sync with 2023.06-software.eessi.io branch

.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

.github/workflows/tests_archdetect.yml

@@ -13,6 +13,8 @@ jobs:
           - x86_64/intel/skylake_avx512/archspec-linux-6132
           - x86_64/amd/zen2/Azure-CentOS7-7V12
           - x86_64/amd/zen3/Azure-CentOS7-7V73X
+          - x86_64/amd/zen4/Azure-Alma8-9V33X
+          - x86_64/amd/zen4/Shinx-RHEL8-9654
           - aarch64/neoverse_n1/Azure-Ubuntu20-Altra
           - aarch64/neoverse_n1/AWS-awslinux-graviton2
           - aarch64/neoverse_v1/AWS-awslinux-graviton3

.github/workflows/tests_scripts.yml

@@ -3,9 +3,9 @@ name: Tests for scripts
 on:
   push:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh
@@ -15,9 +15,9 @@ on:
 
   pull_request:
     paths:
-      - build_container.sh
       - create_directory_tarballs.sh
       - create_lmodsitepackage.py
+      - eessi_container.sh
       - EESSI-install-software.sh
       - install_software_layer.sh
       - load_easybuild_module.sh

EESSI-install-software.sh

@@ -147,6 +147,24 @@ else
   mkdir -p ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
 fi
 
+# if we run the script for the first time, e.g., to start building for a new
+#   stack, we need to ensure certain files are present in
+#   ${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+# - .lmod/lmodrc.lua
+# - .lmod/SitePackage.lua
+_eessi_software_path=${EESSI_PREFIX}/software/${EESSI_OS_TYPE}/${EESSI_SOFTWARE_SUBDIR_OVERRIDE}
+_lmod_cfg_dir=${_eessi_software_path}/.lmod
+_lmod_rc_file=${_lmod_cfg_dir}/lmodrc.lua
+if [ ! -f ${_lmod_rc_file} ]; then
+    command -V python3
+    python3 ${TOPDIR}/create_lmodrc.py ${_eessi_software_path}
+fi
+_lmod_sitepackage_file=${_lmod_cfg_dir}/SitePackage.lua
+if [ ! -f ${_lmod_sitepackage_file} ]; then
+    command -V python3
+    python3 ${TOPDIR}/create_lmodsitepackage.py ${_eessi_software_path}
+fi
+
 # Set all the EESSI environment variables (respecting $EESSI_SOFTWARE_SUBDIR_OVERRIDE)
 # $EESSI_SILENT - don't print any messages
 # $EESSI_BASIC_ENV - give a basic set of environment variables
@@ -203,10 +221,21 @@ ${TOPDIR}/install_scripts.sh --prefix ${EESSI_PREFIX}
 # Hardcode this for now, see if it works
 # TODO: We should make a nice yaml and loop over all CUDA versions in that yaml to figure out what to install
 # Allow skipping CUDA SDK install in e.g. CI environments
+# The install_cuda... script uses EasyBuild. So, we need to check if we have EB
+# or skip this step.
+module_avail_out=$TMPDIR/ml.out
+module avail 2>&1 | grep EasyBuild &> ${module_avail_out}
+if [[ $? -eq 0 ]]; then
+    echo_green ">> Found an EasyBuild module"
+else
+    echo_yellow ">> No EasyBuild module found: skipping step to install CUDA (see output in ${module_avail_out})"
+    export skip_cuda_install=True
+fi
+
 if [ -z "${skip_cuda_install}" ] || [ ! "${skip_cuda_install}" ]; then
     ${EESSI_PREFIX}/scripts/gpu_support/nvidia/install_cuda_host_injections.sh -c 12.1.1 --accept-cuda-eula
 else
-    echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed"
+    echo "Skipping installation of CUDA SDK in host_injections, since the --skip-cuda-install flag was passed OR no EasyBuild module was found"
 fi
 
 # Install drivers in host_injections

create_lmodsitepackage.py

@@ -20,6 +20,28 @@
     return content
 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")
+
+    -- 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
+        -- 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
+
 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.
@@ -153,10 +175,13 @@
 -- 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

eb_hooks.py

@@ -335,6 +335,21 @@ def pre_configure_hook(self, *args, **kwargs):
         PRE_CONFIGURE_HOOKS[self.name](self, *args, **kwargs)
 
 
+def pre_configure_hook_gromacs(self, *args, **kwargs):
+    """
+    Pre-configure hook for GROMACS:
+    - avoid building with SVE instructions on Neoverse V1 as workaround for failing tests,
+      see https://gitlab.com/gromacs/gromacs/-/issues/5057 + https://gitlab.com/eessi/support/-/issues/47
+    """
+    if self.name == 'GROMACS':
+        cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+        if LooseVersion(self.version) <= LooseVersion('2024.1') and cpu_target == CPU_TARGET_NEOVERSE_V1:
+            self.cfg.update('configopts', '-DGMX_SIMD=ARM_NEON_ASIMD')
+            print_msg("Avoiding use of SVE instructions for GROMACS %s by using ARM_NEON_ASIMD as GMX_SIMD value", self.version)
+    else:
+        raise EasyBuildError("GROMACS-specific hook triggered for non-GROMACS easyconfig?!")
+
+
 def pre_configure_hook_openblas_optarch_generic(self, *args, **kwargs):
     """
     Pre-configure hook for OpenBLAS: add DYNAMIC_ARCH=1 to build/test/install options when using --optarch=GENERIC
@@ -597,8 +612,8 @@ def post_sanitycheck_cuda(self, *args, **kwargs):
                 full_path = os.path.join(dir_path, filename)
                 # we only really care about real files, i.e. not symlinks
                 if not os.path.islink(full_path):
-                    # check if the current file is part of the allowlist
-                    basename = os.path.splitext(filename)[0]
+                    # check if the current file name stub is part of the allowlist
+                    basename = filename.split('.')[0]
                     if basename in allowlist:
                         self.log.debug("%s is found in allowlist, so keeping it: %s", basename, full_path)
                     else:
@@ -665,6 +680,7 @@ def inject_gpu_property(ec):
 }
 
 PRE_CONFIGURE_HOOKS = {
+    'GROMACS': pre_configure_hook_gromacs,
     'libfabric': pre_configure_hook_libfabric_disable_psm3_x86_64_generic,
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,

eessi-2023.06-known-issues.yml

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

init/arch_specs/eessi_arch_x86.spec

@@ -1,6 +1,7 @@
 # x86_64 CPU architecture specifications
 # Software path in EESSI 	| Vendor ID 	| List of defining CPU features
-"x86_64/intel/haswell"		"GenuineIntel"	"avx2 fma" 		# Intel Haswell, Broadwell
+"x86_64/intel/haswell"		"GenuineIntel"	"avx2 fma" 						# Intel Haswell, Broadwell
 "x86_64/intel/skylake_avx512"	"GenuineIntel"	"avx2 fma avx512f avx512bw avx512cd avx512dq avx512vl"	# Intel Skylake, Cascade Lake
-"x86_64/amd/zen2"		"AuthenticAMD"	"avx2 fma"		# AMD Rome
-"x86_64/amd/zen3"		"AuthenticAMD"	"avx2 fma vaes"		# AMD Milan, Milan-X
+"x86_64/amd/zen2"		"AuthenticAMD"	"avx2 fma"						# AMD Rome
+"x86_64/amd/zen3"		"AuthenticAMD"	"avx2 fma vaes"						# AMD Milan, Milan-X
+"x86_64/amd/zen4"		"AuthenticAMD"	"avx2 fma vaes avx512f avx512ifma"			# AMD Genoa, Genoa-X

tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.all.output

@@ -0,0 +1 @@
+x86_64/amd/zen4:x86_64/amd/zen3:x86_64/amd/zen2:x86_64/generic

tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.cpuinfo

@@ -0,0 +1,27 @@
+processor       : 0
+vendor_id       : AuthenticAMD
+cpu family      : 25
+model           : 17
+model name      : AMD EPYC 9V33X 96-Core Processor
+stepping        : 1
+microcode       : 0xffffffff
+cpu MHz         : 3705.853
+cache size      : 1024 KB
+physical id     : 0
+siblings        : 88
+core id         : 0
+cpu cores       : 88
+apicid          : 0
+initial apicid  : 0
+fpu             : yes
+fpu_exception   : yes
+cpuid level     : 13
+wp              : yes
+flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl tsc_reliable nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 movbe popcnt aes xsave avx f16c rdrand hypervisor lahf_lm cmp_legacy svm cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw topoext perfctr_core invpcid_single vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid avx512f avx512dq rdseed adx smap avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves avx512_bf16 clzero xsaveerptr arat npt nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold v_vmsave_vmload avx512vbmi umip avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq rdpid fsrm
+bugs            : sysret_ss_attrs null_seg spectre_v1 spectre_v2 spec_store_bypass
+bogomips        : 5100.08
+TLB size        : 3584 4K pages
+clflush size    : 64
+cache_alignment : 64
+address sizes   : 48 bits physical, 48 bits virtual
+power management:

tests/archdetect/x86_64/amd/zen4/Azure-Alma8-9V33X.output

@@ -0,0 +1 @@
+x86_64/amd/zen4

tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.all.output

@@ -0,0 +1 @@
+x86_64/amd/zen4:x86_64/amd/zen3:x86_64/amd/zen2:x86_64/generic

tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.cpuinfo

@@ -0,0 +1,27 @@
+processor	: 0
+vendor_id	: AuthenticAMD
+cpu family	: 25
+model		: 17
+model name	: AMD EPYC 9654 96-Core Processor
+stepping	: 1
+microcode	: 0xa10113e
+cpu MHz		: 3699.993
+cache size	: 1024 KB
+physical id	: 0
+siblings	: 96
+core id		: 0
+cpu cores	: 96
+apicid		: 0
+initial apicid	: 0
+fpu		: yes
+fpu_exception	: yes
+cpuid level	: 16
+wp		: yes
+flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl nonstop_tsc cpuid extd_apicid aperfmperf pni pclmulqdq monitor ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 invpcid_single hw_pstate ssbd mba perfmon_v2 ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 erms invpcid cqm rdt_a avx512f avx512dq rdseed adx avx512ifma clflushopt clwb avx512cd sha_ni avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local avx512_bf16 clzero irperf xsaveerptr wbnoinvd amd_ppin cppc arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif v_spec_ctrl avx512vbmi umip pku ospke avx512_vbmi2 gfni vaes vpclmulqdq avx512_vnni avx512_bitalg avx512_vpopcntdq la57 rdpid overflow_recov succor smca fsrm flush_l1d
+bugs		: sysret_ss_attrs spectre_v1 spectre_v2 spec_store_bypass
+bogomips	: 4799.99
+TLB size	: 3584 4K pages
+clflush size	: 64
+cache_alignment	: 64
+address sizes	: 52 bits physical, 57 bits virtual
+power management: ts ttp tm hwpstate cpb eff_freq_ro [13] [14]

tests/archdetect/x86_64/amd/zen4/Shinx-RHEL8-9654.output

@@ -0,0 +1 @@
+x86_64/amd/zen4