Merge branch 'JCSDA:develop' into develop

Author: rickgrubin-tomorrow

.github/actions/Nightly_07_Cleanup/action.yaml

@@ -8,4 +8,4 @@ runs:
     run: |
       RUNID=$(<RUNID_SAVE.log)
       cd util/weekly_build
-      ./05_BuildCache.sh ${RUNID} ${BASEDIR} ${PLATFORM}
+      ./07_Cleanup.sh ${RUNID} ${BASEDIR} ${PLATFORM}

.github/actions/Nightly_08_Scrubber/action.yaml

@@ -0,0 +1,22 @@
+name: Nightly 08 Scrubber
+
+runs:
+  using: "composite"
+  steps:
+  - name: Nightly 08 Scrubber
+    shell: bash
+    run: |
+      cd ${BASEDIR}
+      pwd
+      # Avoid BASEDIR being deleted
+      touch .
+      # Search for files older than 7 days in in directories 202YMMDD
+      for dir in 202?????; do
+        echo "Scrubbing files older than 7 days in directory ${dir} ..."
+        find ./${dir} -type f -mtime +7 -print0 | xargs -0 rm -f || true
+      done
+      # Search for empty directories older than 7 days in in directories 202YMMDD
+      for dir in 202?????; do
+        echo "Scrubbing empty directories older than 7 days in directory ${dir} ..."
+        find ./${dir} -type d -mtime +7 -empty -print0 | xargs -0 rmdir || true
+      done

configs/common/modules_lmod.yaml

@@ -234,7 +234,7 @@ modules:
         environment:
           set:
             'WGRIB2_INC': '{prefix}/include'
-            'WGRIB2_LIB': '{prefix}/lib/libwgrib2.a'
+            'WGRIB2_LIB': '{prefix}/lib64/libwgrib2.so'
             'WGRIB2': '{prefix}/bin/wgrib2'
       wrf-io:
         environment:

configs/common/modules_tcl.yaml

@@ -236,7 +236,7 @@ modules:
         environment:
           set:
             'WGRIB2_INC': '{prefix}/include'
-            'WGRIB2_LIB': '{prefix}/lib/libwgrib2.a'
+            'WGRIB2_LIB': '{prefix}/lib64/libwgrib2.so'
             'WGRIB2': '{prefix}/bin/wgrib2'
       wrf-io:
         environment:

configs/common/packages.yaml

@@ -71,14 +71,13 @@ packages:
     - any_of: ['fflags="-fp-model precise" cxxflags="-fp-model precise"']
       when: "%intel"
       message: "Extra ESMF compile options for Intel"
+    - '+python'
     #- any_of: ['']
     #  when: "%gcc"
     #  message: "Extra ESMF compile options for GCC"
     #- any_of: ['']
     #  when: "%apple-clang"
     #  message: "Extra ESMF compile options for GCC"
-    prefer:
-    - '+python'
   # To avoid duplicate packages (concretizer bug?)
   expat:
     require:
@@ -104,7 +103,7 @@ packages:
     require:
     - '@3.5.1'
   g2c:
-    require: '@1.6.4'
+    require: '@2.1.0'
   g2tmpl:
     require:
     - '@1.13.0'
@@ -139,7 +138,7 @@ packages:
   hdf-eos2:
     require: '@2.20v1.00'
   ip:
-    require: '@5.1.0 precision=4,d,8'
+    require: '@5.3.0 precision=4,d,8'
   ip2:
     require: '@1.1.2'
   jasper:
@@ -300,7 +299,7 @@ packages:
   # See macOS site config for wgrib2 version/variant overrides
   wgrib2:
     require:
-    - '@3.5.0'
+    - '@3.6.0'
   wrf-io:
     require: '@1.2.0'
   zstd:

configs/containers/docker-ubuntu-gcc11-openmpi.yaml

@@ -0,0 +1,219 @@
+spack:
+  concretizer:
+    unify: true
+
+  config:
+    checksum: false
+    build_jobs: 2
+    connect_timeout: 60
+
+  compilers:
+  - compiler:
+      spec: gcc@11.4.0
+      paths:
+        cc: /usr/bin/gcc
+        cxx: /usr/bin/g++
+        f77: /usr/bin/gfortran
+        fc: /usr/bin/gfortran
+      flags: {}
+      operating_system: ubuntu24.04
+      modules: []
+      environment: {}
+      extra_rpaths: []
+
+  # Basic package config from configs/common/packages.yaml
+  # Additional package config for container
+  packages:
+    all:
+      require: '%gcc'
+      target: [x86_64]
+      providers:
+        mpi: [openmpi@5.0.5]
+      compiler: [gcc@11.4.0]
+    gcc:
+      buildable: false
+      externals:
+      - spec: gcc@11.4.0
+        prefix: /usr
+    gcc-runtime:
+      buildable: false
+      externals:
+      - spec: gcc-runtime@11.4.0
+        prefix: /usr
+    diffutils:
+      buildable: false
+      externals:
+      - spec: diffutils@3.8
+        prefix: /usr
+    git:
+      buildable: false
+      externals:
+      - spec: git@2.34.1~tcltk
+        prefix: /usr
+    git-lfs:
+      buildable: false
+      externals:
+      - spec: git-lfs@3.0.2
+        prefix: /usr
+    llvm:
+      buildable: false
+      externals:
+      - spec: llvm@14.0.6
+        prefix: /usr
+    mysql:
+      buildable: false
+      externals:
+      - spec: mysql@8.0.40
+        prefix: /usr
+    qt:
+      buildable: false
+      externals:
+      - spec: qt@5.15.3
+        prefix: /usr
+      version: [5.15.3]
+    wget:
+      buildable: false
+      externals:
+      - spec: wget@1.21.2
+        prefix: /usr
+
+  specs: []
+
+  container:
+
+    # Select the format of the recipe e.g. docker,
+    # singularity or anything else that is currently supported
+    format: docker
+    # How to use:
+    #$ spack containerize > Dockerfile
+    #$ sudo docker build -t myimage .
+    #$ sudo docker run -it myimage
+
+    #format: singularity
+    # How to use:
+    #$ spack containerize > singularity.def
+    #$ sudo singularity build singularity.sif singularity.def
+
+    # Sets the base images for the stages where Spack builds the
+    # software or where the software gets installed after being built..
+    images:
+      os: ubuntu:24.04
+      spack:
+        url: https://github.com/jcsda/spack
+        ref: spack-stack-dev
+        resolve_sha: true
+
+    # Whether or not to strip binaries
+    strip: false
+
+    ## Additional system packages that are needed at runtime
+    os_packages:
+      build:
+      - bc
+      - cpp-11
+      - g++-11
+      - gcc-11
+      - gfortran-11
+      - git
+      - git-lfs
+      - llvm-14
+      - make
+      - mysql-server
+      - qtbase5-dev
+      - qt5-qmake
+      - libqt5svg5-dev
+      - qt5dxcb-plugin
+      - wget
+
+      final:
+      - bc
+      - cpp-11
+      - g++-11
+      - gcc-11
+      - gfortran-11
+      - git
+      - git-lfs
+      - llvm-14
+      - make
+      - mysql-server
+      - qtbase5-dev
+      - qt5-qmake
+      - libqt5svg5-dev
+      - qt5dxcb-plugin
+      - wget
+      - ca-certificates
+      - curl
+      - file
+      - gnupg2
+      - iproute2
+      - locales
+      - unzip
+      - vim
+      - nano
+      - less
+
+    # Extra instructions
+    extra_instructions:
+      pre_build: |
+        # Copy the spack-stack extension repo into the spack code
+        COPY spack-ext-SPACK_STACK_HASH/repos/spack-stack $SPACK_ROOT/var/spack/repos/spack-stack
+        # Register spack-stack extension repo
+        RUN spack repo add $SPACK_ROOT/var/spack/repos/spack-stack --scope defaults && \
+        update-alternatives --remove-all cpp && \
+        update-alternatives --install /usr/bin/cpp cpp /usr/bin/cpp-11 100 && \
+        update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 100 && \
+        update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 100 && \
+        update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-11 100 && \
+        # Needed by py-llvmlite
+        update-alternatives --install /usr/bin/llvm-config llvm-config /usr/bin/llvm-config-14 100
+      pre_final: |
+        # Set environment variables for installing tzdata
+        ENV DEBIAN_FRONTEND=noninteractive
+        ENV TZ=Etc/UTC
+        ENV CC=gcc
+        ENV CXX=g++
+        ENV FC=gfortran
+      build: |
+        # Put output of spack find into a file
+        RUN cd /opt/spack-environment && \
+        spack env activate -d . && \
+        spack find 2>&1 | tee /root/spack_find.out
+      final: |
+        # Copy spack find output from builder
+        COPY --from=builder /root/spack_find.out /root/spack_find.out
+        # Make a non-root user:nonroot / group:nonroot for running MPI
+        RUN useradd -U -k /etc/skel -s /bin/bash -d /home/nonroot -m nonroot --uid 43891 && \
+        echo "ulimit -s unlimited" >> /home/nonroot/.bashrc && \
+        echo "ulimit -v unlimited" >> /home/nonroot/.bashrc && \
+        echo "export CC=gcc" >> /home/nonroot/.bashrc && \
+        echo "export CXX=g++" >> /home/nonroot/.bashrc && \
+        echo "export FC=gfortran" >> /home/nonroot/.bashrc && \
+        update-alternatives --install /usr/bin/cpp cpp /usr/bin/cpp-11 100 && \
+        update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 100 && \
+        update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 100 && \
+        update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-11 100 && \
+        # Needed by py-llvmlite
+        update-alternatives --install /usr/bin/llvm-config llvm-config /usr/bin/llvm-config-14 100 && \
+        printf "[credential]\n    helper = cache --timeout=7200\n" >> /home/nonroot/.gitconfig && \
+        mkdir /home/nonroot/.pmix && \
+        echo "rmaps_default_mapping_policy=:oversubscribe" >> /home/nonroot/.pmix/mca-params.conf && \
+        chown -R nonroot:nonroot /home/nonroot/.gitconfig /home/nonroot/.pmix
+        # Replicate settings for root user
+        RUN echo "ulimit -s unlimited" >> /root/.bashrc && \
+        echo "ulimit -v unlimited" >> /root/.bashrc && \
+        echo "export CC=gcc" >> /root/.bashrc && \
+        echo "export CXX=g++" >> /root/.bashrc && \
+        echo "export FC=gfortran" >> /root/.bashrc && \
+        printf "[credential]\n    helper = cache --timeout=7200\n" >> /root/.gitconfig && \
+        mkdir /root/.pmix && \
+        echo "rmaps_default_mapping_policy=:oversubscribe" >> /root/.pmix/mca-params.conf
+        # Also set necessary environment variables for openmpi and jedi-cmake.
+        RUN echo "export OMPI_ALLOW_RUN_AS_ROOT=1" >> /root/.bashrc && \
+        echo "export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> /root/.bashrc && \
+        echo "export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe" >> /root/.bashrc && \
+        echo "export jedi_cmake_ROOT=$(ls -d /opt/software/linux-ubuntu*/gcc-*/jedi-cmake-*)" >> /root/.bashrc
+
+    # Labels for the image
+    labels:
+      app: ""
+      mpi: "openmpi"

configs/containers/docker-ubuntu-oneapi-impi.yaml

@@ -97,6 +97,11 @@ spack:
     icu4c:
       require:
       - '%gcc'
+    intel-oneapi-runtime:
+      buildable: false
+      externals:
+      - spec: intel-oneapi-runtime@2024.2.1%oneapi@2024.2.1
+        prefix: /opt/intel/oneapi
     intel-oneapi-mkl:
       buildable: false
       externals:

configs/containers/specs/jedi-ci.yaml

@@ -24,7 +24,7 @@
     gsibec@1.2.1,
     hdf@4.2.15,
     hdf5@1.14.3,
-    ip@5.1.0,
+    ip@5.3.0,
     jasper@2.0.32,
     jedi-cmake@1.4.0,
     libpng@1.6.37,

configs/sites/tier1/acorn/packages.yaml

@@ -41,7 +41,3 @@
       externals:
       - spec: grep@3.1
         prefix: /usr
-    netcdf-c:
-      require:: '@4.9.2 +dap +mpi ~parallel-netcdf ~szip ~parallel_tests build_system=autotools'
-    netcdf-fortran:
-      require:: '@4.6.1 ~parallel_tests'

configs/sites/tier1/acorn/packages_intel.yaml

@@ -16,6 +16,7 @@
         - libfabric
         - craype-network-ofi
         - cray-mpich/8.1.9
+        - cray-pals
     intel-oneapi-mkl:
       # Remove buildable: False and configure+uncomment externals section below to use intel-oneapi-mkl
       buildable: False
@@ -32,8 +33,7 @@
     py-numpy:
       require::
       - '^[virtuals=lapack,blas] openblas'
-      - '@1.26'
-      - '%gcc'
+      - '@1.26 %gcc'
     # *DH
     eckit:
       require: