Merge release/2.1 into develop

.dockerignore

@@ -0,0 +1,19 @@
+# .dockerignore
+
+# Log files. 
+log.*
+*.log
+
+# spack-stack environments and builds.
+envs/
+.env/
+build/
+cache/
+
+# Misc.
+.vscode
+.Trashes
+.github/
+venv/
+.venv/
+

.gitmodules

@@ -4,5 +4,7 @@
   branch = spack-stack-dev
 [submodule "repos/builtin"]
   path = repos/builtin
-  url = https://github.com/jcsda/spack-packages
-  branch = spack-stack-dev
+  #url = https://github.com/jcsda/spack-packages
+  #branch = spack-stack-dev
+  url = https://github.com/climbfuji/spack-packages
+  branch = feature/merge_rel21_into_spack_stack_dev

configs/sites/tier1/container/Dockerfile.gcc

@@ -34,10 +34,6 @@ RUN set -euo pipefail; \
         # External dependencies.
         libcurl4-openssl-dev \
         libmysqlclient-dev \
-        libqt5svg5-dev \
-        qt5-qmake \
-        qt5dxcb-plugin \
-        qtbase5-dev \
         zstd \
         # Shell tools, source retrieval and networking.
         sed \
@@ -72,10 +68,15 @@ FROM ubuntu_base AS builder
 ENV SPACK_STACK_DIR=/opt/spack-stack \
     SPACK_ROOT=/opt/spack-stack/spack
 
-
 # Copy spack-stack from build context. Note the build context must be the
 # root of the spack-stack repository (see the README.md for details).
-COPY . ${SPACK_STACK_DIR}
+# Do not copy the dockerfiles into the container.
+COPY --exclude=configs/sites/tier1/container/Dockerfile.oneapi \
+    --exclude=configs/sites/tier1/container/Dockerfile.gcc \
+    --exclude=configs/sites/tier1/container/packages_oneapi.yaml \
+    --exclude=envs/** \
+    --exclude=cache/** \
+    . ${SPACK_STACK_DIR}
 
 # Create spack-stack environment
 WORKDIR /opt/spack-stack
@@ -89,12 +90,19 @@ RUN mkdir -p /tmp/spack-stack && \
         --compiler $COMPILER && \
     cd ${SPACK_STACK_DIR}/envs/container && \
     spack env activate . && \
-    spack concretize 2>&1 | tee log.concretize && \
-    spack install --fail-fast -j ${BUILD_JOBS} 2>&1 | tee log.install && \
+    spack concretize 2>&1 | tee log.concretize
+
+# Build the spack environment.
+RUN  source setup.sh &&  cd ${SPACK_STACK_DIR}/envs/container && spack env activate . && \
+        spack install --fail-fast -j ${BUILD_JOBS} 2>&1 | tee log.install
+
+# Setup modules and meta-modules.
+RUN source setup.sh &&  cd ${SPACK_STACK_DIR}/envs/container && spack env activate . && \
     spack module tcl refresh -y && \
     spack stack setup-meta-modules && \
     # Save output of spack find.
     spack find 2>&1 | tee /opt/spack-software/spack_find.out && \
+    cp ./log.concretize /opt/spack-software/log.concretize && \
     spack clean --all
 
 ## ---------- Create runtime container ----------
@@ -118,7 +126,20 @@ RUN echo "ulimit -s unlimited" > /etc/spack_container_rc.sh \
     && echo "export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe" >> /etc/spack_container_rc.sh \
     && echo "# TCL module path for the spack-stack environment." >> /etc/spack_container_rc.sh \
     && echo "source /etc/profile.d/modules.sh" >> /etc/spack_container_rc.sh \
-    && echo "module use /opt/spack-software/modules/Core" >> /etc/spack_container_rc.sh \
+    && echo "module use /opt/spack-software/modulefiles" >> /etc/spack_container_rc.sh \
+    && echo "module use /opt/spack-software/modulefiles/Core" >> /etc/spack_container_rc.sh \
+    && echo "# Bash function to load modules necessary to build the JEDI bundle." >> /etc/spack_container_rc.sh \
+    && echo "load_jedi_bundle_env() {" >> /etc/spack_container_rc.sh \
+    && echo "    module purge" >> /etc/spack_container_rc.sh \
+    && echo "    module load stack-gcc" >> /etc/spack_container_rc.sh \
+    && echo "    module load stack-openmpi" >> /etc/spack_container_rc.sh \
+    && echo "    module load base-env" >> /etc/spack_container_rc.sh \
+    && echo "    module load jedi-mpas-env" >> /etc/spack_container_rc.sh \
+    && echo "    module load py-fortranformat" >> /etc/spack_container_rc.sh \
+    && echo "    module load jedi-fv3-env" >> /etc/spack_container_rc.sh \
+    && echo "    module load ewok-env" >> /etc/spack_container_rc.sh \
+    && echo "    module load ip" >> /etc/spack_container_rc.sh \
+    && echo "}" >> /etc/spack_container_rc.sh \ \
     && echo "source /etc/spack_container_rc.sh" >> /etc/bash.bashrc \
     && printf "[credential]\n    helper = cache --timeout=7200\n" >> /root/.gitconfig \
     && mkdir /root/.pmix \

configs/sites/tier1/container/Dockerfile.oneapi

@@ -34,10 +34,6 @@ RUN set -euo pipefail; \
         # External dependencies.
         libcurl4-openssl-dev \
         libmysqlclient-dev \
-        libqt5svg5-dev \
-        qt5-qmake \
-        qt5dxcb-plugin \
-        qtbase5-dev \
         zstd \
         # Shell tools, source retrieval and networking.
         sed \
@@ -91,7 +87,13 @@ ENV SPACK_STACK_DIR=/opt/spack-stack \
 
 # Copy spack-stack from build context. Note the build context must be the
 # root of the spack-stack repository (see the README.md for details).
-COPY . ${SPACK_STACK_DIR}
+# Do not copy the dockerfiles into the container.
+COPY --exclude=configs/sites/tier1/container/Dockerfile.oneapi \
+    --exclude=configs/sites/tier1/container/Dockerfile.gcc \
+    --exclude=configs/sites/tier1/container/packages_gcc.yaml \
+    --exclude=envs/** \
+    --exclude=cache/** \
+    . ${SPACK_STACK_DIR}
 
 # Create spack-stack environment
 WORKDIR /opt/spack-stack
@@ -105,12 +107,19 @@ RUN mkdir -p /tmp/spack-stack && \
         --compiler oneapi && \
     cd ${SPACK_STACK_DIR}/envs/container && \
     spack env activate . && \
-    spack concretize 2>&1 | tee log.concretize && \
-    spack install --fail-fast -j ${BUILD_JOBS} 2>&1 | tee log.install && \
+    spack concretize 2>&1 | tee log.concretize
+
+# Build the spack environment.
+RUN  source setup.sh &&  cd ${SPACK_STACK_DIR}/envs/container && spack env activate . && \
+        spack install --fail-fast -j ${BUILD_JOBS} 2>&1 | tee log.install
+
+# Setup modules and meta-modules.
+RUN source setup.sh &&  cd ${SPACK_STACK_DIR}/envs/container && spack env activate . && \
     spack module tcl refresh -y && \
     spack stack setup-meta-modules && \
     # Save output of spack find.
     spack find 2>&1 | tee /opt/spack-software/spack_find.out && \
+    cp ./log.concretize /opt/spack-software/log.concretize && \
     spack clean --all
 
 ## ---------- Create runtime container ----------
@@ -129,10 +138,22 @@ RUN echo "ulimit -s unlimited" > /etc/spack_container_rc.sh \
     && echo "export CXX=icpx" >> /etc/spack_container_rc.sh \
     && echo "export FC=ifx" >> /etc/spack_container_rc.sh \
     && echo "# TCL module path for the spack-stack environment." >> /etc/spack_container_rc.sh \
-    && echo "export MODULEPATH=/opt/spack-software/modules/Core" >> /etc/spack_container_rc.sh \
     && echo "source /etc/profile.d/modules.sh" >> /etc/spack_container_rc.sh \
     && echo "module use /opt/intel/oneapi/modulefiles" >> /etc/spack_container_rc.sh \
-    && echo "module use /opt/spack-software/modules/Core" >> /etc/spack_container_rc.sh \
+    && echo "module use /opt/spack-software/modulefiles" >> /etc/spack_container_rc.sh \
+    && echo "module use /opt/spack-software/modulefiles/Core" >> /etc/spack_container_rc.sh \
+    && echo "# Bash function to load modules necessary to build the JEDI bundle." >> /etc/spack_container_rc.sh \
+    && echo "load_jedi_bundle_env() {" >> /etc/spack_container_rc.sh \
+    && echo "    module purge" >> /etc/spack_container_rc.sh \
+    && echo "    module load stack-intel-oneapi-compilers" >> /etc/spack_container_rc.sh \
+    && echo "    module load stack-intel-oneapi-mpi" >> /etc/spack_container_rc.sh \
+    && echo "    module load base-env" >> /etc/spack_container_rc.sh \
+    && echo "    module load jedi-mpas-env" >> /etc/spack_container_rc.sh \
+    && echo "    module load py-fortranformat" >> /etc/spack_container_rc.sh \
+    && echo "    module load jedi-fv3-env" >> /etc/spack_container_rc.sh \
+    && echo "    module load ewok-env" >> /etc/spack_container_rc.sh \
+    && echo "    module load ip" >> /etc/spack_container_rc.sh \
+    && echo "}" >> /etc/spack_container_rc.sh \ \
     && echo "source /etc/spack_container_rc.sh" >> /etc/bash.bashrc \
     && printf "[credential]\n    helper = cache --timeout=7200\n" >> /root/.gitconfig \
     && mkdir /root/.pmix

configs/sites/tier1/container/packages.yaml

@@ -1,30 +1,54 @@
 packages:
   all:
-    target: [core2]
+    target: [x86_64_v3]
+  awscli-v2:
+    require:
+    - "@2.22.4"
+  cairo:
+    variants: +pic
+  ewok-env:
+    require:
+    - +ecflow
+  fontconfig:
+    variants: +pic
   met:
     variants: +python +grib2 +graphics +lidar2nc +modis
+  parallelio:
+    require:
+    - +pnetcdf
+  pixman:
+    variants: +pic
+  py-awscrt:
+    require:
+    - "@0.19.19"
+  py-botocore:
+    require:
+    - "@1.34.162"
+  py-boto3:
+    require:
+    - "@1.34.162"
+  py-netcdf4:
+    require:
+    - "@1.7.2"
+
   # System packages installed during the container build.
-  grep:
-    externals:
-    - spec: grep@3.11
-      prefix: /usr
-  findutils:
+  autoconf:
     externals:
-    - spec: findutils@4.9.0
+    - spec: autoconf@2.71
       prefix: /usr
   coreutils:
     externals:
     - spec: coreutils@9.4
       prefix: /usr
-  autoconf:
-    externals:
-    - spec: autoconf@2.71
-      prefix: /usr
   diffutils:
     buildable: false
     externals:
     - spec: diffutils@3.10
       prefix: /usr
+  findutils:
+    externals:
+    - spec: findutils@4.9.0
+      prefix: /usr
   git:
     buildable: false
     externals:
@@ -35,24 +59,17 @@ packages:
     externals:
     - spec: git-lfs@3.4.1
       prefix: /usr
-  llvm:
-    buildable: false
-    externals:
-    - spec: llvm@14.0.6
-      prefix: /usr
-  qt:
-    buildable: false
+  grep:
     externals:
-    - spec: qt@5.15.3
+    - spec: grep@3.11
       prefix: /usr
-    version: [5.15.3]
-  wget:
+  llvm:
     buildable: false
     externals:
-    - spec: wget@1.21.4
+    - spec: llvm@14.0.6
       prefix: /usr
   perl:
     buildable: false
     externals:
     - spec: perl@5.38.2
-      prefix: /usr
+      prefix: /usr

configs/sites/tier1/container/packages_oneapi.yaml

@@ -15,8 +15,8 @@ packages:
       modules:
       - umf/1.0.2
       - tbb/2022.3
-      - compiler-rt/2025.3.0
-      - compiler/2025.3.0
+      - compiler-rt/2025.3.2
+      - compiler/2025.3.2
       extra_attributes:
         compilers:
           c: /opt/intel/oneapi/compiler/2025.3/bin/icx

configs/sites/tier1/derecho/packages.yaml

@@ -1,7 +1,8 @@
 packages:
 # Modification of common packages
-  zlib-api:
-    buildable: False
+  all:
+    providers:
+      zlib-api:: [zlib]
   # Tell esmf that this is not a 'normal' Cray ...
   esmf:
     require:
@@ -113,5 +114,5 @@ packages:
   zlib:
     buildable: False
     externals:
-    - spec: zlib@1.2.11
+    - spec: zlib@1.2.13
       prefix: /usr

configs/sites/tier1/derecho/packages_gcc-13.3.1.yaml

@@ -32,6 +32,9 @@ packages:
     - spec: cray-mpich@8.1.32 +wrappers
       prefix: /opt/cray/pe/mpich/8.1.32/ofi/gnu/12.3
       modules:
+      - crayenv/25.03
+      - PrgEnv-gnu/8.6.0
+      - gcc-native/13.2
       - craype-network-ofi
       - cray-mpich/8.1.32
       - libfabric/1.22.0

configs/sites/tier1/derecho/packages_oneapi-2025.3.1.yaml

@@ -15,9 +15,9 @@ packages:
     - spec: intel-oneapi-compilers@2025.3.1
       prefix: /glade/work/epicufsrt/contrib/spack-stack/derecho/installs/oneapi-2025.3.1
       modules:
-        - crayenv/25.03
-        - PrgEnv-intel/8.6.0
-        - intel/2025.3.1
+      - crayenv/25.03
+      - PrgEnv-intel/8.6.0
+      - intel/2025.3.1
       extra_attributes:
         compilers:
           c: /glade/work/epicufsrt/contrib/spack-stack/derecho/installs/oneapi-2025.3.1/compiler/2025.3/bin/icx
@@ -54,6 +54,9 @@ packages:
     - spec: cray-mpich@8.1.32 +wrappers
       prefix: /opt/cray/pe/mpich/8.1.32/ofi/intel/2022.1
       modules:
+      - crayenv/25.03
+      - PrgEnv-intel/8.6.0
+      - intel/2025.3.1
       - craype-network-ofi
       - cray-mpich/8.1.32
       - libfabric/1.22.0

configs/sites/tier1/discover-scu17/mirrors.yaml

@@ -1,18 +1,2 @@
 mirrors:
-  local-source:
-    fetch:
-      url: file:///discover/swdev/jcsda/spack-stack/source-cache
-      access_pair:
-      - null
-      - null
-      access_token: null
-      profile: null
-      endpoint_url: null
-    push:
-      url: file:///discover/swdev/jcsda/spack-stack/source-cache
-      access_pair:
-      - null
-      - null
-      access_token: null
-      profile: null
-      endpoint_url: null
+  local-source: file:///discover/swdev/jcsda/spack-stack/source-cache

configs/sites/tier1/discover-scu17/packages.yaml

@@ -1,5 +1,8 @@
 packages:
 ### Modification of common packages
+  ewok-env:
+    require:
+    - '+ecflow'
   # Problems building shared hdf-eos2 with Intel, not needed
   hdf-eos2:
     variants: ~shared

configs/sites/tier1/discover-scu17/packages_gcc.yaml

@@ -8,7 +8,7 @@ packages:
   openmpi:
     buildable: False
     externals:
-    - spec: openmpi@4.1.6 ~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath
+    - spec: openmpi@4.1.6 ~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath+two_level_namespace
         fabrics=ucx schedulers=slurm
       prefix: /discover/swdev/gmao_SIteam/MPI/openmpi/4.1.6-SLES15/gcc-13.4.0
       modules:

configs/sites/tier1/discover-scu17/packages_oneapi.yaml

@@ -1,5 +1,7 @@
 packages:
   all:
+    prefer:
+    - '%oneapi'
     providers:
       mpi:: [intel-oneapi-mpi@2021.13]
   mpi:
@@ -28,15 +30,16 @@ packages:
         extra_rpaths:
         - /usr/local/other/gcc/12.3.0/lib64
   intel-oneapi-mpi:
+    buildable: False
     externals:
-    - spec: intel-oneapi-mpi@2021.13%oneapi@2024.2.0
+    - spec: intel-oneapi-mpi@2021.13
       prefix: /usr/local/intel/oneapi/2024
       modules:
       - mpi/impi/2021.13
   intel-oneapi-mkl:
     buildable: false
     externals:
-    - spec: intel-oneapi-mkl@2024.2.0%oneapi@2024.2.0
+    - spec: intel-oneapi-mkl@2024.2.0
       prefix: /usr/local/intel/oneapi/2024
   gcc:
     externals: