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 01/47] 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 02/47] 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 03/47] 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 04/47] 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 05/47] 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 06/47] 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 07/47] 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 08/47] 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 09/47] 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 10/47] 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 11/47] 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 12/47] 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 13/47] 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 14/47] 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 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 15/47] 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 16/47] 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 17/47] 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 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 18/47] 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 19/47] 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 20/47] 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 21/47] 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 22/47] 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 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 23/47] 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 24/47] 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 25/47] 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 26/47] 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 27/47] 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 28/47] 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 29/47] 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 30/47] 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 31/47] 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 32/47] 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 33/47] 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 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 34/47] 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 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 35/47] 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 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 36/47] 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 37/47] 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 38/47] 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 39/47] 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 40/47] 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 41/47] 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 42/47] 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 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 43/47] 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 44/47] 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 45/47] 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 46/47] 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 47/47] 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