Merge remote-tracking branch 'jcsda/develop' into revert_modules_mods

.github/workflows/macos-ci-aarch64.yaml

@@ -56,7 +56,9 @@ jobs:
           export SPACK_SYSTEM_CONFIG_PATH="${ENVDIR}/site"
 
           # Find external packages
-          spack external find --scope system --exclude bison --exclude openssl
+          spack external find --scope system \
+              --exclude bison --exclude openssl \
+              --exclude python
           spack external find --scope system perl
           spack external find --scope system wget
           PATH="/opt/homebrew/opt/curl/bin:$PATH" \
@@ -77,7 +79,7 @@ jobs:
           # *DH
 
           # Set compiler and MPI
-          spack config add "packages:all:providers:mpi:[openmpi@4.1.6]"
+          spack config add "packages:all:providers:mpi:[openmpi@5.0.1]"
           spack config add "packages:all:compiler:[apple-clang@14.0.3]"
           sed -i '' "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%apple-clang'\]/g" $ENVDIR/spack.yaml
 
@@ -136,7 +138,7 @@ jobs:
 
           module use ${ENVDIR}/install/modulefiles/Core
           module load stack-apple-clang/14.0.3
-          module load stack-openmpi/4.1.6
+          module load stack-openmpi/5.0.1
           module load stack-python/3.10.13
           module available
 

.github/workflows/macos-ci-x86_64.yaml

@@ -49,7 +49,11 @@ jobs:
           export SPACK_SYSTEM_CONFIG_PATH="${ENVDIR}/site"
 
           # Find external packages
-          spack external find --scope system --exclude bison --exclude openssl
+          spack external find --scope system \
+              --exclude bison --exclude openssl  \
+              --exclude python --exclude gettext
+          # Need to find gettext outside of default (presumed to be a system) path for krb5
+          spack external find --path=/usr/local/Cellar/gettext/0.21.1 gettext
           spack external find --scope system perl
           spack external find --scope system wget
           PATH="/usr/local/opt/curl/bin:$PATH" \
@@ -70,7 +74,7 @@ jobs:
           # *DH
 
           # Set compiler and MPI
-          spack config add "packages:all:providers:mpi:[openmpi@4.1.6]"
+          spack config add "packages:all:providers:mpi:[openmpi@5.0.1]"
           spack config add "packages:all:compiler:[apple-clang@14.0.0]"
           sed -i '' "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%apple-clang'\]/g" $ENVDIR/spack.yaml
 
@@ -127,7 +131,7 @@ jobs:
 
           module use ${ENVDIR}/install/modulefiles/Core
           module load stack-apple-clang/14.0.0
-          module load stack-openmpi/4.1.6
+          module load stack-openmpi/5.0.1
           module load stack-python/3.10.13
           module available
 

.github/workflows/ubuntu-ci-containers-x86_64.yaml

@@ -63,9 +63,9 @@ jobs:
           spack stack create ctr --container ${CONTAINER} --specs ${SPECS}
 
           cd ${ENVDIR}
-          # mapl doesn't build with mpich - https://github.com/JCSDA/spack-stack/issues/608
+          # mapl@:2.41 doesn't build with mpich@4 - https://github.com/JCSDA/spack-stack/issues/608
           if [[ "${CONTAINER}" == *"mpich"* ]]; then
-              sed -i 's/- mapl@2.35.2/#- mapl@2.35.2/g' spack.yaml
+              sed -i 's/- mapl@/#- mapl@/g' spack.yaml
           fi
           spack containerize > Dockerfile
           docker build -t ${CONTAINER}-${SPECS} .

.github/workflows/ubuntu-ci-x86_64.yaml

@@ -49,12 +49,12 @@ jobs:
           export SPACK_SYSTEM_CONFIG_PATH="${ENVDIR}/site"
 
           # Find external packages
-          spack external find --scope system --exclude bison --exclude openssl
+          spack external find --scope system \
+              --exclude bison --exclude openssl \
+              --exclude curl --exclude python
           spack external find --scope system sed
           spack external find --scope system perl
           spack external find --scope system wget
-          PATH="/usr/local/opt/curl/bin:$PATH" \
-              spack external find --scope system curl
           PATH="/usr/local/opt/qt5/bin:$PATH" \
               spack external find --scope system qt
           spack external find --scope system texlive
@@ -70,7 +70,7 @@ jobs:
           echo "  intel-oneapi-mpi:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
           echo "    buildable: false" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
           echo "    externals:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
-          echo "    - spec: intel-oneapi-mpi@2021.6.0%intel@2022.1.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
+          echo "    - spec: intel-oneapi-mpi@2021.6.0%intel@2021.6.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
           echo "      prefix: /opt/intel" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
           echo "      modules:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
           echo "      - libfabric-aws/1.16.0~amzn4.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
@@ -84,7 +84,7 @@ jobs:
           echo "" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "compilers:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "- compiler:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
-          echo "    spec: intel@2022.1.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
+          echo "    spec: intel@2021.6.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "    paths:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "      cc: /opt/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/icc" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "      cxx: /opt/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/icpc" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
@@ -110,15 +110,15 @@ jobs:
 
           # Set compiler and MPI
           spack config add "packages:all:providers:mpi:[intel-oneapi-mpi@2021.6.0]"
-          spack config add "packages:all:compiler:[intel@2022.1.0]"
+          spack config add "packages:all:compiler:[intel@2021.6.0]"
           sed -i "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%intel'\]/g" $ENVDIR/spack.yaml
 
           # Add additional variants for MET packages, different from config/common/packages.yaml
           spack config add "packages:met:variants:+python +grib2 +graphics +lidar2nc +modis"
 
           # Concretize and check for duplicates
-          spack concretize 2>&1 | tee log.concretize.intel-2022.1.0
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.intel-2022.1.0 -i fms -i crtm -i esmf -i mapl
+          spack concretize 2>&1 | tee log.concretize.intel-2021.6.0
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.intel-2021.6.0 -i fms -i crtm -i esmf -i mapl
 
           # Add and update source cache
           spack mirror add local-source file:///home/ubuntu/spack-stack/source-cache/
@@ -136,12 +136,12 @@ jobs:
 
           # base-env
           echo "base-env ..."
-          spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.intel-2022.1.0.base-env
+          spack install --fail-fast --source --no-check-signature base-env 2>&1 | tee log.install.intel-2021.6.0.base-env
           spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ base-env
 
           # the rest
           echo "${{ inputs.template || 'unified-dev' }} ..."
-          spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.intel@2022.1.0.${{ inputs.template || 'unified-dev' }}
+          spack install --fail-fast --source --no-check-signature 2>&1 | tee log.install.intel@2021.6.0.${{ inputs.template || 'unified-dev' }}
           spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/
 
           # Next steps: synchronize source and build cache to a central/combined mirror?
@@ -181,7 +181,7 @@ jobs:
           ls -l ${ENVDIR}/install/modulefiles/Core
 
           module use ${ENVDIR}/install/modulefiles/Core
-          module load stack-intel/2022.1.0
+          module load stack-intel/2021.6.0
           module load stack-intel-oneapi-mpi/2021.6.0
           module load stack-python/3.10.13
           module available

.github/workflows/ubuntu-rnd-x86_64.yaml

@@ -188,7 +188,7 @@ jobs:
           ls -l /home/ubuntu/spack-stack/CI/unified-env/${TODAY}/modulefiles/Core
 
           module use /home/ubuntu/spack-stack/CI/unified-env/${TODAY}/modulefiles/Core
-          module load stack-intel/2022.1.0
+          module load stack-intel/2021.6.0
           module load stack-intel-oneapi-mpi/2021.6.0
           module load stack-python/3.10.13
           module available

configs/common/modules_lmod.yaml

@@ -141,6 +141,7 @@ modules:
         environment:
           set:
             'OMPI_MCA_rmaps_base_oversubscribe': '1'
+            'PRTE_MCA_rmaps_default_mapping_policy': ':oversubscribe'
       p4est:
         environment:
           set:
@@ -285,5 +286,3 @@ modules:
       - PKG_CONFIG_PATH
       lib64/pkgconfig:
       - PKG_CONFIG_PATH
-      '':
-      - CMAKE_PREFIX_PATH

configs/common/modules_tcl.yaml

@@ -143,6 +143,7 @@ modules:
         environment:
           set:
             'OMPI_MCA_rmaps_base_oversubscribe': '1'
+            'PRTE_MCA_rmaps_default_mapping_policy': ':oversubscribe'
       p4est:
         environment:
           set:
@@ -284,5 +285,3 @@ modules:
       - PKG_CONFIG_PATH
       lib64/pkgconfig:
       - PKG_CONFIG_PATH
-      '':
-      - CMAKE_PREFIX_PATH

configs/common/packages.yaml

@@ -10,7 +10,7 @@
         jpeg: [libjpeg-turbo]
         lapack: [openblas]
         yacc: [bison]
-        zlib-api: [zlib]
+        zlib-api: [zlib-ng]
     #
     # This version of awscli goes with py-pyyaml@5.4.1
     awscli:
@@ -20,8 +20,7 @@
     bison:
       version: ['3.8.2']
     boost:
-      version: ['1.83.0']
-      variants: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=17 visibility=hidden
+      require: "@1.83: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=17 visibility=hidden"
     bufr:
       version: ['12.0.1']
       variants: +python
@@ -40,7 +39,7 @@
     ecbuild:
       version: ['3.7.2']
     eccodes:
-      version: ['2.32.0']
+      version: ['2.33.0']
       variants: +png
     ecflow:
       version: ['5.11.4']
@@ -49,7 +48,7 @@
       version: ['1.24.5']
       variants: linalg=eigen,lapack compression=lz4,bzip2
     ecmwf-atlas:
-      version: ['0.35.1']
+      version: ['0.36.0']
       variants: +fckit +trans +tesselation +fftw
     ectrans:
       version: ['1.2.0']
@@ -113,8 +112,8 @@
       version: ['4.2.15']
       variants: +external-xdr ~fortran ~netcdf
     hdf5:
-      version: ['1.14.0']
-      variants: +hl +fortran +mpi ~threadsafe +szip
+      version: ['1.14.3']
+      variants: +hl +fortran +mpi ~threadsafe ~szip
     ip:
       version: ['4.3.0']
       variants: precision=4,d,8
@@ -124,8 +123,6 @@
       version: ['2.0.32']
     jedi-cmake:
       version: ['1.4.0']
-    jpeg:
-      version: ['9.1.0']
     landsfcutil:
       version: ['2.4.1']
     libjpeg-turbo:
@@ -138,7 +135,7 @@
     mapl:
       version: ['2.40.3']
       variants: +shared +pflogger ~f2py
-    # If making changes here, also check the Discover site config and the CI workflows
+    # If making changes here, also check the Discover site configs and the CI workflows
     met:
       version: ['11.1.0']
       variants: +python +grib2
@@ -148,10 +145,8 @@
       require: "+int64 +real64"
     mpich:
       variants: ~hwloc +two_level_namespace
-    mysql:
-      variants: +download_boost
     nco:
-      version: ['5.0.6']
+      version: ['5.1.6']
       variants: ~doc
     # ncview - when adding information here, also check Orion
     # and Discover site configs
@@ -166,7 +161,7 @@
     netcdf-c:
       version: ['4.9.2']
       # If using 4.9.1, turn off byterange variant to fix compile error: ~byterange
-      variants: +dap +mpi ~parallel-netcdf
+      variants: +dap +mpi ~parallel-netcdf ~szip
     netcdf-cxx4:
       version: ['4.3.1']
     netcdf-fortran:
@@ -183,17 +178,17 @@
       version: ['0.3.24']
       variants: +noavx512
     openmpi:
-      variants: +internal-hwloc +two_level_namespace
+      variants: ~internal-hwloc +two_level_namespace
     # Pin openssl to avoid duplicate packages being built
     openssl:
       variants: +shared
     p4est:
       version: ['2.8']
     parallelio:
-      version: ['2.5.10']
+      version: ['2.6.2']
       variants: +pnetcdf
     parallel-netcdf:
-      version: ['1.12.2']
+      version: ['1.12.3']
     pflogger:
       version: ['1.12.0']
       variants: +mpi
@@ -221,6 +216,9 @@
     # to avoid duplicate packages being built (cylc dependencies soft-want @3:)
     py-cython:
       require: "@0.29.36"
+    ## https://github.com/JCSDA/spack-stack/issues/980
+    #py-gitpython:
+    #  require: "@3.1.27"
     py-h5py:
       version: ['3.7.0']
       variants: ~mpi
@@ -237,9 +235,6 @@
       require: ['@1.22.3']
     py-pandas:
       variants: +excel
-    # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer
-    # versions of py-poetry-core when using external/homebrew Python as
-    # we do at the moment in spack-stack.
     # Pin the py-setuptools version to avoid duplicate Python packages
     py-setuptools:
       require: ['@63.4.3']
@@ -263,6 +258,7 @@
       variants: precision=4,d,8
     udunits:
       version: ['2.2.28']
+    # Note - we can remove upp from stack at some point?
     upp:
       version: ['10.0.10']
     w3emc:
@@ -278,9 +274,7 @@
     wrf-io:
       version: ['1.2.0']
     yafyaml:
-      version: ['0.5.1']
-    zlib:
-      version: ['1.2.13']
+      version: ['1.2.0']
     zstd:
       version: ['1.5.2']
       variants: +programs