resolve merge conflixt

Author: laraPPr

.github/workflows/scripts/test_init_scripts.sh

@@ -26,7 +26,7 @@ if [ ! -d assert.sh ]; then
 fi
 . assert.sh/assert.sh
 
-TEST_SHELLS=("bash" "zsh" "fish" "ksh" "csh")
+TEST_SHELLS=("bash" "zsh" "fish" "ksh" "csh" "sh")
 SHELLS=$@
 
 for shell in ${SHELLS[@]}; do
@@ -43,7 +43,11 @@ for shell in ${SHELLS[@]}; do
 
     # TEST 1: Source Script and check Module Output
     expected_pattern=".*EESSI has selected $EESSI_SOFTWARE_SUBDIR_OVERRIDE as the compatible CPU target for EESSI/$EESSI_VERSION.*"
-    assert_raises "$shell -c 'source init/lmod/$shell' 2>&1 | grep -E \"${expected_pattern}\""
+    if [ "$shell" = "csh" ]; then
+      assert_raises "$shell -c 'source init/lmod/$shell' 2>&1 | grep -E \"${expected_pattern}\""
+    else
+      assert_raises "$shell -c '. init/lmod/$shell' 2>&1 | grep -E \"${expected_pattern}\""
+    fi
 
     # TEST 2: Check if module overviews first section is the loaded EESSI module
     if [ "$shell" = "csh" ]; then
@@ -53,7 +57,7 @@ for shell in ${SHELLS[@]}; do
       echo "source init/lmod/$shell" > ~/.cshrc
       MODULE_SECTIONS=($($shell -c "module ov" 2>&1 | grep -e '---'))
     else
-      MODULE_SECTIONS=($($shell -c "source init/lmod/$shell >/dev/null 2>&1; module ov 2>&1 | grep -e '---'"))
+      MODULE_SECTIONS=($($shell -c ". init/lmod/$shell >/dev/null 2>&1; module ov 2>&1 | grep -e '---'"))
     fi
     PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/$EESSI_SOFTWARE_SUBDIR_OVERRIDE/modules/all"
     assert_raises 'echo "${MODULE_SECTIONS[1]}" | grep -E "$PATTERN"'
@@ -68,7 +72,7 @@ for shell in ${SHELLS[@]}; do
       echo "source init/lmod/$shell" > ~/.cshrc
       command="$shell -c 'module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; eb --version' | tail -n 1 | awk '{print \$4}'"
     else
-      command="$shell -c 'source init/lmod/$shell >/dev/null 2>&1; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; eb --version' | tail -n 1 | awk '{print \$4}'"
+      command="$shell -c '. init/lmod/$shell >/dev/null 2>&1; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; eb --version' | tail -n 1 | awk '{print \$4}'"
     fi
     assert "$command" "$EXPECTED_EASYBUILD_VERSION"
 
@@ -77,7 +81,7 @@ for shell in ${SHELLS[@]}; do
       echo "source init/lmod/$shell" > ~/.cshrc
       EASYBUILD_PATH=$($shell -c "module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; which eb")
     else
-      EASYBUILD_PATH=$($shell -c "source init/lmod/$shell 2>/dev/null; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; which eb")
+      EASYBUILD_PATH=$($shell -c ". init/lmod/$shell 2>/dev/null; module load EasyBuild/${EXPECTED_EASYBUILD_VERSION}; which eb")
     fi
     # escape the dots in ${EASYBUILD_VERSION}
     PATTERN="/cvmfs/software\.eessi\.io/versions/$EESSI_VERSION/software/linux/$EESSI_SOFTWARE_SUBDIR_OVERRIDE/software/EasyBuild/${EXPECTED_EASYBUILD_VERSION//./\\.}/bin/eb"
@@ -97,8 +101,8 @@ for shell in ${SHELLS[@]}; do
       TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'set -x EESSI_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $LMOD_SYSTEM_DEFAULT_MODULES')
       TEST_MODULEPATH=$($shell -c 'set -x EESSI_DEFAULT_MODULES_APPEND append_module ; set -x EESSI_DEFAULT_MODULES_PREPEND prepend_module ; set -x EESSI_EXTRA_MODULEPATH .github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
     else
-      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' ; echo $LMOD_SYSTEM_DEFAULT_MODULES')
-      TEST_MODULEPATH=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; source init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
+      TEST_LMOD_SYSTEM_DEFAULT_MODULES=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; . init/lmod/'"$shell"' ; echo $LMOD_SYSTEM_DEFAULT_MODULES')
+      TEST_MODULEPATH=$($shell -c 'export EESSI_DEFAULT_MODULES_APPEND=append_module ; export EESSI_DEFAULT_MODULES_PREPEND=prepend_module ; export EESSI_EXTRA_MODULEPATH=.github/workflows/modules ; . init/lmod/'"$shell"' 2>/dev/null; echo $MODULEPATH')
     fi
     LMOD_SYSTEM_DEFAULT_MODULES_PATTERN='^prepend_module:.*:append_module$'
     # echo "$TEST_LMOD_SYSTEM_DEFAULT_MODULES" AND "$LMOD_SYSTEM_DEFAULT_MODULES_PATTERN"
@@ -126,8 +130,8 @@ for shell in ${SHELLS[@]}; do
           TEST_EESSI_WITH_PURGE=$($shell -c "source $LMOD_PKG/init/$shell 2>/dev/null ; source init/lmod/$shell 2>/dev/null")
           TEST_EESSI_WITHOUT_PURGE=$($shell -c "set -x EESSI_NO_MODULE_PURGE_ON_INIT 1 ; source $LMOD_PKG/init/$shell 2>/dev/null ; source init/lmod/$shell 2>/dev/null")
         else
-          TEST_EESSI_WITH_PURGE=$($shell -c "source $LMOD_PKG/init/$shell 2>/dev/null ; source init/lmod/$shell 2>/dev/null")
-          TEST_EESSI_WITHOUT_PURGE=$($shell -c "export EESSI_NO_MODULE_PURGE_ON_INIT=1 ; source $LMOD_PKG/init/$shell 2>/dev/null ; source init/lmod/$shell 2>/dev/null")
+          TEST_EESSI_WITH_PURGE=$($shell -c ". $LMOD_PKG/init/$shell 2>/dev/null ; . init/lmod/$shell 2>/dev/null")
+          TEST_EESSI_WITHOUT_PURGE=$($shell -c "export EESSI_NO_MODULE_PURGE_ON_INIT=1 ; . $LMOD_PKG/init/$shell 2>/dev/null ; . init/lmod/$shell 2>/dev/null")
         fi
         # In the first case we should have the test and in the second case we shouldn't
         pattern="Modules purged before initialising EESSI"
@@ -139,13 +143,18 @@ for shell in ${SHELLS[@]}; do
     fi
 
     # Optional test 10, check if the prompt has been updated
-    if [ "$shell" = "bash" ] || [ "$shell" = "ksh" ] || [ "$shell" = "zsh" ]; then
+    if [ "$shell" = "bash" ] || [ "$shell" = "ksh" ] || [ "$shell" = "zsh" ] || [ "$shell" = "sh" ]; then
         # Typically this is a non-interactive shell, so manually unset PS1 and reset to a non-exported variable when testing
-        TEST_EESSI_PS1_UPDATE=$($shell -c "unset PS1 ; PS1='$ ' ; source init/lmod/$shell 2>/dev/null ; echo \"\$PS1\"")
-        TEST_EESSI_NO_PS1_UPDATE=$($shell -c "unset PS1 ; source init/lmod/$shell 2>/dev/null ; echo \"\$PS1\"")
+        TEST_EESSI_PS1_UPDATE=$($shell -c "unset PS1 ; PS1='$ ' ; . init/lmod/$shell 2>/dev/null ; echo \"\$PS1\"")
+        TEST_EESSI_NO_PS1_UPDATE=$($shell -c "unset PS1 ; . init/lmod/$shell 2>/dev/null ; echo \"\$PS1\"")
         pattern="{EESSI/${EESSI_VERSION}} "
         assert_raises 'echo "$TEST_EESSI_PS1_UPDATE" | grep "$pattern"'
         assert_raises 'echo "$TEST_EESSI_NO_PS1_UPDATE" | grep "$pattern"' 1
+        # Also check when we explicitly ask for it not to be updated
+        TEST_EESSI_EXPLICIT_NO_PS1_UPDATE=$($shell -c "unset PS1 ; PS1='test> ' ; export EESSI_MODULE_UPDATE_PS1=0 ; . init/lmod/$shell 2>/dev/null ; echo \"\$PS1\"")
+        TEST_EESSI_EXPLICIT_NO_PS1_UPDATE_CALLED_TWICE=$($shell -c "unset PS1 ; PS1='$ ' ; export EESSI_MODULE_UPDATE_PS1=0 ; . init/lmod/$shell 2>/dev/null ; . init/lmod/$shell 2>/dev/null ; echo \"\$PS1\"")
+        assert_raises 'echo "$TEST_EESSI_EXPLICIT_NO_PS1_UPDATE" | grep "$pattern"' 1
+        assert_raises 'echo "$TEST_EESSI_EXPLICIT_NO_PS1_UPDATE_CALLED_TWICE" | grep "$pattern"' 1
     fi
 
     # End Test Suite

.github/workflows/tests_init_module.yml

@@ -57,6 +57,7 @@ jobs:
       - name: Install missing shells
         run: |
           sudo apt update
+          # We're in Ubuntu so dash is already installed (and is symlinked to sh)
           sudo apt install zsh ksh fish tcsh
           echo "# INIT ZSH" > ~/.zshrc
 
@@ -65,7 +66,7 @@ jobs:
           export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
           export EESSI_VERSION=${{matrix.EESSI_VERSION}}
           export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
-          .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"
+          .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh" "sh"
       - name: Run tests for available shells with system Lmod
         run: |
           # We also want to perform the same test when there is an Lmod version available on the system
@@ -76,4 +77,4 @@ jobs:
           export EESSI_SOFTWARE_SUBDIR_OVERRIDE=${{matrix.EESSI_SOFTWARE_SUBDIR_OVERRIDE}}
           export EESSI_VERSION=${{matrix.EESSI_VERSION}}
           export EXPECTED_EASYBUILD_VERSION=${{matrix.EXPECTED_EASYBUILD_VERSION}}
-          .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh"
+          .github/workflows/scripts/test_init_scripts.sh "bash" "zsh" "ksh" "fish" "csh" "sh"

create_lmodsitepackage.py

@@ -124,7 +124,7 @@
     if packagesList[simpleName] then
         -- simpleName is a module in packagesList
         -- first, check the old host_injections path prior to https://github.com/EESSI/software-layer-scripts/pull/59
-        -- If that exists, print a more targetted, explanatory warning
+        -- If that exists, print a more targeted, explanatory warning
         local previousHostInjections = string.gsub(os.getenv('EESSI_SOFTWARE_PATH') or "", 'versions', 'host_injections')
         local previousPackageEasyBuildDir = previousHostInjections .. "/software/" .. t.modFullName .. "/easybuild"
         local previousPackageDirExists = isDir(previousPackageEasyBuildDir)
@@ -161,24 +161,38 @@
     local checkGpu = mt:haveProperty(simpleName,"arch","gpu")
     local overrideGpuCheck = os.getenv("EESSI_OVERRIDE_GPU_CHECK")
     if checkGpu and (overrideGpuCheck == nil) then
-        local arch = os.getenv("EESSI_CPU_FAMILY") or ""
-        local cvmfs_repo = os.getenv("EESSI_CVMFS_REPO") or ""
-        local cudaVersionFile = cvmfs_repo .. "/host_injections/nvidia/" .. arch .. "/latest/cuda_version.txt"
-        local cudaDriverFile = cvmfs_repo .. "/host_injections/nvidia/" .. arch .. "/latest/libcuda.so"
+        local eessi_version = os.getenv('EESSI_VERSION') or ""
+        local eessi_eprefix = os.getenv("EESSI_EPREFIX") or ""
+        if eessi_eprefix == nil or eessi_version == nil then
+            LmodError("EESSI_VERSION and EESSI_EPREFIX must be defined for GPU driver check to work\\n")
+        end
+        local cudaDriverDir = nil
+        if eessi_version == "2023.06" then
+            cudaDriverDir = string.gsub(eessi_eprefix, 'versions', 'host_injections') .. "/lib"
+        else
+            cudaDriverDir = eessi_eprefix .. "/lib/nvidia"
+        end
+        local cudaVersionFile = cudaDriverDir .. "/cuda_version.txt"
+        local cudaDriverFile = cudaDriverDir .. "/libcuda.so"
         local cudaDriverExists = isFile(cudaDriverFile)
         local singularityCudaExists = isFile("/.singularity.d/libs/libcuda.so")
         if not (cudaDriverExists or singularityCudaExists)  then
             local advice = "which relies on the CUDA runtime environment and driver libraries. "
             advice = advice .. "In order to be able to use the module, you will need "
-            advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system. You can "
-            advice = advice .. "override this check by setting the environment variable EESSI_OVERRIDE_GPU_CHECK but "
+            advice = advice .. "to make sure EESSI can find the GPU driver libraries on your host system. "
+            advice = advice .. "The file being checked for on your system is \\n" .. cudaDriverFile .. "\\n"
+            advice = advice .. "You can override this check by setting the environment variable "
+            advice = advice .. "EESSI_OVERRIDE_GPU_CHECK but "
             advice = advice .. "the loaded application will not be able to execute on your system.\\n"
             advice = advice .. refer_to_docs
             LmodError("\\nYou requested to load ", simpleName, " ", advice)
         else
             -- CUDA driver exists, now we check its version to see if an update is needed
             if cudaDriverExists then
                 local cudaVersion = read_file(cudaVersionFile)
+                if not cudaVersion then
+                    LmodError("No CUDA version file\\n" .. cudaVersionFile .. "\\nfound. " .. refer_to_docs)
+                end
                 local cudaVersion_req = os.getenv("EESSICUDAVERSION")
                 -- driver CUDA versions don't give a patch version for CUDA
                 local major, minor = string.match(cudaVersion, "(%d+)%.(%d+)")

eb_hooks.py

@@ -1575,23 +1575,6 @@ def pre_test_hook_ignore_failing_tests_OpenBabel_a64fx(self, *args, **kwargs):
         self.cfg['testopts'] = "|| echo ignoring failing tests"
 
 
-def pre_test_hook_ignore_failing_tests_LAMMPS_ARM_generic(self, *args, **kwargs):
-    """
-    Pre-test hook for LAMMPS: skip failing ctest for selected LAMMPS version on ARM generic.
-
-    See: https://github.com/lammps/lammps/issues/4926
-    """
-    print('build option before pre_test_hooki: ', build_option('ignore_test_failure'))
-    if self.name == 'LAMMPS' and self.version in ('22Jul2025'):
-        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
-        print('Debug: ', cpu_target)
-        if cpu_target == CPU_TARGET_AARCH64_GENERIC:
-            print('I will reset ignore_test_failure')
-            self.orig_ignore_test_failure = build_option('ignore_test_failure')
-            update_build_option('ignore_test_failure', True)
-            print(build_option('ignore_test_failure'))
-
-
 def pre_single_extension_hook(ext, *args, **kwargs):
     """Main pre-extension: trigger custom functions based on software name."""
     if ext.name in PRE_SINGLE_EXTENSION_HOOKS:
@@ -1939,23 +1922,23 @@ def post_easyblock_hook(self, *args, **kwargs):
                 post_easyblock_hook_copy_easybuild_subdir(self, *args, **kwargs)
         else:
             self.log.debug("No CVMFS/site installation requested, not running post_easyblock_hook_copy_easybuild_subdir.")
-
-        # If self.orig_ignore_test_failure is set return it to its original value.
-        if hasattr(self, "orig_ignore_test_failure") and self.orig_ignore_test_failure != build_option('ignore_test_failure'):
-            update_build_option('ignore_test_failure', self.orig_ignore_test_failure)
 else:
     print_warning(f"Not enabling the post_easybuild_hook, as it requires EasyBuild 5.1.1 or newer (you are using {EASYBUILD_VERSION}).")
 
 
 def pre_run_shell_cmd_hook(cmd, work_dir=None, **kwargs):
     """Main pre_shell_cmd_hook: trigger custom funtions based on software name."""
+    
     # Ignore failing ctest for LAMMPS/22Jul2025 on aarch64/generic
     cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
     if cpu_target == CPU_TARGET_AARCH64_GENERIC:
         if bool(re.search('LAMMPS', work_dir)) and bool(re.search('22Jul2025', work_dir)):
             if isinstance(cmd, str) and cmd.startswith('ctest') and '-LE unstable' in cmd:
                 cmd = cmd + ' || true'
 
+
+
+
 PARSE_HOOKS = {
     'casacore': parse_hook_casacore_disable_vectorize,
     'CGAL': parse_hook_cgal_toolchainopts_precise,
@@ -2016,7 +1999,6 @@ def pre_run_shell_cmd_hook(cmd, work_dir=None, **kwargs):
     'netCDF': pre_test_hook_ignore_failing_tests_netCDF,
     'OpenBabel': pre_test_hook_ignore_failing_tests_OpenBabel_a64fx,
     'PyTorch': pre_test_hook_increase_max_failed_tests_arm_PyTorch,
-    'LAMMPS': pre_test_hook_ignore_failing_tests_LAMMPS_ARM_generic,
 }
 
 PRE_SINGLE_EXTENSION_HOOKS = {