCESS}" # use globally defined access mode
+    fi
+    # obtain cvmfs_repo_name from EESSI_REPOS_CFG_FILE if cvmfs_repo is in cfg_cvmfs_repos
+    if [[ ${cfg_cvmfs_repos[${cvmfs_repo_name}]} ]]; then
+        [[ ${VERBOSE} -eq 1 ]] && echo "repo '${cvmfs_repo_name}' is not an EESSI CVMFS repository..."
+        # cvmfs_repo_name is actually a repository ID, use that to obtain
+	#   the actual name from the EESSI_REPOS_CFG_FILE
+        cfg_repo_id=${cvmfs_repo_name}
+        cvmfs_repo_name=$(cfg_get_value ${cfg_repo_id} "repo_name")
+    fi
 
-if [[ "${ACCESS}" == "rw" ]]; then
-  mkdir -p ${EESSI_TMPDIR}/overlay-upper
-  mkdir -p ${EESSI_TMPDIR}/overlay-work
+    # add fusemount options depending on requested access mode ('ro' - read-only; 'rw' - read & write)
+    if [[ ${cvmfs_repo_access} == "ro" ]] ; then
+        export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs/${cvmfs_repo_name}"
 
-  # set environment variables for fuse mounts in Singularity container
-  export EESSI_READONLY="container:cvmfs2 ${repo_name} /cvmfs_ro/${repo_name}"
+        EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+        export EESSI_FUSE_MOUNTS
+    elif [[ ${cvmfs_repo_access} == "rw" ]] ; then
+        # use repo-specific overlay directories
+        mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}/overlay-upper
+        mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}/overlay-work
 
-  EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
+        # set environment variables for fuse mounts in Singularity container
+        export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
 
-  EESSI_WRITABLE_OVERLAY="container:fuse-overlayfs"
-  EESSI_WRITABLE_OVERLAY+=" -o lowerdir=/cvmfs_ro/${repo_name}"
-  EESSI_WRITABLE_OVERLAY+=" -o upperdir=${TMP_IN_CONTAINER}/overlay-upper"
-  EESSI_WRITABLE_OVERLAY+=" -o workdir=${TMP_IN_CONTAINER}/overlay-work"
-  EESSI_WRITABLE_OVERLAY+=" ${EESSI_CVMFS_REPO}"
-  export EESSI_WRITABLE_OVERLAY
+        EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_READONLY}")
 
-  EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_WRITABLE_OVERLAY}")
-  export EESSI_FUSE_MOUNTS
-fi
+        EESSI_WRITABLE_OVERLAY="container:fuse-overlayfs"
+        EESSI_WRITABLE_OVERLAY+=" -o lowerdir=/cvmfs_ro/${cvmfs_repo_name}"
+        EESSI_WRITABLE_OVERLAY+=" -o upperdir=${TMP_IN_CONTAINER}/${cvmfs_repo_name}/overlay-upper"
+        EESSI_WRITABLE_OVERLAY+=" -o workdir=${TMP_IN_CONTAINER}/${cvmfs_repo_name}/overlay-work"
+        EESSI_WRITABLE_OVERLAY+=" /cvmfs/${cvmfs_repo_name}"
+        export EESSI_WRITABLE_OVERLAY
 
+        EESSI_FUSE_MOUNTS+=("--fusemount" "${EESSI_WRITABLE_OVERLAY}")
+        export EESSI_FUSE_MOUNTS
+    else
+        echo -e "ERROR: access mode '${cvmfs_repo_access}' for CVMFS repository\n  '${cvmfs_repo_name}' is not known"
+	exit ${REPOSITORY_ERROR_EXITCODE}
+    fi
+done
 
 # 5. run container
-# final settings
-if [[ -z ${SINGULARITY_BIND} ]]; then
-    export SINGULARITY_BIND="${BIND_PATHS}"
-else
-    export SINGULARITY_BIND="${SINGULARITY_BIND},${BIND_PATHS}"
-fi
 [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
 
 # pass $EESSI_SOFTWARE_SUBDIR_OVERRIDE into build container (if set)

From 32f413328cd3b8f1da7ea7521f7458c20cd7232b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Wed, 19 Jun 2024 16:02:40 +0200
Subject: [PATCH 162/203] revert back changes related to BIND_PATHS and
 SINGULARITY_BIND + some polishing

---
 eessi_container.sh | 46 ++++++++++++++++++++++++----------------------
 1 file changed, 24 insertions(+), 22 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index c549d04d8c..163792f622 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -416,12 +416,10 @@ fi
 #      |-${CVMFS_VAR_LIB}
 #      |-${CVMFS_VAR_RUN}
 #      |-CVMFS_REPO_1
-#      |   |-repo_settings (name, access_mode, host_injections)
 #      |   |-overlay-upper
 #      |   |-overlay-work
 #      |   |-opt-eessi (unless otherwise specificed for host_injections)
 #      |-CVMFS_REPO_n
-#          |-repo_settings (name, access_mode, host_injections)
 #          |-overlay-upper
 #          |-overlay-work
 #          |-opt-eessi (unless otherwise specificed for host_injections)
@@ -526,18 +524,15 @@ fi
 [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_HOME=${SINGULARITY_HOME}"
 
 # define paths to add to SINGULARITY_BIND (added later when all BIND mounts are defined)
-if [[ -z ${SINGULARITY_BIND} ]] ; then
-    SINGULARITY_BIND="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
-else
-    SINGULARITY_BIND="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi,${SINGULARITY_BIND}"
-fi
+BIND_PATHS="${EESSI_CVMFS_VAR_LIB}:/var/lib/cvmfs,${EESSI_CVMFS_VAR_RUN}:/var/run/cvmfs,${HOST_INJECTIONS}:/opt/eessi"
+
 # provide a '/tmp' inside the container
-SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
+BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}:${TMP_IN_CONTAINER}"
 if [[ ! -z ${EXTRA_BIND_PATHS} ]]; then
-    SINGULARITY_BIND="${SINGULARITY_BIND},${EXTRA_BIND_PATHS}"
+    BIND_PATHS="${BIND_PATHS},${EXTRA_BIND_PATHS}"
 fi
 
-[[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
+[[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
 
 declare -a ADDITIONAL_CONTAINER_OPTIONS=()
 
@@ -558,8 +553,8 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         EESSI_USR_LOCAL_CUDA=${EESSI_TMPDIR}/usr-local-cuda
         mkdir -p ${EESSI_VAR_LOG}
         mkdir -p ${EESSI_USR_LOCAL_CUDA}
-        SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
-        [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
+        BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
+        [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
         if [[ "${NVIDIA_MODE}" == "install" ]] ; then
             # No GPU so we need to "trick" Lmod to allow us to load CUDA modules even without a CUDA driver
             # (this variable means EESSI_OVERRIDE_GPU_CHECK=1 will be set inside the container)
@@ -577,7 +572,7 @@ fi
 # arg -r|--repository is used)
 mkdir -p ${EESSI_TMPDIR}/repos_cfg
 [[ ${VERBOSE} -eq 1 ]] && echo
-[[ ${VERBOSE} -eq 1 ]] && echo -e "SINGULARITY_BIND before processing REPOSITORIES\n  SINGULARITY_BIND=${SINGULARITY_BIND}"
+[[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS before processing REPOSITORIES\n  BIND_PATHS=${BIND_PATHS}"
 [[ ${VERBOSE} -eq 1 ]] && echo
 # iterate over repositories in array REPOSITORIES
 for cvmfs_repo in "${REPOSITORIES[@]}"
@@ -668,20 +663,20 @@ do
         do
             target=${cfg_file_map[${src}]}
             # if target is alreay BIND mounted, exit with an error
-            if [[ ${SINGULARITY_BIND} =~ "${target}" ]]; then
-                fatal_error "target '${target}' is already listed in paths to bind mount into the container ('${SINGULARITY_BIND}')" ${REPOSITORY_ERROR_EXITCODE}
+            if [[ ${BIND_PATHS} =~ "${target}" ]]; then
+                fatal_error "target '${target}' is already listed in paths to bind mount into the container ('${BIND_PATHS}')" ${REPOSITORY_ERROR_EXITCODE}
             fi
-            export SINGULARITY_BIND="${SINGULARITY_BIND},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
+            BIND_PATHS="${BIND_PATHS},${EESSI_TMPDIR}/repos_cfg/${src}:${target}"
         done
     fi
-    [[ ${VERBOSE} -eq 1 ]] && echo -e "SINGULARITY_BIND after processing '${cvmfs_repo}'\n  SINGULARITY_BIND=${SINGULARITY_BIND}"
+    [[ ${VERBOSE} -eq 1 ]] && echo -e "BIND_PATHS after processing '${cvmfs_repo}'\n  BIND_PATHS=${BIND_PATHS}"
     [[ ${VERBOSE} -eq 1 ]] && echo
 done
 
 # if http_proxy is not empty, we assume that the machine accesses internet
 # via a proxy. then we need to add CVMFS_HTTP_PROXY to
 # ${EESSI_TMPDIR}/repos_cfg/default.local on the host (and possibly add a BIND
-# MOUNT if it was not yet in SINGULARITY_BIND)
+# MOUNT if it was not yet in BIND_PATHS)
 if [[ ! -z ${http_proxy} ]]; then
     # TODO tolerate other formats for proxy URLs, for now assume format is
     # http://SOME_HOSTNAME:SOME_PORT/
@@ -697,13 +692,13 @@ if [[ ! -z ${http_proxy} ]]; then
     [[ ${VERBOSE} -eq 1 ]] && echo "contents of default.local"
     [[ ${VERBOSE} -eq 1 ]] && cat ${EESSI_TMPDIR}/repos_cfg/default.local
 
-    # if default.local is not BIND mounted into container, add it to SINGULARITY_BIND
+    # if default.local is not BIND mounted into container, add it to BIND_PATHS
     src=${EESSI_TMPDIR}/repos_cfg/default.local
     target=/etc/cvmfs/default.local
-    if [[ ${SINGULARITY_BIND} =~ "${target}" ]]; then
-        fatal_error "BIND target in '${src}:${target}' is already in paths to be bind mounted into the container ('${SINGULARITY_BIND}')" ${REPOSITORY_ERROR_EXITCODE}
+    if [[ ${BIND_PATHS} =~ "${target}" ]]; then
+        fatal_error "BIND target in '${src}:${target}' is already in paths to be bind mounted into the container ('${BIND_PATHS}')" ${REPOSITORY_ERROR_EXITCODE}
     fi
-    export SINGULARITY_BIND="${SINGULARITY_BIND},${src}:${target}"
+    BIND_PATHS="${BIND_PATHS},${src}:${target}"
 fi
 
 # 4. set up vars and dirs specific to a scenario
@@ -744,6 +739,7 @@ do
         # use repo-specific overlay directories
         mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}/overlay-upper
         mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}/overlay-work
+	[[ ${VERBOSE} -eq 1 ]] && echo -e "TMP directory contents:\n$(ls -l ${EESSI_TMPDIR})"
 
         # set environment variables for fuse mounts in Singularity container
         export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs_ro/${cvmfs_repo_name}"
@@ -766,6 +762,12 @@ do
 done
 
 # 5. run container
+# final settings
+if [[ -z ${SINGULARITY_BIND} ]]; then
+    export SINGULARITY_BIND="${BIND_PATHS}"
+else
+    export SINGULARITY_BIND="${SINGULARITY_BIND},${BIND_PATHS}"
+fi
 [[ ${VERBOSE} -eq 1 ]] && echo "SINGULARITY_BIND=${SINGULARITY_BIND}"
 
 # pass $EESSI_SOFTWARE_SUBDIR_OVERRIDE into build container (if set)

From 07de7008e60586d146cd4986de9d0a4f7e505731 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Thu, 20 Jun 2024 09:07:24 +0200
Subject: [PATCH 163/203] store repository settings under tmp

---
 eessi_container.sh | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/eessi_container.sh b/eessi_container.sh
index 163792f622..eaa4f59af9 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -416,10 +416,12 @@ fi
 #      |-${CVMFS_VAR_LIB}
 #      |-${CVMFS_VAR_RUN}
 #      |-CVMFS_REPO_1
+#      |   |-repo_settings.sh (name, id, access, host_injections)
 #      |   |-overlay-upper
 #      |   |-overlay-work
 #      |   |-opt-eessi (unless otherwise specificed for host_injections)
 #      |-CVMFS_REPO_n
+#          |-repo_settings.sh (name, id, access, host_injections)
 #          |-overlay-upper
 #          |-overlay-work
 #          |-opt-eessi (unless otherwise specificed for host_injections)
@@ -711,6 +713,7 @@ EESSI_FUSE_MOUNTS+=("--fusemount" "container:cvmfs2 cvmfs-config.cern.ch /cvmfs/
 # iterate over REPOSITORIES and either use repository-specific access mode or global setting (possibly a global default)
 for cvmfs_repo in "${REPOSITORIES[@]}"
 do
+    unset cfg_repo_id
     [[ ${VERBOSE} -eq 1 ]] && echo "add fusemount options for CVMFS repo '${cvmfs_repo}'"
     # split into name and access mode if ',access=' in $cvmfs_repo
     if [[ ${cvmfs_repo} == *",access="* ]] ; then
@@ -729,6 +732,9 @@ do
         cvmfs_repo_name=$(cfg_get_value ${cfg_repo_id} "repo_name")
     fi
 
+    # always create a directory for the repository (e.g., to store settings, ...)
+    mkdir -p ${EESSI_TMPDIR}/${cvmfs_repo_name}
+
     # add fusemount options depending on requested access mode ('ro' - read-only; 'rw' - read & write)
     if [[ ${cvmfs_repo_access} == "ro" ]] ; then
         export EESSI_READONLY="container:cvmfs2 ${cvmfs_repo_name} /cvmfs/${cvmfs_repo_name}"
@@ -759,6 +765,20 @@ do
         echo -e "ERROR: access mode '${cvmfs_repo_access}' for CVMFS repository\n  '${cvmfs_repo_name}' is not known"
 	exit ${REPOSITORY_ERROR_EXITCODE}
     fi
+    # create repo_settings.sh file in ${EESSI_TMPDIR}/${cvmfs_repo_name} to store
+    #   (intention is that the file could be just sourced to obtain the settings)
+    # repo_name = ${cvmfs_repo_name}
+    # repo_id = ${cfg_repo_id} # empty if not an EESSI repo
+    # repo_access = ${cvmfs_repo_access}
+    # repo_host_injections = [ {"src_path":"target_path"}... ] # TODO
+    settings=
+    #[[ -n ${cfg_repo_id} ]] && settings="[${cvmfs_repo_name}]\n" || settings="[${cfg_repo_id}]\n"
+    settings="${settings}repo_name = ${cvmfs_repo_name}\n"
+    settings="${settings}repo_id = ${cfg_repo_id}\n"
+    settings="${settings}repo_access = ${cvmfs_repo_access}\n"
+    # TODO iterate over host_injections (first need means to define them (globally and/or per repository)
+    # settings="${settings}repo_host_injections = ${host_injections}\n"
+    echo -e "${settings}" > ${EESSI_TMPDIR}/${cvmfs_repo_name}/repo_settings.sh
 done
 
 # 5. run container

From 3da63162f66480d4c4430e6725800fc0769e90f1 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 24 Jun 2024 18:18:49 +0200
Subject: [PATCH 164/203] {2023.06,a64fx}[2023a] OpenMPI 4.1.5

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml              | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
new file mode 100644
index 0000000000..1475ad0866
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - OpenMPI-4.1.5-GCC-12.3.0.eb

From 871586fbb055a07ad7250a48a3a06c3ffec1d8b2 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 24 Jun 2024 18:49:22 +0200
Subject: [PATCH 165/203] use latest Ubuntu in CI workflows

---
 .github/workflows/test-software.eessi.io.yml      | 2 +-
 .github/workflows/test_eessi_container_script.yml | 2 +-
 .github/workflows/test_licenses.yml               | 2 +-
 .github/workflows/tests.yml                       | 2 +-
 .github/workflows/tests_archdetect.yml            | 2 +-
 .github/workflows/tests_init.yml                  | 2 +-
 .github/workflows/tests_readme.yml                | 2 +-
 .github/workflows/tests_scripts.yml               | 2 +-
 8 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test-software.eessi.io.yml b/.github/workflows/test-software.eessi.io.yml
index 8cfb023bc6..06c02c8834 100644
--- a/.github/workflows/test-software.eessi.io.yml
+++ b/.github/workflows/test-software.eessi.io.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   check_missing:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index 32120d0087..d31feb23fe 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   eessi_container_script:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
diff --git a/.github/workflows/test_licenses.yml b/.github/workflows/test_licenses.yml
index 3b9675d523..6b6387d47d 100644
--- a/.github/workflows/test_licenses.yml
+++ b/.github/workflows/test_licenses.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index faa7eb82ff..6af6a83e96 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [3.6, 3.7, 3.8, 3.9, '3.10']
diff --git a/.github/workflows/tests_archdetect.yml b/.github/workflows/tests_archdetect.yml
index bee348995d..4f5d3d174d 100644
--- a/.github/workflows/tests_archdetect.yml
+++ b/.github/workflows/tests_archdetect.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         proc_cpuinfo:
diff --git a/.github/workflows/tests_init.yml b/.github/workflows/tests_init.yml
index 053acb9730..aabe37de44 100644
--- a/.github/workflows/tests_init.yml
+++ b/.github/workflows/tests_init.yml
@@ -5,7 +5,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         python: [3.6, 3.7, 3.8, 3.9, '3.10']
diff --git a/.github/workflows/tests_readme.yml b/.github/workflows/tests_readme.yml
index efdb796e5e..76f46a8abe 100644
--- a/.github/workflows/tests_readme.yml
+++ b/.github/workflows/tests_readme.yml
@@ -14,7 +14,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
         - name: Check out software-layer repository
           uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
diff --git a/.github/workflows/tests_scripts.yml b/.github/workflows/tests_scripts.yml
index 76d19d29fe..6413fcf86f 100644
--- a/.github/workflows/tests_scripts.yml
+++ b/.github/workflows/tests_scripts.yml
@@ -28,7 +28,7 @@ permissions:
   contents: read # to fetch code (actions/checkout)
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     steps:
     - name: checkout
       uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1

From 70878f66586c49b0a2412754a7937482f7910803 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Mon, 24 Jun 2024 18:58:42 +0200
Subject: [PATCH 166/203] only run CI workflows with Python >= 3.7

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 .github/workflows/tests.yml      | 2 +-
 .github/workflows/tests_init.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 6af6a83e96..8249e50d9b 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10']
+        python: [3.7, 3.8, 3.9, '3.10']
       fail-fast: false
     steps:
     - name: checkout
diff --git a/.github/workflows/tests_init.yml b/.github/workflows/tests_init.yml
index aabe37de44..6c356a9184 100644
--- a/.github/workflows/tests_init.yml
+++ b/.github/workflows/tests_init.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: [3.6, 3.7, 3.8, 3.9, '3.10']
+        python: [3.7, 3.8, 3.9, '3.10']
       fail-fast: false
     steps:
     - name: checkout

From 0cb1d2af5ad9ad8f2ccdb7e9da9d2614c61781d0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 25 Jun 2024 09:29:21 +0200
Subject: [PATCH 167/203] implement hook to inject -DCACHE_SECTOR_SIZE_READONLY
 in $CFLAGS when building BLIS 0.9.0 on A64FX

---
 eb_hooks.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 8b0a11b0ed..fd3e0830ee 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -23,6 +23,7 @@
 CPU_TARGET_NEOVERSE_N1 = 'aarch64/neoverse_n1'
 CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1'
 CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic'
+CPU_TARGET_A64FX = 'aarch64/a64fx'
 
 EESSI_RPATH_OVERRIDE_ATTR = 'orig_rpath_override_dirs'
 
@@ -335,6 +336,19 @@ def pre_configure_hook(self, *args, **kwargs):
         PRE_CONFIGURE_HOOKS[self.name](self, *args, **kwargs)
 
 
+def pre_configure_hook_BLIS_a64fx(self, *args, **kwargs):
+    """
+    Pre-configure hook for BLIS when building for A64FX:
+    - add -DCACHE_SECTOR_SIZE_READONLY to $CFLAGS for BLIS 0.9.0, cfr. https://github.com/flame/blis/issues/800
+    """
+    if self.name == 'BLIS':
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if self.version == '0.9.0' and cpu_target == CPU_TARGET_A64FX:
+            self.cfg.update('configopts', 'CFLAGS="$CFLAGS -DCACHE_SECTOR_SIZE_READONLY"')
+    else:
+        raise EasyBuildError("BLIS-specific hook triggered for non-BLIS easyconfig?!")
+
+
 def pre_configure_hook_gromacs(self, *args, **kwargs):
     """
     Pre-configure hook for GROMACS:
@@ -680,12 +694,13 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
+    'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
+    'BLIS': pre_configure_hook_BLIS_a64fx,
     'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,
     'WRF': pre_configure_hook_wrf_aarch64,
-    'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
 }
 
 PRE_TEST_HOOKS = {

From 3aac7ea854e8f4613ad89fc8e15e2ca26df0af6f Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 25 Jun 2024 09:29:38 +0200
Subject: [PATCH 168/203] {2023.06,a64fx} foss/2023a

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
index 1475ad0866..3a060e30a7 100644
--- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - OpenMPI-4.1.5-GCC-12.3.0.eb
+  - foss-2023a.eb

From d9c1fb1104f19e741b8ac2a5a652eb22e07bf241 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Tue, 25 Jun 2024 10:17:51 +0200
Subject: [PATCH 169/203] removed unnecessary variable

---
 eessi_container.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index eaa4f59af9..4b7b4eb719 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -48,9 +48,6 @@ HTTPS_PROXY_ERROR_EXITCODE=$((${ANY_ERROR_EXITCODE} << 10))
 RUN_SCRIPT_MISSING_EXITCODE=$((${ANY_ERROR_EXITCODE} << 11))
 NVIDIA_MODE_UNKNOWN_EXITCODE=$((${ANY_ERROR_EXITCODE} << 12))
 
-# we use an associative array for storing sets of settings per CVMFS repository
-declare -A cvmfs_repo_settings
-
 # CernVM-FS settings
 CVMFS_VAR_LIB="var-lib-cvmfs"
 CVMFS_VAR_RUN="var-run-cvmfs"

From e25cd1e720a3a0e787409093d561d5892929d10a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Thomas=20R=C3=B6blitz?= <thomas.roblitz@uib.no>
Date: Tue, 25 Jun 2024 10:23:18 +0200
Subject: [PATCH 170/203] add more information about repository-specific access
 modes

---
 eessi_container.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 4b7b4eb719..9d2ce6c25f 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -70,7 +70,8 @@ export EESSI_REPOS_CFG_FILE="${EESSI_REPOS_CFG_DIR}/repos.cfg"
 display_help() {
   echo "usage: $0 [OPTIONS] [[--] SCRIPT or COMMAND]"
   echo " OPTIONS:"
-  echo "  -a | --access {ro,rw}   - ro (read-only), rw (read & write) [default: ro]"
+  echo "  -a | --access {ro,rw}   - sets access globally for all CVMFS repositories:"
+  echo "                            ro (read-only), rw (read & write) [default: ro]"
   echo "  -b | --extra-bind-paths - specify extra paths to be bound into the container."
   echo "                            To specify multiple bind paths, separate by comma."
   echo "                            Example: '/src:/dest:ro,/src2:/dest2:rw'"
@@ -89,7 +90,9 @@ display_help() {
   echo "                            MODE==install for a CUDA installation, MODE==run to"
   echo "                            attach a GPU, MODE==all for both [default: false]"
   echo "  -r | --repository CFG   - configuration file or identifier defining the"
-  echo "                            repository to use; can be given multiple times"
+  echo "                            repository to use; can be given multiple times;"
+  echo "                            CFG may include a suffix ';access={ro,rw}' to"
+  echo "                            overwrite the global access mode for this repository"
   echo "                            [default: software.eessi.io via CVMFS config available"
   echo "                            via default container, see --container]"
   echo "  -u | --resume DIR/TGZ   - resume a previous run from a directory or tarball,"

From da1b6710152dcf912db34147e88c739914e0290d Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Tue, 25 Jun 2024 18:16:24 +0200
Subject: [PATCH 171/203] fix hook to tweak BLIS configure command when
 building for A64FX

---
 eb_hooks.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index fd3e0830ee..b14c799eae 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -344,7 +344,12 @@ def pre_configure_hook_BLIS_a64fx(self, *args, **kwargs):
     if self.name == 'BLIS':
         cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
         if self.version == '0.9.0' and cpu_target == CPU_TARGET_A64FX:
-            self.cfg.update('configopts', 'CFLAGS="$CFLAGS -DCACHE_SECTOR_SIZE_READONLY"')
+            # last argument of BLIS' configure command is configuration target (usually 'auto' for auto-detect),
+            # specifying of variables should be done before that
+            config_opts = self.cfg['configopts'].split(' ')
+            cflags_var = 'CFLAGS="$CFLAGS -DCACHE_SECTOR_SIZE_READONLY"'
+            config_target = config_opts[-1]
+            self.cfg['configopts'] = ' '.join(config_opts[:-1] + [cflags_var, config_target])
     else:
         raise EasyBuildError("BLIS-specific hook triggered for non-BLIS easyconfig?!")
 

From 80d8d6e5789a972342fd57532e84d8df3a39bb88 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 26 Jun 2024 11:46:11 +0200
Subject: [PATCH 172/203] ignore scipy test failures when installing
 SciPy-bundle for A64FX

---
 eb_hooks.py                    | 22 ++++++++++++++++------
 eessi-2023.06-known-issues.yml |  7 +++++++
 2 files changed, 23 insertions(+), 6 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index b14c799eae..e6f0cf0dd2 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -488,20 +488,30 @@ def pre_test_hook_ignore_failing_tests_FFTWMPI(self, *args, **kwargs):
 def pre_test_hook_ignore_failing_tests_SciPybundle(self, *args, **kwargs):
     """
     Pre-test hook for SciPy-bundle: skip failing tests for selected SciPy-bundle versions
-    In version 2021.10, 2 failing tests in scipy 1.6.3:
+    In version 2021.10 on neoverse_v1, 2 failing tests in scipy 1.6.3:
         FAILED optimize/tests/test_linprog.py::TestLinprogIPSparse::test_bug_6139 - A...
         FAILED optimize/tests/test_linprog.py::TestLinprogIPSparsePresolve::test_bug_6139
         = 2 failed, 30554 passed, 2064 skipped, 10992 deselected, 76 xfailed, 7 xpassed, 40 warnings in 380.27s (0:06:20) =
-    In versions 2023.02, 2023.07, and 2023.11, 2 failing tests in scipy (versions 1.10.1, 1.11.1, 1.11.4):
+    In versions 2023.02 + 2023.07 + 2023.11 on neoverse_v1, 2 failing tests in scipy (versions 1.10.1, 1.11.1, 1.11.4):
         FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris
         FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris_float32
         = 2 failed, 54409 passed, 3016 skipped, 223 xfailed, 13 xpassed, 10917 warnings in 892.04s (0:14:52) =
-    In previous versions we were not as strict yet on the numpy/SciPy tests
+    In version 2023.07 on a64fx, 4 failing tests in scipy 1.11.1:
+        FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparse::test_bug_6139
+        FAILED scipy/optimize/tests/test_linprog.py::TestLinprogIPSparsePresolve::test_bug_6139
+        FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris
+        FAILED scipy/spatial/tests/test_distance.py::TestPdist::test_pdist_correlation_iris_float32
+        = 4 failed, 54407 passed, 3016 skipped, 223 xfailed, 13 xpassed, 10917 warnings in 6068.43s (1:41:08) =
+    (in previous versions we were not as strict yet on the numpy/SciPy tests)
     """
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-    scipy_bundle_versions = ('2021.10', '2023.02', '2023.07', '2023.11')
-    if self.name == 'SciPy-bundle' and self.version in scipy_bundle_versions and cpu_target == CPU_TARGET_NEOVERSE_V1:
-        self.cfg['testopts'] = "|| echo ignoring failing tests"
+    scipy_bundle_versions_nv1 = ('2021.10', '2023.02', '2023.07', '2023.11')
+    scipy_bundle_versions_a64fx = ('2023.07', '2023.11')
+    if self.name == 'SciPy-bundle':
+        if cpu_target == CPU_TARGET_NEOVERSE_V1 and self.version in scipy_bundle_versions_nv1:
+            self.cfg['testopts'] = "|| echo ignoring failing tests"
+        elif cpu_target == CPU_TARGET_A64FX and self.version in scipy_bundle_versions_a64fx:
+            self.cfg['testopts'] = "|| echo ignoring failing tests"
 
 def pre_test_hook_ignore_failing_tests_netCDF(self, *args, **kwargs):
     """
diff --git a/eessi-2023.06-known-issues.yml b/eessi-2023.06-known-issues.yml
index 2d1256354f..c5cdc68941 100644
--- a/eessi-2023.06-known-issues.yml
+++ b/eessi-2023.06-known-issues.yml
@@ -1,3 +1,10 @@
+- aarch64/a64x:
+  - SciPy-bundle-2023.07-gfbf-2023a:
+    - issue: https://github.com/EESSI/software-layer/issues/318
+    - info: "4 failing tests (vs 54407 passed) in scipy test suite"
+  - SciPy-bundle-2023.11-gfbf-2023b:
+    - issue: https://github.com/EESSI/software-layer/issues/318
+    - info: "3 failing tests (vs 54875 passed) in scipy test suite"
 - aarch64/generic:
   - PyTorch-2.1.2-foss-2023a:
     - issue: https://github.com/EESSI/software-layer/issues/461

From f07fd8567f1154cb8b4f0ab338979caff4dbfcce Mon Sep 17 00:00:00 2001
From: torri <torri@disroot.org>
Date: Wed, 26 Jun 2024 14:03:51 +0200
Subject: [PATCH 173/203] fix for broken curl installation

---
 init/eessi_environment_variables | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index 78851a9c95..d6e5b75dce 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -15,6 +15,20 @@ function show_msg {
   fi
 }
 
+function check_rhel_ca {
+
+  os=$(grep -oP '(?<=^ID_LIKE=).+' /etc/os-release | tr -d '"')
+
+  version_id=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
+  version_major=${version_id%\.*}
+
+  if [[ $os =~ "rhel" ]] && [ $version_major -gt 7 ]
+  then
+        export CURL_CA_BUNDLE=/etc/pki/tls/certs/ca-bundle.crt
+  fi
+}
+
+
 # set up minimal environment: $EESSI_PREFIX, $EESSI_VERSION, $EESSI_OS_TYPE, $EESSI_CPU_FAMILY, $EPREFIX
 source $EESSI_INIT_DIR_PATH/minimal_eessi_env
 
@@ -106,6 +120,8 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
+        # Fix wrong path for RHEL >=8 libcurl 
+	check_rhel_ca
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From 8ed871b53b4bcca8a55f9365b7aaaf0288dc36c9 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 26 Jun 2024 15:43:38 +0200
Subject: [PATCH 174/203] {2023.06,a64fx}[foss/2023a] SciPy-bundle 2023.07

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
index 3a060e30a7..5326f6c493 100644
--- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,3 +1,4 @@
 easyconfigs:
   - OpenMPI-4.1.5-GCC-12.3.0.eb
   - foss-2023a.eb
+  - SciPy-bundle-2023.07-gfbf-2023a.eb

From 69c059b758c29400ac7039cf1ee03af5eba2515c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 26 Jun 2024 22:29:52 +0200
Subject: [PATCH 175/203] {2023.06,a64fx}[foss/2023a] ESPResSo 4.2.2

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
index 5326f6c493..3fe1e43d3f 100644
--- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - OpenMPI-4.1.5-GCC-12.3.0.eb
   - foss-2023a.eb
   - SciPy-bundle-2023.07-gfbf-2023a.eb
+  - ESPResSo-4.2.2-foss-2023a.eb

From 69a812962486940fe553facc459939af8f6549fe Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 27 Jun 2024 13:27:48 +0200
Subject: [PATCH 176/203] {2023.06,a64fx} foss/2023b

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml          | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml
new file mode 100644
index 0000000000..c7411ada0a
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -0,0 +1,6 @@
+easyconfigs:
+  - OpenBLAS-0.3.24-GCC-13.2.0.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20820
+        from-commit: 1fc885b35dacdeb2feef4af207a2daa2502bae08
+  - foss-2023b.eb

From 36dea35585cbc86b7044ec454593a00307c130f9 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 1 Jul 2024 08:45:07 +0000
Subject: [PATCH 177/203] {2023.06}[GCC/12.3.0] BCFtools v1.18

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml  | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
new file mode 100644
index 0000000000..ade226c217
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -0,0 +1,2 @@
+easyconfigs:
+  - BCFtools-1.18-GCC-12.3.0.eb

From 9747ee497161f23dd999094e78bae6c863c5a9fb Mon Sep 17 00:00:00 2001
From: torri <torri@disroot.org>
Date: Mon, 1 Jul 2024 16:31:37 +0200
Subject: [PATCH 178/203] simplified the implementation

---
 init/eessi_environment_variables | 20 +++++---------------
 1 file changed, 5 insertions(+), 15 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index d6e5b75dce..c28ddb45d9 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -15,20 +15,6 @@ function show_msg {
   fi
 }
 
-function check_rhel_ca {
-
-  os=$(grep -oP '(?<=^ID_LIKE=).+' /etc/os-release | tr -d '"')
-
-  version_id=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
-  version_major=${version_id%\.*}
-
-  if [[ $os =~ "rhel" ]] && [ $version_major -gt 7 ]
-  then
-        export CURL_CA_BUNDLE=/etc/pki/tls/certs/ca-bundle.crt
-  fi
-}
-
-
 # set up minimal environment: $EESSI_PREFIX, $EESSI_VERSION, $EESSI_OS_TYPE, $EESSI_CPU_FAMILY, $EPREFIX
 source $EESSI_INIT_DIR_PATH/minimal_eessi_env
 
@@ -121,7 +107,11 @@ if [ -d $EESSI_PREFIX ]; then
           fi
 
         # Fix wrong path for RHEL >=8 libcurl 
-	check_rhel_ca
+	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
+        if [ -f $rhel_libcurl_file ]; then
+          show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
+          export CURL_CA_BUNDLE=$rhel_libcurl_file
+        fi
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From 51c6b1c998a69d8dd4a75f4f83b101b5ba81f1b4 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Jul 2024 10:51:41 +0200
Subject: [PATCH 179/203] improve comment that explains setting of
 `$CURL_CA_BUNDLE` on RHEL-based systems

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 init/eessi_environment_variables | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index c28ddb45d9..f5bb387955 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -107,6 +107,9 @@ if [ -d $EESSI_PREFIX ]; then
           fi
 
         # Fix wrong path for RHEL >=8 libcurl 
+	# This is required here because we ship curl in our compat layer. If we only provided
+	# curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
+	# hook (or via an Lmod hook)
 	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
         if [ -f $rhel_libcurl_file ]; then
           show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"

From 84de38a958417daf880c347dba0e9ae728d0e3f0 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Wed, 3 Jul 2024 21:37:43 +0200
Subject: [PATCH 180/203] {2023.06,zen4}[foss/2023a] ParaView 5.11.2

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml                | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
index 09f525364f..d4c70c562d 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -2,3 +2,4 @@ easyconfigs:
   - ESPResSo-4.2.2-foss-2023a.eb
   - TensorFlow-2.13.0-foss-2023a.eb
   - R-4.3.2-gfbf-2023a.eb
+  - ParaView-5.11.2-foss-2023a.eb

From c895bf16668c588d7eec827092849d883ce10bf2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Jul 2024 13:24:12 +0200
Subject: [PATCH 181/203] remove TODO for using separate cache dirs for each
 repo

---
 eessi_container.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 9d2ce6c25f..94de82df0f 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -510,7 +510,6 @@ fi
 [[ ${VERBOSE} -eq 1 ]] && echo "CONTAINER=${CONTAINER}"
 
 # set env vars and create directories for CernVM-FS
-# TODO need to use separate values for separate repos?
 EESSI_CVMFS_VAR_LIB=${EESSI_TMPDIR}/${CVMFS_VAR_LIB}
 EESSI_CVMFS_VAR_RUN=${EESSI_TMPDIR}/${CVMFS_VAR_RUN}
 mkdir -p ${EESSI_CVMFS_VAR_LIB}

From 417f4dd9b82795520e5923a9c1532ed04f384747 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Jul 2024 13:24:44 +0200
Subject: [PATCH 182/203] fix usage line for access permissions

---
 eessi_container.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eessi_container.sh b/eessi_container.sh
index 94de82df0f..e404b7ee18 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -91,7 +91,7 @@ display_help() {
   echo "                            attach a GPU, MODE==all for both [default: false]"
   echo "  -r | --repository CFG   - configuration file or identifier defining the"
   echo "                            repository to use; can be given multiple times;"
-  echo "                            CFG may include a suffix ';access={ro,rw}' to"
+  echo "                            CFG may include a suffix ',access={ro,rw}' to"
   echo "                            overwrite the global access mode for this repository"
   echo "                            [default: software.eessi.io via CVMFS config available"
   echo "                            via default container, see --container]"

From d8cf6a60540b36b5c3e64c687af5d1482df021a5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Jul 2024 13:41:40 +0200
Subject: [PATCH 183/203] check for software.eessi.io in the default
 --list-repos output

---
 .github/workflows/test_eessi_container_script.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index d31feb23fe..c0346774cb 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -45,7 +45,8 @@ jobs:
               elif [[ ${{matrix.SCRIPT_TEST}} == 'listrepos_default' ]]; then
                 outfile=out_listrepos.txt
                 ./eessi_container.sh --verbose --list-repos | tee ${outfile}
-                grep "EESSI" ${outfile}
+                # make sure that the default EESSI software repository is available
+                grep "software.eessi.io" ${outfile}
 
               # test use of --list-repos with custom repos.cfg
               elif [[ ${{matrix.SCRIPT_TEST}} == 'listrepos_custom' ]]; then

From aa9895e44ac1afd5a44524d004161f3804449a90 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Thu, 4 Jul 2024 15:27:27 +0200
Subject: [PATCH 184/203] fix regex to find the custom EESSI version in the
 output of --list-repos

---
 .github/workflows/test_eessi_container_script.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test_eessi_container_script.yml b/.github/workflows/test_eessi_container_script.yml
index c0346774cb..d44788927f 100644
--- a/.github/workflows/test_eessi_container_script.yml
+++ b/.github/workflows/test_eessi_container_script.yml
@@ -58,11 +58,12 @@ jobs:
                 echo "[EESSI/20HT.TP]" >> cfg/repos.cfg
                 echo "repo_version = 20HT.TP" >> cfg/repos.cfg
                 ./eessi_container.sh --verbose --list-repos | tee ${outfile}
-                grep "EESSI" ${outfile}
+                # make sure that the default EESSI software repository is available
+                grep "software.eessi.io" ${outfile}
 
                 export EESSI_REPOS_CFG_DIR_OVERRIDE=${PWD}/cfg
                 ./eessi_container.sh --verbose --list-repos | tee ${outfile2}
-                grep "[EESSI/2023.02]" ${outfile2}
+                grep "EESSI/20AB.CD" ${outfile2}
 
               # test use of --mode run
               elif [[ ${{matrix.SCRIPT_TEST}} == 'run' ]]; then

From cbedafef9f104540151ca9093bc2e95b178036b3 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 21:07:39 +0200
Subject: [PATCH 185/203] {2023.06,a64fx}[foss/2023a] ParaView 5.11.2

---
 .../2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
index 3fe1e43d3f..5521b92398 100644
--- a/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/a64fx/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -3,3 +3,4 @@ easyconfigs:
   - foss-2023a.eb
   - SciPy-bundle-2023.07-gfbf-2023a.eb
   - ESPResSo-4.2.2-foss-2023a.eb
+  - ParaView-5.11.2-foss-2023a.eb

From c97dd7ed8e9d7cc23436927f4dfff00fae93d623 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 21:58:10 +0200
Subject: [PATCH 186/203] add missing /cvmfs/ in $EESSI_CVMFS_REPO_OVERRIDE
 defined by bot/build.sh and bot/test.sh

---
 bot/build.sh | 2 +-
 bot/test.sh  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index c9a362fdca..145be740d3 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -138,7 +138,7 @@ echo "bot/build.sh: EESSI_VERSION_OVERRIDE='${EESSI_VERSION_OVERRIDE}'"
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
 # "source init/eessi_defaults" via sourcing init/minimal_eessi_env
-export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+export EESSI_CVMFS_REPO_OVERRIDE=/cvmfs/$(cfg_get_value "repository" "repo_name")
 echo "bot/build.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
 
 # determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}
diff --git a/bot/test.sh b/bot/test.sh
index 04bff346cd..d3f3630ea8 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -160,7 +160,7 @@ echo "bot/test.sh: EESSI_PILOT_VERSION_OVERRIDE='${EESSI_PILOT_VERSION_OVERRIDE}
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
 # "source init/eessi_defaults" via sourcing init/minimal_eessi_env
-export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+export EESSI_CVMFS_REPO_OVERRIDE=/cvmfs/$(cfg_get_value "repository" "repo_name")
 echo "bot/test.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
 
 # determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}

From 3bae44ca2c8ee6cf0b53f753b74f47314d532222 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Thu, 4 Jul 2024 21:58:10 +0200
Subject: [PATCH 187/203] add missing /cvmfs/ in $EESSI_CVMFS_REPO_OVERRIDE
 defined by bot/build.sh and bot/test.sh

---
 bot/build.sh | 2 +-
 bot/test.sh  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/bot/build.sh b/bot/build.sh
index c9a362fdca..145be740d3 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -138,7 +138,7 @@ echo "bot/build.sh: EESSI_VERSION_OVERRIDE='${EESSI_VERSION_OVERRIDE}'"
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
 # "source init/eessi_defaults" via sourcing init/minimal_eessi_env
-export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+export EESSI_CVMFS_REPO_OVERRIDE=/cvmfs/$(cfg_get_value "repository" "repo_name")
 echo "bot/build.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
 
 # determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}
diff --git a/bot/test.sh b/bot/test.sh
index 04bff346cd..d3f3630ea8 100755
--- a/bot/test.sh
+++ b/bot/test.sh
@@ -160,7 +160,7 @@ echo "bot/test.sh: EESSI_PILOT_VERSION_OVERRIDE='${EESSI_PILOT_VERSION_OVERRIDE}
 # determine CVMFS repo to be used from .repository.repo_name in ${JOB_CFG_FILE}
 # here, just set EESSI_CVMFS_REPO_OVERRIDE, a bit further down
 # "source init/eessi_defaults" via sourcing init/minimal_eessi_env
-export EESSI_CVMFS_REPO_OVERRIDE=$(cfg_get_value "repository" "repo_name")
+export EESSI_CVMFS_REPO_OVERRIDE=/cvmfs/$(cfg_get_value "repository" "repo_name")
 echo "bot/test.sh: EESSI_CVMFS_REPO_OVERRIDE='${EESSI_CVMFS_REPO_OVERRIDE}'"
 
 # determine architecture to be used from entry .architecture in ${JOB_CFG_FILE}

From 3fc6cdc1558e21005470e815adeb3f8620ec53e8 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Fri, 5 Jul 2024 08:18:27 +0200
Subject: [PATCH 188/203] reduce parallellism when building Qt5 on A64FX
 systems, due to scarce memory

---
 eb_hooks.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index e6f0cf0dd2..40071ea067 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -81,8 +81,11 @@ def post_ready_hook(self, *args, **kwargs):
     """
     # 'parallel' easyconfig parameter is set via EasyBlock.set_parallel in ready step based on available cores.
     # here we reduce parallellism to only use half of that for selected software,
-    # to avoid failing builds/tests due to out-of-memory problems
-    if self.name in ['TensorFlow', 'libxc']:
+    # to avoid failing builds/tests due to out-of-memory problems;
+    memory_hungry_build = self.name in ['libxc', 'TensorFlow']
+    # on A64FX systems, (HBM) memory is typically scarce, so we need to use fewer cores for some builds
+    memory_hungry_build_a64fx = self.name in ['Qt5']
+    if memory_hungry_build or memory_hungry_build_a64fx:
         parallel = self.cfg['parallel']
         if parallel > 1:
             self.cfg['parallel'] = parallel // 2

From a74669585a742ca83e9b976d7f6854a20570460f Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Fri, 5 Jul 2024 12:24:01 +0000
Subject: [PATCH 189/203] {2023.06}[GCCcore/12.3.0-GCC/12.3.0-gompi/2023a]
 bio-packages

---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023a.yml      | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index ade226c217..7fc42e2e34 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -1,2 +1,17 @@
 easyconfigs:
   - BCFtools-1.18-GCC-12.3.0.eb
+  - BWA-0.7.18-GCCcore-12.3.0.eb
+  - CapnProto-1.0.1-GCCcore-12.3.0.eb
+  - DendroPy-4.6.1-GCCcore-12.3.0.eb
+  - DIAMOND-2.1.8-GCC-12.3.0.eb
+  - FastME-2.1.6.3-GCC-12.3.0.eb
+  - fastp-0.23.4-GCC-12.3.0.eb
+  - HMMER-3.4-gompi-2023a.eb
+  - IQ-TREE-2.3.5-gompi-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20955
+        from-commit: 185f88b9a03d65a7fb74edc7acb4221e87e90784      
+  - KronaTools-2.8.1-GCCcore-12.3.0.eb
+  - LSD2-2.4.1-GCCcore-12.3.0.eb
+  - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
+  - ncbi-vdb-3.0.10-gompi-2023a.e

From 4d9390ef015f03abe54ca3f61cd84ca6b1164c07 Mon Sep 17 00:00:00 2001
From: TopRichard <121792457+TopRichard@users.noreply.github.com>
Date: Fri, 5 Jul 2024 14:30:32 +0200
Subject: [PATCH 190/203] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index 7fc42e2e34..34ec3257e8 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -14,4 +14,4 @@ easyconfigs:
   - KronaTools-2.8.1-GCCcore-12.3.0.eb
   - LSD2-2.4.1-GCCcore-12.3.0.eb
   - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
-  - ncbi-vdb-3.0.10-gompi-2023a.e
+  - ncbi-vdb-3.0.10-gompi-2023a.eb

From 868a8a8c94e932762299aabc6c6ed4eca749ef42 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 16:07:05 +0200
Subject: [PATCH 191/203] /tmp/overlay-upper should now be
 /tmp/<repo-name>/overlay-upper

---
 create_tarball.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 0a7669f73f..ed999cde89 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -26,7 +26,7 @@ if [ ! -d ${software_dir} ]; then
     exit 2
 fi
 
-overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
+overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo}/overlay-upper"
 
 software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then

From d5ecd74837cde2feb834275632e327beb182c00f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 21:58:23 +0200
Subject: [PATCH 192/203] remove /cvmfs/ from cvmfs_repo variable

---
 create_tarball.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index ed999cde89..2dee665060 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -26,7 +26,8 @@ if [ ! -d ${software_dir} ]; then
     exit 2
 fi
 
-overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo}/overlay-upper"
+cvmfs_repo_name=${cvmfs_repo#/cvmfs/}
+overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo_name}/overlay-upper"
 
 software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then

From 49cbcc8de452e9cc51a3969b860932caf109a9bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= <b.e.droge@rug.nl>
Date: Fri, 5 Jul 2024 22:02:31 +0200
Subject: [PATCH 193/203] implement changes from
 https://github.com/EESSI/software-layer/pull/635 and
 https://github.com/EESSI/software-layer/pull/636

---
 create_tarball.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/create_tarball.sh b/create_tarball.sh
index 0a7669f73f..2dee665060 100755
--- a/create_tarball.sh
+++ b/create_tarball.sh
@@ -26,7 +26,8 @@ if [ ! -d ${software_dir} ]; then
     exit 2
 fi
 
-overlay_upper_dir="${eessi_tmpdir}/overlay-upper"
+cvmfs_repo_name=${cvmfs_repo#/cvmfs/}
+overlay_upper_dir="${eessi_tmpdir}/${cvmfs_repo_name}/overlay-upper"
 
 software_dir_overlay="${overlay_upper_dir}/versions/${eessi_version}"
 if [ ! -d ${software_dir_overlay} ]; then

From 88eebb9ee7245c56e4ad623c4055b8f4c365b59a Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 6 Jul 2024 11:26:40 +0200
Subject: [PATCH 194/203] rebuild OpenFOAM-10-foss-2023a.eb and
 OpenFOAM-11-foss-2023a.eb without -ftree-vectorize

---
 ...20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 easystacks/software.eessi.io/2023.06/rebuilds/20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml

diff --git a/easystacks/software.eessi.io/2023.06/rebuilds/20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml b/easystacks/software.eessi.io/2023.06/rebuilds/20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml
new file mode 100644
index 0000000000..c12d244790
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/rebuilds/20240706-eb-4.9.2-OpenFOAM-no-ftree-vectorize.yml
@@ -0,0 +1,12 @@
+# 2024.07.06
+# OpenFOAM 10 and 11 built with GCC 11.3.0 or 12.3.0 and -ftree-vectorize yields incorrect results,
+# see https://github.com/easybuilders/easybuild-easyconfigs/issues/20927
+easyconfigs:
+  - OpenFOAM-10-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
+        from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f
+  - OpenFOAM-11-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
+        from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f

From f2507201e02ea6da362f784fad1bbb5b27caa4a7 Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sat, 6 Jul 2024 11:29:01 +0200
Subject: [PATCH 195/203] {2023.06,zen4}[foss/2023a] OpenFOAM 10 + 11

---
 .../2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml         | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
index d4c70c562d..65a12695e4 100644
--- a/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/zen4/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -3,3 +3,11 @@ easyconfigs:
   - TensorFlow-2.13.0-foss-2023a.eb
   - R-4.3.2-gfbf-2023a.eb
   - ParaView-5.11.2-foss-2023a.eb
+  - OpenFOAM-10-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
+        from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f
+  - OpenFOAM-11-foss-2023a.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20958
+        from-commit: dbadb2074464d816740ee0e95595c2cb31b6338f

From b07445e75cb874fb87003df1d92a5ba879deac4c Mon Sep 17 00:00:00 2001
From: Kenneth Hoste <kenneth.hoste@ugent.be>
Date: Sun, 7 Jul 2024 21:56:20 +0200
Subject: [PATCH 196/203] only use half the cores for Qt5 when building for
 A64FX

---
 eb_hooks.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 40071ea067..3b381e5963 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -84,7 +84,8 @@ def post_ready_hook(self, *args, **kwargs):
     # to avoid failing builds/tests due to out-of-memory problems;
     memory_hungry_build = self.name in ['libxc', 'TensorFlow']
     # on A64FX systems, (HBM) memory is typically scarce, so we need to use fewer cores for some builds
-    memory_hungry_build_a64fx = self.name in ['Qt5']
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    memory_hungry_build_a64fx = cpu_target == CPU_TARGET_A64FX and self.name in ['Qt5']
     if memory_hungry_build or memory_hungry_build_a64fx:
         parallel = self.cfg['parallel']
         if parallel > 1:

From d6d5a2bb5c2eead7cd931ea307ea4cd3b44bf9db Mon Sep 17 00:00:00 2001
From: Helena Vela Beltran <47674829+hvelab@users.noreply.github.com>
Date: Mon, 8 Jul 2024 17:18:02 +0200
Subject: [PATCH 197/203] Update init/eessi_environment_variables

Add bigger comment

Co-authored-by: ocaisa <alan.ocais@cecam.org>
---
 init/eessi_environment_variables | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/init/eessi_environment_variables b/init/eessi_environment_variables
index f5bb387955..9417d5b2a2 100644
--- a/init/eessi_environment_variables
+++ b/init/eessi_environment_variables
@@ -106,15 +106,15 @@ if [ -d $EESSI_PREFIX ]; then
             false
           fi
 
-        # Fix wrong path for RHEL >=8 libcurl 
-	# This is required here because we ship curl in our compat layer. If we only provided
-	# curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
-	# hook (or via an Lmod hook)
-	rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
-        if [ -f $rhel_libcurl_file ]; then
-          show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
-          export CURL_CA_BUNDLE=$rhel_libcurl_file
-        fi
+          # Fix wrong path for RHEL >=8 libcurl 
+	  # This is required here because we ship curl in our compat layer. If we only provided
+	  # curl as a module file we could instead do this via a `modluafooter` in an EasyBuild
+	  # hook (or via an Lmod hook)
+	  rhel_libcurl_file="/etc/pki/tls/certs/ca-bundle.crt"
+          if [ -f $rhel_libcurl_file ]; then
+            show_msg "Found libcurl CAs file at RHEL location, setting CURL_CA_BUNDLE"
+            export CURL_CA_BUNDLE=$rhel_libcurl_file
+          fi
 
         else
           error "EESSI software layer at $EESSI_SOFTWARE_PATH not found!"

From 28eabaaefcde5b112b60e8c94f46494ab7b0944e Mon Sep 17 00:00:00 2001
From: Xin An <xina@int5.local.snellius.surf.nl>
Date: Fri, 12 Jul 2024 12:11:19 +0200
Subject: [PATCH 198/203] {2023.06}[gfbf/2023b] Pystencils 1.3.4

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 15c02951d7..3963f79ecd 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,3 +58,4 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb

From 2ca3684b845165425af638daaea27897fd1cbe7e Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 14:29:19 +0200
Subject: [PATCH 199/203] Update
 easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Bob Dröge <b.e.droge@rug.nl>
---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 3963f79ecd..8d9779c59c 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,4 +58,7 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
-  - pystencils-1.3.4-gfbf-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
+        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From 641288af0c2bc1d1e35d411815465abdeb8a1ddc Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:08:14 +0200
Subject: [PATCH 200/203] Update eessi-2023.06-eb-4.9.0-2023b.yml

Remove pystencils
---
 .../2023.06/eessi-2023.06-eb-4.9.0-2023b.yml                  | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
index 8d9779c59c..15c02951d7 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023b.yml
@@ -58,7 +58,3 @@ easyconfigs:
       options:
         from-pr: 20201
   - OSU-Micro-Benchmarks-7.2-gompi-2023b.eb
-  - pystencils-1.3.4-gfbf-2023b.eb:
-      options:
-        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
-        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From bb8b4aa1442c032b88d6cacc94b2d8f42cce3721 Mon Sep 17 00:00:00 2001
From: Xin An <34663977+xinan1911@users.noreply.github.com>
Date: Fri, 12 Jul 2024 16:10:02 +0200
Subject: [PATCH 201/203] add pystencils

update eessi-2023.06-eb-4.9.2-2023b
---
 .../2023.06/eessi-2023.06-eb-4.9.2-2023b.yml                  | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
index 38bfa81142..e0057f18ab 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023b.yml
@@ -1,3 +1,7 @@
 easyconfigs:
   - IPython-8.17.2-GCCcore-13.2.0.eb
   - dlb-3.4-gompi-2023b.eb
+  - pystencils-1.3.4-gfbf-2023b.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20889
+        from-commit: c66c4788a17f7e4f55aa23f9fdb782aad97c9ce7

From f204afa5d804dee715476ac3d2a96e8e69fa6842 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Mon, 15 Jul 2024 10:47:34 +0200
Subject: [PATCH 202/203] Add MetalWalls to easystack file

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 4b58cb6106..0cdbd4b5b3 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -74,3 +74,4 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
+  - MetalWalls-21.06.1-foss-2023a.eb

From 58fb56f2a8f2fb11d5df2b8332388ace82eda993 Mon Sep 17 00:00:00 2001
From: crivella <davide.grassano@epfl.ch>
Date: Tue, 16 Jul 2024 14:41:39 +0200
Subject: [PATCH 203/203] Switch target to EB 4.9.2

---
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml   | 1 -
 .../software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml   | 1 +
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
index 0cdbd4b5b3..4b58cb6106 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.0-2023a.yml
@@ -74,4 +74,3 @@ easyconfigs:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/20238
         from-pr: 20238
-  - MetalWalls-21.06.1-foss-2023a.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
index 34ec3257e8..e7730d1eb6 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-4.9.2-2023a.yml
@@ -15,3 +15,4 @@ easyconfigs:
   - LSD2-2.4.1-GCCcore-12.3.0.eb
   - MAFFT-7.520-GCC-12.3.0-with-extensions.eb
   - ncbi-vdb-3.0.10-gompi-2023a.eb
+  - MetalWalls-21.06.1-foss-2023a.eb