Merge branch 'develop' of https://github.com/jcsda/spack-stack into f…

…eature/version_updates_20230817
climbfuji · Aug 23, 2023 · aa0115a · aa0115a
2 parents 7c5277c + f00d250
commit aa0115a
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diff --git a/.github/workflows/ubuntu-ci-x86_64.yaml b/.github/workflows/ubuntu-ci-x86_64.yaml
@@ -80,10 +80,10 @@ 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@2021.4.0%intel@2021.4.0" >> ${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 "      prefix: /opt/intel" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
           echo "      modules:" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
-          echo "      - libfabric-aws/1.16.0~amzn3.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
+          echo "      - libfabric-aws/1.16.0~amzn4.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
           echo "      - intelmpi" >> ${SPACK_SYSTEM_CONFIG_PATH}/packages.yaml
 
           # For GNU
@@ -94,19 +94,19 @@ 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@2021.4.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
+          echo "    spec: intel@2022.1.0" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "    paths:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
-          echo "      cc: /opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64/icc" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
-          echo "      cxx: /opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64/icpc" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
-          echo "      f77: /opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64/ifort" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
-          echo "      fc: /opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64/ifort" >> ${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
+          echo "      f77: /opt/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/ifort" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
+          echo "      fc: /opt/intel/oneapi/compiler/2022.1.0/linux/bin/intel64/ifort" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "    flags: {}" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "    operating_system: ubuntu20.04" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "    target: x86_64" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "    modules: []" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "    environment:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "      prepend_path:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
-          echo "        LD_LIBRARY_PATH: '/opt/intel/oneapi/compiler/2021.4.0/linux/compiler/lib/intel64_lin'" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
+          echo "        LD_LIBRARY_PATH: '/opt/intel/oneapi/compiler/2022.1.0/linux/compiler/lib/intel64_lin'" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "      set:" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "        I_MPI_PMI_LIBRARY: '/opt/slurm/lib/libpmi.so'" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
           echo "    extra_rpaths: []" >> ${SPACK_SYSTEM_CONFIG_PATH}/compilers.yaml
@@ -119,12 +119,15 @@ jobs:
           # *DH
 
           # Set compiler and MPI
-          spack config add "packages:all:providers:mpi:[intel-oneapi-mpi@2021.4.0]"
-          spack config add "packages:all:compiler:[intel@2021.4.0]"
+          spack config add "packages:all:providers:mpi:[intel-oneapi-mpi@2021.6.0]"
+          spack config add "packages:all:compiler:[intel@2022.1.0]"
           sed -i "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%intel'\]/g" $ENVDIR/spack.yaml
 
-          spack concretize 2>&1 | tee log.concretize.intel-2021.4.0
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -d log.concretize.intel-2021.4.0 -i fms -i crtm
+          # Switch from default tcl to lmod modules
+          sed -i "s/tcl/lmod/g" $ENVDIR/site/modules.yaml
+
+          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
 
           # Add and update source cache
           spack mirror add local-source file:///home/ubuntu/spack-stack/source-cache/
@@ -145,21 +148,21 @@ jobs:
           # base-env
           echo "base-env ..."
           # DH* 20230721 - todo remove --no-checksum
-          spack install --fail-fast --source --no-check-signature --no-checksum base-env 2>&1 | tee log.install.intel-2021.4.0.base-env
+          spack install --fail-fast --source --no-check-signature --no-checksum base-env 2>&1 | tee log.install.intel-2022.1.0.base-env
           # DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
           spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ || true
 
           # the rest
           echo "${{ inputs.template || 'unified-dev' }} ..."
           # DH* 20230721 - todo remove --no-checksum
-          spack install --fail-fast --source --no-check-signature --no-checksum 2>&1 | tee log.install.intel@2021.4.0.${{ inputs.template || 'unified-dev' }}
+          spack install --fail-fast --source --no-check-signature --no-checksum 2>&1 | tee log.install.intel@2022.1.0.${{ inputs.template || 'unified-dev' }}
           # DH* 20230721 - todo remove || true (this was here all the time, but should not be needed if spack creates buildcaches correctly)
           spack buildcache create -a -u /home/ubuntu/spack-stack/build-cache/ || true
 
           # Next steps: synchronize source and build cache to a central/combined mirror?
           echo "Next steps ..."
           spack clean -a
-          spack module tcl refresh -y
+          spack module lmod refresh -y
           spack stack setup-meta-modules
           spack env deactivate
 
@@ -177,7 +180,10 @@ jobs:
 
       - name: test-env
         run: |
-          source /etc/profile.d/modules.sh
+          source /etc/profile.d/z00_lmod.sh
+          module use /usr/share/modules/modulefiles
+          module use /opt/intel/mpi/2021.6.0/modulefiles
+          module use /home/ubuntu/jedi/modulefiles
 
           # DH* 20230302 - to avoid using padded_length for build caches,
           # always build in the same environment so that the length of the
@@ -189,8 +195,8 @@ jobs:
           ls -l ${ENVDIR}/install/modulefiles/Core
 
           module use ${ENVDIR}/install/modulefiles/Core
-          module load stack-intel/2021.4.0
-          module load stack-intel-oneapi-mpi/2021.4.0
+          module load stack-intel/2022.1.0
+          module load stack-intel-oneapi-mpi/2021.6.0
           module load stack-python/3.10.8
           module available
 

diff --git a/doc/source/NewSiteConfigs.rst b/doc/source/NewSiteConfigs.rst
@@ -143,6 +143,14 @@ These instructions are meant to be a reference that users can follow to set up t
    brew install qt@5
    brew install mysql
 
+.. note::
+  On an Intel based Mac, you will need to also install pkg-config using homebrew.
+  This is done to work around an issue where libraries (eg, openssl) cannot be properly found during code compilation.
+
+.. code-block:: console
+
+  brew install pkg-config  # Intel based Mac only
+
 4. Configure your terminal to use the homebrew installed bash
 
   After installing bash with homebrew, you need to change your terminal application's default command to use :code:`$HOMEBREW_ROOT/bin/bash`.
@@ -220,6 +228,14 @@ Remember to activate the ``lua`` module environment and have MacTeX in your sear
    # The texlive bin directory must have been added to PATH (see above)
    spack external find --scope system texlive
 
+.. note::
+  On an Intel based Mac, you need to add the following spack config command to prevent spack from building pkg-config.
+  This will force spack to use the pkg-config installed by homebrew (see above).
+
+.. code-block:: console
+
+  spack config --scope system add packages:pkg-config:buildable:false  # Intel based Mac only
+
 5. Find compilers, add to site config's ``compilers.yaml``
 
 .. code-block:: console