From f3c638f9e9cc13f91a1e680827f2e2ca5cb5b267 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Wed, 17 Apr 2024 10:34:18 +0200
Subject: [PATCH 01/18] {2023.06}[foss/2023b] Qt5 v5.15.13

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
index 6af367229c..45123e5fdb 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023b.yml
@@ -1,2 +1,3 @@
 easyconfigs:
   - CDO-2.2.2-gompi-2023b.eb
+  - Qt5-5.15.13-GCCcore-13.2.0.eb

From f60ecd8529985dcc2c73044e1ee671aa67d51e0e Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 23 May 2024 09:16:08 +0200
Subject: [PATCH 02/18] {2023.06}[foss/2023a] PyTorch v2.1.2 with CUDA/12.1.1

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index aeaf710837..c70385abaf 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -36,3 +36,4 @@ easyconfigs:
         from-pr: 19451
   - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb
   - ABySS-2.3.7-foss-2023a.eb
+  - PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb

From 31eef035269187f96ad97abafda7ea180f2c1f1d Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 23 May 2024 15:01:21 +0200
Subject: [PATCH 03/18] add compute capability setting (just 7.0 for now)

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml   | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index c70385abaf..d49004d02c 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -36,4 +36,6 @@ easyconfigs:
         from-pr: 19451
   - OSU-Micro-Benchmarks-7.2-gompi-2023a-CUDA-12.1.1.eb
   - ABySS-2.3.7-foss-2023a.eb
-  - PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb
+  - PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb:
+      options:
+        cuda-compute-capabilities: 7.0

From fcc0eaf8e4fb00b4b47f110e9d3e002964f66193 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 23 May 2024 18:43:33 +0200
Subject: [PATCH 04/18] add CUPTI lib path to LIBRARY_PATH

---
 eb_hooks.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/eb_hooks.py b/eb_hooks.py
index c7b2a62f64..c4c2a0261e 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -425,6 +425,28 @@ def pre_configure_hook_openblas_optarch_generic(self, *args, **kwargs):
         raise EasyBuildError("OpenBLAS-specific hook triggered for non-OpenBLAS easyconfig?!")
 
 
+def pre_configure_hook_pytorch_add_cupti_libdir(self, *args, **kwargs):
+    """
+    Pre-configure hook for PyTorch: add directory $EESSI_SOFTWARE_PATH/CUDA/12.1.1/extras/CUPTI/lib64 to LIBRARY_PATH
+    """
+    #if self.name == 'PyTorch' and 'CUDA' in self.versionsuffix:
+    if self.name == 'PyTorch':
+        library_path = os.getenv('LIBRARY_PATH')
+        print_msg("library_path: '%s'", library_path)
+        #lib_dirs = library_path.split(':')
+        eessi_software_path = os.getenv('EESSI_SOFTWARE_PATH')
+        print_msg("eessi_software_path: '%s'", eessi_software_path)
+        #for lib_dir in lib_dirs:
+        #    if lib_dir.startswith(eessi_software_path + '/CUDA'):
+        #
+        cupti_lib_dir = os.path.join(eessi_software_path, 'CUDA', '12.1.1', 'extras', 'CUPTI', 'lib64')
+        print_msg("cupti_lib_dir: '%s'", cupti_lib_dir)
+        env.setvar('LIBRARY_PATH', ':'.join([library_path, cupti_lib_dir]))
+        print_msg("LIBRARY_PATH: '%s'", os.getenv('LIBRARY_PATH'))
+    else:
+        raise EasyBuildError("PyTorch-specific hook triggered for non-PyTorch easyconfig?!")
+
+
 def pre_configure_hook_libfabric_disable_psm3_x86_64_generic(self, *args, **kwargs):
     """Add --disable-psm3 to libfabric configure options when building with --optarch=GENERIC on x86_64."""
     if self.name == 'libfabric':
@@ -851,6 +873,7 @@ def inject_gpu_property(ec):
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,
+    'PyTorch': pre_configure_hook_pytorch_add_cupti_libdir,
     'WRF': pre_configure_hook_wrf_aarch64,
     'at-spi2-core': pre_configure_hook_atspi2core_filter_ld_library_path,
 }

From de17ad31d0c21d70ab2973e94463db6b2382681d Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 23 May 2024 19:51:31 +0200
Subject: [PATCH 05/18] add missing 'software' to library path

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

diff --git a/eb_hooks.py b/eb_hooks.py
index c4c2a0261e..7b5c082ddc 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -427,7 +427,7 @@ def pre_configure_hook_openblas_optarch_generic(self, *args, **kwargs):
 
 def pre_configure_hook_pytorch_add_cupti_libdir(self, *args, **kwargs):
     """
-    Pre-configure hook for PyTorch: add directory $EESSI_SOFTWARE_PATH/CUDA/12.1.1/extras/CUPTI/lib64 to LIBRARY_PATH
+    Pre-configure hook for PyTorch: add directory $EESSI_SOFTWARE_PATH/software/CUDA/12.1.1/extras/CUPTI/lib64 to LIBRARY_PATH
     """
     #if self.name == 'PyTorch' and 'CUDA' in self.versionsuffix:
     if self.name == 'PyTorch':
@@ -439,7 +439,7 @@ def pre_configure_hook_pytorch_add_cupti_libdir(self, *args, **kwargs):
         #for lib_dir in lib_dirs:
         #    if lib_dir.startswith(eessi_software_path + '/CUDA'):
         #
-        cupti_lib_dir = os.path.join(eessi_software_path, 'CUDA', '12.1.1', 'extras', 'CUPTI', 'lib64')
+        cupti_lib_dir = os.path.join(eessi_software_path, 'software', 'CUDA', '12.1.1', 'extras', 'CUPTI', 'lib64')
         print_msg("cupti_lib_dir: '%s'", cupti_lib_dir)
         env.setvar('LIBRARY_PATH', ':'.join([library_path, cupti_lib_dir]))
         print_msg("LIBRARY_PATH: '%s'", os.getenv('LIBRARY_PATH'))

From b053cbd960f6f0308f8364c7969a0420d4068b06 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Thu, 23 May 2024 23:03:45 +0200
Subject: [PATCH 06/18] nvcc sanity check

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

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 6c59f46570..11b2b3069e 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -208,6 +208,9 @@ if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
         -e ${EESSI_PREFIX}/scripts/gpu_support/nvidia/eessi-2023.06-cuda-and-libraries.yml \
         -t /tmp/temp \
         --accept-cuda-eula
+    ml CUDA/12.1.1
+    command -V nvcc
+    ml rm CUDA/12.1.1
 else
     echo "Skipping installation of CUDA SDK and cu* libraries in host_injections, since the --skip-cuda-install flag was passed"
 fi

From 8951b4f2f721fc50e5a4eba084f8f83935902a44 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 25 May 2024 11:13:53 +0200
Subject: [PATCH 07/18] improve hook to add CUPTI/lib64 dir to LIBRARY_PATH

---
 eb_hooks.py | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/eb_hooks.py b/eb_hooks.py
index 7b5c082ddc..f01e1ca55c 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -429,20 +429,21 @@ def pre_configure_hook_pytorch_add_cupti_libdir(self, *args, **kwargs):
     """
     Pre-configure hook for PyTorch: add directory $EESSI_SOFTWARE_PATH/software/CUDA/12.1.1/extras/CUPTI/lib64 to LIBRARY_PATH
     """
-    #if self.name == 'PyTorch' and 'CUDA' in self.versionsuffix:
     if self.name == 'PyTorch':
-        library_path = os.getenv('LIBRARY_PATH')
-        print_msg("library_path: '%s'", library_path)
-        #lib_dirs = library_path.split(':')
-        eessi_software_path = os.getenv('EESSI_SOFTWARE_PATH')
-        print_msg("eessi_software_path: '%s'", eessi_software_path)
-        #for lib_dir in lib_dirs:
-        #    if lib_dir.startswith(eessi_software_path + '/CUDA'):
-        #
-        cupti_lib_dir = os.path.join(eessi_software_path, 'software', 'CUDA', '12.1.1', 'extras', 'CUPTI', 'lib64')
-        print_msg("cupti_lib_dir: '%s'", cupti_lib_dir)
-        env.setvar('LIBRARY_PATH', ':'.join([library_path, cupti_lib_dir]))
-        print_msg("LIBRARY_PATH: '%s'", os.getenv('LIBRARY_PATH'))
+        if 'cudaver' in self.cfg.template_values and self.cfg.template_values['cudaver'] == '12.1.1':
+            _cudaver = self.cfg.template_values['cudaver']
+            print_msg("pre_configure_hook_pytorch_add_cupti_libdir: CUDA version: '%s'" % _cudaver)
+            _library_path = os.getenv('LIBRARY_PATH')
+            print_msg("pre_configure_hook_pytorch_add_cupti_libdir: library_path: '%s'", _library_path)
+            _eessi_software_path = os.getenv('EESSI_SOFTWARE_PATH')
+            print_msg("pre_configure_hook_pytorch_add_cupti_libdir: eessi_software_path: '%s'", _eessi_software_path)
+            _cupti_lib_dir = os.path.join(_eessi_software_path, 'software', 'CUDA', _cudaver, 'extras', 'CUPTI', 'lib64')
+            print_msg("pre_configure_hook_pytorch_add_cupti_libdir: cupti_lib_dir: '%s'", _cupti_lib_dir)
+            if _library_path:
+                env.setvar('LIBRARY_PATH', ':'.join([_library_path, _cupti_lib_dir]))
+            else:
+                env.setvar('LIBRARY_PATH', _cupti_lib_dir)
+            print_msg("pre_configure_hook_pytorch_add_cupti_libdir: LIBRARY_PATH: '%s'", os.getenv('LIBRARY_PATH'))
     else:
         raise EasyBuildError("PyTorch-specific hook triggered for non-PyTorch easyconfig?!")
 

From 0e4e8243e54ba5ded373b9a5697de278f9cffbbd Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sat, 25 May 2024 11:17:46 +0200
Subject: [PATCH 08/18] don't load/unload CUDA

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

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 11b2b3069e..6c59f46570 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -208,9 +208,6 @@ if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
         -e ${EESSI_PREFIX}/scripts/gpu_support/nvidia/eessi-2023.06-cuda-and-libraries.yml \
         -t /tmp/temp \
         --accept-cuda-eula
-    ml CUDA/12.1.1
-    command -V nvcc
-    ml rm CUDA/12.1.1
 else
     echo "Skipping installation of CUDA SDK and cu* libraries in host_injections, since the --skip-cuda-install flag was passed"
 fi

From 47eeac1b0739d3155a374a3c42f64159da0fc1e4 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sun, 26 May 2024 08:10:15 +0200
Subject: [PATCH 09/18] sync with state of relevant EESSI PRs (579, 581, 586)

---
 EESSI-install-software.sh  | 70 +++++++++++++++++++++++---------------
 bot/build.sh               |  5 +++
 eessi_container.sh         |  6 ----
 install_scripts.sh         |  2 --
 run_in_compat_layer_env.sh |  3 ++
 5 files changed, 51 insertions(+), 35 deletions(-)

diff --git a/EESSI-install-software.sh b/EESSI-install-software.sh
index 6c59f46570..ca6fed71d5 100755
--- a/EESSI-install-software.sh
+++ b/EESSI-install-software.sh
@@ -17,6 +17,11 @@ display_help() {
   echo "  --skip-cuda-install    -  disable installing a full CUDA SDK in the host_injections prefix (e.g. in CI)"
 }
 
+# Function to check if a command exists
+function command_exists() {
+    command -v "$1" >/dev/null 2>&1
+}
+
 function copy_build_log() {
     # copy specified build log to specified directory, with some context added
     build_log=${1}
@@ -147,6 +152,39 @@ else
   mkdir -p ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
+# We need to ensure that certain files are present or updated before we source
+#   $TOPDIR/init/eessi_environment_variables
+# Particularly the files we need to have present/updated in
+#   ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+#   are:
+#     - .lmod/lmodrc.lua
+#     - .lmod/SitePackage.lua
+# We run scripts to create them if they don't exist or if the scripts have been
+# changed in the PR.
+
+# Set base directory for software and for Lmod config files
+_eessi_software_path=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+_lmod_cfg_dir=${_eessi_software_path}/.lmod
+
+# We assume there's only one diff file that corresponds to the PR patch file
+pr_diff=$(ls [0-9]*.diff | head -1)
+
+# Create or update ${_eessi_software_path}/.lmod/lmodrc.lua
+_lmodrc_file=${_lmod_cfg_dir}/lmodrc.lua
+_lmodrc_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodrc.py$' > /dev/null; echo $?)
+if [ ! -f "${_lmodrc_file}" ] || [ "${_lmodrc_changed}" == '0' ]; then
+    python3 ${TOPDIR}/create_lmodrc.py ${_eessi_software_path}
+    check_exit_code $? "${_lmodrc_file} created/updated" "Failed to create/update ${_lmodrc_file}"
+fi
+
+# Create or update ${_eessi_software_path}/.lmod/SitePackage.lua
+_lmod_sitepackage_file=${_lmod_cfg_dir}/SitePackage.lua
+_sitepackage_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodsitepackage.py$' > /dev/null; echo $?)
+if [ ! -f "${_lmod_sitepackage_file}" ] || [ "${_sitepackage_changed}" == '0' ]; then
+    python3 ${TOPDIR}/create_lmodsitepackage.py ${_eessi_software_path}
+    check_exit_code $? "${_lmod_sitepackage_file} created/updated" "Failed to create/update ${_lmod_sitepackage_file}"
+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
@@ -212,13 +250,11 @@ else
     echo "Skipping installation of CUDA SDK and cu* libraries in host_injections, since the --skip-cuda-install flag was passed"
 fi
 
-# Install drivers in host_injections
-# TODO: this is commented out for now, because the script assumes that nvidia-smi is available and works;
-#       if not, an error is produced, and the bot flags the whole build as failed (even when not installing GPU software)
-# ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
-
-# Don't run the Lmod GPU driver check when doing builds (may not have a GPU, and it's not relevant for vanilla builds anyway)
-export EESSI_OVERRIDE_GPU_CHECK=1
+# Install NVIDIA drivers in host_injections (if they exist)
+if command_exists "nvidia-smi"; then
+    echo "Command 'nvidia-smi' found. Installing NVIDIA drivers for use in prefix shell..."
+    ${EESSI_PREFIX}/scripts/gpu_support/nvidia/link_nvidia_host_libraries.sh
+fi
 
 # use PR patch file to determine in which easystack files stuff was added
 changed_easystacks=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^easystacks/.*yml$' | egrep -v 'known-issues|missing') 
@@ -268,25 +304,5 @@ else
     done
 fi
 
-### add packages here
-
-echo ">> Creating/updating Lmod RC file..."
-export LMOD_CONFIG_DIR="${EASYBUILD_INSTALLPATH}/.lmod"
-lmod_rc_file="$LMOD_CONFIG_DIR/lmodrc.lua"
-lmodrc_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodrc.py$' > /dev/null; echo $?)
-if [ ! -f $lmod_rc_file ] || [ ${lmodrc_changed} == '0' ]; then
-    python3 $TOPDIR/create_lmodrc.py ${EASYBUILD_INSTALLPATH}
-    check_exit_code $? "$lmod_rc_file created" "Failed to create $lmod_rc_file"
-fi
-
-echo ">> Creating/updating Lmod SitePackage.lua ..."
-export LMOD_PACKAGE_PATH="${EASYBUILD_INSTALLPATH}/.lmod"
-lmod_sitepackage_file="$LMOD_PACKAGE_PATH/SitePackage.lua"
-sitepackage_changed=$(cat ${pr_diff} | grep '^+++' | cut -f2 -d' ' | sed 's@^[a-z]/@@g' | grep '^create_lmodsitepackage.py$' > /dev/null; echo $?)
-if [ ! -f "$lmod_sitepackage_file" ] || [ "${sitepackage_changed}" == '0' ]; then
-    python3 $TOPDIR/create_lmodsitepackage.py ${EASYBUILD_INSTALLPATH}
-    check_exit_code $? "$lmod_sitepackage_file created" "Failed to create $lmod_sitepackage_file"
-fi
-
 echo ">> Cleaning up ${TMPDIR}..."
 rm -r ${TMPDIR}
diff --git a/bot/build.sh b/bot/build.sh
index 23f5fd952b..6e835cb6aa 100755
--- a/bot/build.sh
+++ b/bot/build.sh
@@ -271,6 +271,11 @@ if [[ ! -z ${SHARED_FS_PATH} ]]; then
     BUILD_STEP_ARGS+=("--host-injections" "${SHARED_FS_PATH}/host-injections")
 fi
 
+# Don't run the Lmod GPU driver check when doing builds (may not have a GPU, and it's not relevant for vanilla builds anyway)
+echo "EESSI_OVERRIDE_GPU_CHECK='${EESSI_OVERRIDE_GPU_CHECK}'"
+export EESSI_OVERRIDE_GPU_CHECK=1
+echo "EESSI_OVERRIDE_GPU_CHECK='${EESSI_OVERRIDE_GPU_CHECK}'"
+
 # create tmp file for output of build step
 build_outerr=$(mktemp build.outerr.XXXX)
 
diff --git a/eessi_container.sh b/eessi_container.sh
index c9ed97e5c6..a9405b6d8e 100755
--- a/eessi_container.sh
+++ b/eessi_container.sh
@@ -477,12 +477,6 @@ if [[ ${SETUP_NVIDIA} -eq 1 ]]; then
         mkdir -p ${EESSI_USR_LOCAL_CUDA}
         BIND_PATHS="${BIND_PATHS},${EESSI_VAR_LOG}:/var/log,${EESSI_USR_LOCAL_CUDA}:/usr/local/cuda"
         [[ ${VERBOSE} -eq 1 ]] && echo "BIND_PATHS=${BIND_PATHS}"
-        if [[ "${NVIDIA_MODE}" == "install" ]] ; then
-            # We need to "trick" our LMOD_RC file to allow us to load CUDA modules even without a CUDA driver
-            # (this works because we build within a container and the LMOD_RC recognises that)
-            touch ${EESSI_TMPDIR}/libcuda.so
-            export SINGULARITY_CONTAINLIBS="${EESSI_TMPDIR}/libcuda.so"
-        fi
     fi
 fi
 
diff --git a/install_scripts.sh b/install_scripts.sh
index 17712a0ae7..07643a39e6 100755
--- a/install_scripts.sh
+++ b/install_scripts.sh
@@ -112,8 +112,6 @@ copy_files_by_list ${TOPDIR}/scripts ${INSTALL_PREFIX}/scripts "${script_files[@
 nvidia_files=(
     eessi-2023.06-cuda-and-libraries.yml
     install_cuda_and_libraries.sh
-    install_cuda_host_injections.sh
-    install_cuDNN_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[@]}"
diff --git a/run_in_compat_layer_env.sh b/run_in_compat_layer_env.sh
index efd30e7cc0..393956a0c1 100755
--- a/run_in_compat_layer_env.sh
+++ b/run_in_compat_layer_env.sh
@@ -29,6 +29,9 @@ fi
 if [ ! -z ${http_proxy} ]; then
     INPUT="export http_proxy=${http_proxy}; ${INPUT}"
 fi
+if [ ! -z ${EESSI_OVERRIDE_GPU_CHECK} ]; then
+    INPUT="export EESSI_OVERRIDE_GPU_CHECK=${EESSI_OVERRIDE_GPU_CHECK}; ${INPUT}"
+fi
 if [ ! -z ${https_proxy} ]; then
     INPUT="export https_proxy=${https_proxy}; ${INPUT}"
 fi

From be1de45639066705785e1000bce9c128dd8e46f3 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Sun, 26 May 2024 08:11:50 +0200
Subject: [PATCH 10/18] building for all relevant compute capabilities

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index 4b2965554e..bd0de1a6c8 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -41,4 +41,4 @@ easyconfigs:
         from-pr: 20540
   - PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb:
       options:
-        cuda-compute-capabilities: 7.0
+        cuda-compute-capabilities: 6.0,6.1,7.0,7.5,8.0,8.6,8.9,9.0

From 179e7d1e3114043acce6e6025bc4bc43d778fd3d Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Sun, 26 May 2024 19:23:24 +0000
Subject: [PATCH 11/18] {2023.06}[foss/2022b] ParaView V5.11.1

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index f388a327f6..f9bfaca153 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -6,3 +6,4 @@ easyconfigs:
   - bokeh-3.2.1-foss-2022b.eb
   - MDAnalysis-2.4.2-foss-2022b.eb
   - arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb
+  - ParaView-5.11.1-foss-2022b.eb

From c1d63dcc08fb74d98c42a385848b72d45a64fc1e Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 28 May 2024 10:54:05 +0000
Subject: [PATCH 12/18] {2023.06}[foss/2022b] R-bundle-Bioconductor V3.16 R
 V4.2.2

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index ecfa63223f..7321390a5f 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -7,3 +7,4 @@ easyconfigs:
   - MDAnalysis-2.4.2-foss-2022b.eb
   - arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb
   - biom-format-2.1.15-foss-2022b.eb
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb

From c40fe9d5d4eae584938067ffdb0ea889fec26f79 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 28 May 2024 11:48:16 +0000
Subject: [PATCH 13/18] {2023.06}[gfbf/2022b] ASE V3.22.1

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index ecfa63223f..193a18cc70 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -7,3 +7,4 @@ easyconfigs:
   - MDAnalysis-2.4.2-foss-2022b.eb
   - arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb
   - biom-format-2.1.15-foss-2022b.eb
+  - ASE-3.22.1-gfbf-2022b.eb

From 794a6f5d2266b658f1dbb83382a924346c05b35d Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Wed, 29 May 2024 06:55:08 +0000
Subject: [PATCH 14/18] {2023.06}[foss/2023a] ESPResSo V4.2.2

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml    | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
index e12d4a680a..ba42cffaa6 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2023a.yml
@@ -49,3 +49,6 @@ easyconfigs:
         from-pr: 20540
   - WhatsHap-2.2-foss-2023a.eb
   - GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb
+  - ESPResSo-4.2.2-foss-2023a.eb:
+      options:
+        from-pr: 20595

From f82c93b310ca90dbad7d50fa314b22b486edbcc7 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Wed, 29 May 2024 07:17:14 +0000
Subject: [PATCH 15/18] Added --from-pr option

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml   | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index 7321390a5f..3aa77363e2 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -7,4 +7,6 @@ easyconfigs:
   - MDAnalysis-2.4.2-foss-2022b.eb
   - arrow-R-11.0.0.3-foss-2022b-R-4.2.2.eb
   - biom-format-2.1.15-foss-2022b.eb
-  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb
+  - R-bundle-Bioconductor-3.16-foss-2022b-R-4.2.2.eb:
+      options:
+        from-pr: 20379

From f780ca552270086f34798c4500978be453fe4ef8 Mon Sep 17 00:00:00 2001
From: Thomas Roeblitz <thomas.roblitz@uib.no>
Date: Wed, 29 May 2024 23:11:47 +0200
Subject: [PATCH 16/18] run PyTorch tests sequentially

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

diff --git a/eb_hooks.py b/eb_hooks.py
index f01e1ca55c..e4a957acdc 100644
--- a/eb_hooks.py
+++ b/eb_hooks.py
@@ -583,6 +583,12 @@ def pre_test_hook_increase_max_failed_tests_arm_PyTorch(self, *args, **kwargs):
     """
     if self.name == 'PyTorch' and self.version == '2.1.2' and get_cpu_architecture() == AARCH64:
         self.cfg['max_failed_tests'] = 10
+        if 'cudaver' in self.cfg.template_values and self.cfg.template_values['cudaver'] == '12.1.1':
+            _cudaver = self.cfg.template_values['cudaver']
+            _runtest = self.cfg['runtest']
+            self.cfg['runtest'] = _runtest.replace(
+                                      'PYTHONUNBUFFERED',
+                                      'PYTORCH_TEST_RUN_EVERYTHING_IN_SERIAL=1 PYTHONUNBUFFERED')
 
 
 def pre_single_extension_hook(ext, *args, **kwargs):

From 441a7c4455e6290d2d46ca2b518ed84408714699 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Mon, 3 Jun 2024 07:42:44 +0000
Subject: [PATCH 17/18] Use LmodMessage instead of LmodWarning on loading
 ESPResSo v4.2.1

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

diff --git a/create_lmodsitepackage.py b/create_lmodsitepackage.py
index 20c4098b8f..6ba0b6ebfb 100755
--- a/create_lmodsitepackage.py
+++ b/create_lmodsitepackage.py
@@ -178,9 +178,26 @@
     end
 end
 
+local function eessi_espresso_deprecated_message(t)
+    local frameStk  = require("FrameStk"):singleton()
+    local mt        = frameStk:mt()
+    local simpleName = string.match(t.modFullName, "(.-)/")
+    local version = string.match(t.modFullName, "%d.%d.%d")
+    if simpleName == 'ESPResSo' and version == '4.2.1' then
+    -- Print a message on loading ESPreSso v <= 4.2.1 recommending using v 4.2.2 and above.
+    -- A message and not a warning as the exit code would break CI runs otherwise.
+        local advice = 'Prefer versions  >= 4.2.2 which include important bugfixes.\\n'
+        advice = advice .. 'For details see https://github.com/espressomd/espresso/releases/tag/4.2.2\\n'
+        advice = advice .. 'Use version 4.2.1 at your own risk!\\n'
+        LmodWarning("\\nESPResSo v4.2.1 has known issues and has been deprecated. ", advice)
+        LmodMessage("\\nESPResSo v4.2.1 has known issues and has been deprecated. ", advice)
+    end
+end
+
 -- Combine both functions into a single one, as we can only register one function as load hook in lmod
 -- Also: make it non-local, so it can be imported and extended by other lmodrc files if needed
 function eessi_load_hook(t)
+    eessi_espresso_deprecated_message(t)
     -- Only apply CUDA and libraries hook if the loaded module is in the NESSI prefix
     -- This avoids getting an Lmod Error when trying to load a CUDA or library module from a local software stack
     if from_eessi_prefix(t) then

From ff690cdfbe1a5821e4cee289308e71a338a020a2 Mon Sep 17 00:00:00 2001
From: Richard Top <richard.topouchian@uib.no>
Date: Tue, 4 Jun 2024 07:07:07 +0000
Subject: [PATCH 18/18] {2023.06}[foss/2022b] SEPP V4.5.1

---
 .../pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
index 57366995c2..1bca410982 100644
--- a/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
+++ b/easystacks/pilot.nessi.no/2023.06/eessi-2023.06-eb-4.9.1-2022b.yml
@@ -12,3 +12,4 @@ easyconfigs:
       options:
         from-pr: 20379
   - ParaView-5.11.1-foss-2022b.eb
+  - SEPP-4.5.1-foss-2022b.eb