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 01/37] 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 02/37] 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 03/37] 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 04/37] 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 05/37] 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 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 06/37] 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 07/37] 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 08/37] 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 09/37] 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 10/37] 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 11/37] 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 12/37] 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 13/37] 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 14/37] 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 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 15/37] 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 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 16/37] 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 17/37] 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 18/37] 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 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 19/37] 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 20/37] 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 21/37] 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 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 22/37] 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 23/37] 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 24/37] 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 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 25/37] 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 26/37] 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 27/37] 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 28/37] 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 29/37] 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 30/37] 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 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 31/37] 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 32/37] 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 33/37] 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 34/37] 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 35/37] 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 36/37] 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 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 37/37] 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