Merge branch '2023.06-software.eessi.io' into 2023.06-eessi.io

.github/workflows/tests_readme.yml

@@ -19,10 +19,10 @@ jobs:
         - name: Check out software-layer repository
           uses: actions/checkout@93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8 # v3.1.0
 
-        - name: verify if README.md is consistent with EESSI_PILOT_VERSION from init/eessi_defaults
+        - name: verify if README.md is consistent with EESSI_VERSION from init/eessi_defaults
           run: |
             source init/eessi_defaults
-            grep "${EESSI_PILOT_VERSION}" README.md
+            grep "${EESSI_VERSION}" README.md
 
         - name: verify if README.md is consistent with EESSI_CVMFS_REPO from init/eessi_defaults
           run: |

configure_easybuild

@@ -25,8 +25,7 @@ fi
 
 # note: filtering Bison may break some installations, like Qt5 (see https://github.com/EESSI/software-layer/issues/49)
 # filtering pkg-config breaks R-bundle-Bioconductor installation (see also https://github.com/easybuilders/easybuild-easyconfigs/pull/11104)
-# problems occur when filtering pkg-config with gnuplot too (picks up Lua 5.1 from $EPREFIX rather than from Lua 5.3 dependency)
-DEPS_TO_FILTER=Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,Lua,M4,makeinfo,ncurses,util-linux,XZ,zlib
+DEPS_TO_FILTER=Autoconf,Automake,Autotools,binutils,bzip2,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,M4,makeinfo,ncurses,util-linux,XZ,zlib
 # For aarch64 we need to also filter out Yasm.
 # See https://github.com/easybuilders/easybuild-easyconfigs/issues/11190
 if [[ "$EESSI_CPU_FAMILY" == "aarch64" ]]; then

eb_hooks.py

@@ -19,6 +19,7 @@
 
 
 CPU_TARGET_NEOVERSE_V1 = 'aarch64/neoverse_v1'
+CPU_TARGET_AARCH64_GENERIC = 'aarch64/generic' 
 
 EESSI_RPATH_OVERRIDE_ATTR = 'orig_rpath_override_dirs'
 
@@ -268,6 +269,24 @@ def pre_configure_hook_wrf_aarch64(self, *args, **kwargs):
         raise EasyBuildError("WRF-specific hook triggered for non-WRF easyconfig?!")
 
 
+def pre_configure_hook_LAMMPS_aarch64(self, *args, **kwargs):
+    """
+    pre-configure hook for LAMMPS:
+    - set kokkos_arch on Aarch64
+    """
+
+    cpu_target = get_eessi_envvar('EESSI_SOFTWARE_SUBDIR')
+    if self.name == 'LAMMPS':
+        if self.version == '23Jun2022':
+            if  get_cpu_architecture() == AARCH64:
+                if cpu_target == CPU_TARGET_AARCH64_GENERIC:
+                    self.cfg['kokkos_arch'] = 'ARM80'
+                else:
+                    self.cfg['kokkos_arch'] = 'ARM81'
+    else:
+        raise EasyBuildError("LAMMPS-specific hook triggered for non-LAMMPS easyconfig?!")
+
+
 def pre_test_hook(self,*args, **kwargs):
     """Main pre-test hook: trigger custom functions based on software name."""
     if self.name in PRE_TEST_HOOKS:
@@ -346,6 +365,7 @@ def pre_single_extension_isoband(ext, *args, **kwargs):
     'MetaBAT': pre_configure_hook_metabat_filtered_zlib_dep,
     'OpenBLAS': pre_configure_hook_openblas_optarch_generic,
     'WRF': pre_configure_hook_wrf_aarch64,
+    'LAMMPS': pre_configure_hook_LAMMPS_aarch64,
 }
 
 PRE_TEST_HOOKS = {

eessi-2023.06-eb-4.8.0-2021b.yml

@@ -4,4 +4,9 @@ easyconfigs:
       # see https://github.com/easybuilders/easybuild-easyconfigs/pull/18746
       options:
         from-pr: 18746
+  - gnuplot-5.4.2-GCCcore-11.2.0.eb:
+      # make sure that Lua dependency is correctly picked up,
+      # see https://github.com/easybuilders/easybuild-easyconfigs/pull/19261
+      options:
+        from-pr: 19261
   - OpenFOAM-v2112-foss-2021b.eb

eessi-2023.06-eb-4.8.1-2021b.yml

@@ -5,3 +5,11 @@ easyconfigs:
       options:
         from-pr: 18834
   - R-4.2.0-foss-2021b.eb
+  - PLUMED-2.7.3-foss-2021b.eb:
+      # the --enable-asmjit is not supported on Aarch64
+      options:
+        from-pr: 19110
+  - LAMMPS-23Jun2022-foss-2021b-kokkos.eb:
+      # TBB and ScaFaCos are optional dependencies when building on Intel arch
+      options:
+        from-pr: 19246

eessi-2023.06-eb-4.8.2-2021b.yml

@@ -0,0 +1,6 @@
+easyconfigs:
+  - Pillow-8.3.2-GCCcore-11.2.0.eb:
+      # avoid that hardcoded paths like /usr/include are used in build commands
+      options:
+        from-pr: 19226
+  - matplotlib-3.4.3-foss-2021b.eb

eessi-2023.06-eb-4.8.2-2022a.yml

@@ -5,27 +5,6 @@ easyconfigs:
   - AOFlagger-3.4.0-foss-2022a:
       options:
         from-pr: 19119
-        # Exclude Lua from `filter-deps` as the compat layer version is too old for the software
-        filter-deps:
-          - Autoconf
-          - Automake
-          - Autotools
-          - binutils
-          - bzip2
-          - DBus
-          - flex
-          - gettext
-          - gperf
-          - help2man
-          - intltool
-          - libreadline
-          - libtool
-          - ncurses
-          - M4
-          - makeinfo
-          - util-linux
-          - XZ
-          - zlib
   - EveryBeam-0.5.2-foss-2022a:
       options:
         from-pr: 19119
@@ -35,3 +14,8 @@ easyconfigs:
   - WSClean-3.4-foss-2022a:
       options:
         from-pr: 19119
+  - Pillow-9.1.1-GCCcore-11.3.0.eb:
+      # avoid that hardcoded paths like /usr/include are used in build commands
+      options:
+        from-pr: 19226
+  - matplotlib-3.5.2-foss-2022a.eb

init/eessi_defaults

@@ -11,5 +11,5 @@
 export EESSI_CVMFS_REPO="${EESSI_CVMFS_REPO_OVERRIDE:=/cvmfs/software.eessi.io}"
 export EESSI_VERSION="${EESSI_VERSION_OVERRIDE:=2023.06}"
 # use archdetect by default, unless otherwise specified
-export EESSI_USE_ARCHDETECT="${EESSI_USE_ARCHDETECT:=0}"
-export EESSI_USE_ARCHSPEC="${EESSI_USE_ARCHSPEC:=1}"
+export EESSI_USE_ARCHDETECT="${EESSI_USE_ARCHDETECT:=1}"
+export EESSI_USE_ARCHSPEC="${EESSI_USE_ARCHSPEC:=0}"