Merge release/2.2 into develop

.gitmodules

@@ -5,4 +5,5 @@
 [submodule "repos/builtin"]
   path = repos/builtin
   url = https://github.com/jcsda/spack-packages
-  branch = spack-stack-dev
+  #branch = spack-stack-dev
+  branch = feature/merge_rel22_to_spackstackdev

configs/common/modules_lmod.yaml

@@ -143,6 +143,10 @@ modules:
             'MADIS_ROOT': '{prefix}'
       mapl:
         suffixes:
+          ^esmf@=8.9.1~debug ~openmp: 'esmf-8.9.1-noopenmp'
+          ^esmf@=8.9.1+debug ~openmp: 'esmf-8.9.1-debug-noopenmp'
+          ^esmf@=8.9.1~debug +openmp: 'esmf-8.9.1'
+          ^esmf@=8.9.1+debug +openmp: 'esmf-8.9.1-debug'
           ^esmf@=9.0.0~debug ~openmp: 'esmf-9.0.0-noopenmp'
           ^esmf@=9.0.0+debug ~openmp: 'esmf-9.0.0-debug-noopenmp'
           ^esmf@=9.0.0~debug +openmp: 'esmf-9.0.0'

configs/common/modules_tcl.yaml

@@ -162,6 +162,10 @@ modules:
             'MADIS_ROOT': '{prefix}'
       mapl:
         suffixes:
+          ^esmf@=8.9.1~debug ~openmp: 'esmf-8.9.1-noopenmp'
+          ^esmf@=8.9.1+debug ~openmp: 'esmf-8.9.1-debug-noopenmp'
+          ^esmf@=8.9.1~debug +openmp: 'esmf-8.9.1'
+          ^esmf@=8.9.1+debug +openmp: 'esmf-8.9.1-debug'
           ^esmf@=9.0.0~debug ~openmp: 'esmf-9.0.0-noopenmp'
           ^esmf@=9.0.0+debug ~openmp: 'esmf-9.0.0-debug-noopenmp'
           ^esmf@=9.0.0~debug +openmp: 'esmf-9.0.0'

configs/common/packages.yaml

@@ -151,6 +151,7 @@ packages:
       - +shared
       - +external-parallelio
       - any_of:
+        - '@=8.9.1'
         - '@=9.0.0b17'
         - '@=9.0.0b18'
       - any_of:

configs/sites/tier1/aws-ubuntu/config.yaml

@@ -0,0 +1,7 @@
+config:
+  build_jobs: 8
+
+  # Build stage and caches use the common defaults under
+  # ${SPACK_STACK_DIR}/cache on the root disk. Don't point them at /tmp: on
+  # Ubuntu 26.04 /tmp is a RAM-backed tmpfs (half of RAM, with per-user quotas),
+  # and a unified-env build fills it ("Disk quota exceeded").

configs/sites/tier1/aws-ubuntu/packages.yaml

@@ -0,0 +1,121 @@
+packages:
+  # Package constraints.
+  ewok-env:
+    require:
+    - +ecflow
+  # Soft preference, as on other tier1 sites. With gcc 14, +lidar2nc and +modis
+  # are dropped: they need hdf-eos2, and common pins hdf-eos2@2.20v1.00, which
+  # conflicts with %gcc@14: (3.0+ is required).
+  met:
+    variants: +python +grib2 +graphics +lidar2nc +modis
+  py-netcdf4:
+    require:
+    - "@1.7.2"
+  jedi-base-env:
+    require: [+fftw, +hdf4]
+  # jedi-ufs-env needs +bufrquery; unconstrained, the root splits in two.
+  jedi-python-env:
+    require: [+bufrquery]
+  # Unconstrained, jedi-tools-env falls back to py-myst-parser@1/py-sphinx@6,
+  # which cap py-attrs@:21 and py-docutils@:0.19 and split py-attrs, py-eccodes,
+  # py-rasterio, jedi-python-env and awscli-v2. common/packages_oneapi.yaml
+  # already requires py-sphinx@9: for the same reason.
+  py-myst-parser:
+    require: ['@5:']
+  py-sphinx:
+    require: ['@9:']
+  fontconfig:
+    variants: +pic
+  pixman:
+    variants: +pic
+  cairo:
+    variants: +pic
+
+  # System packages (Ubuntu 26.04). Derived with `spack external find`
+  # excluding cmake, curl, openssl, openssh, python and zlib (the multiarch
+  # libdir breaks pmix's zlib detection). coreutils (uutils) and binutils
+  # (2.46, no gold) aren't detected and are left for spack to build if needed.
+  autoconf:
+    externals:
+    - spec: autoconf@2.72
+      prefix: /usr
+  automake:
+    externals:
+    - spec: automake@1.18.1
+      prefix: /usr
+  diffutils:
+    externals:
+    - spec: diffutils@3.12
+      prefix: /usr
+  findutils:
+    externals:
+    - spec: findutils@4.10.0
+      prefix: /usr
+  flex:
+    externals:
+    - spec: flex@2.6.4+lex
+      prefix: /usr
+  gawk:
+    externals:
+    - spec: gawk@5.3.2
+      prefix: /usr
+  gettext:
+    externals:
+    - spec: gettext@0.23.2
+      prefix: /usr
+  git:
+    externals:
+    - spec: git@2.53.0~tcltk
+      prefix: /usr
+  git-lfs:
+    externals:
+    - spec: git-lfs@3.7.1
+      prefix: /usr
+  gmake:
+    externals:
+    - spec: gmake@4.4.1
+      prefix: /usr
+  grep:
+    externals:
+    - spec: grep@3.12
+      prefix: /usr
+  groff:
+    externals:
+    - spec: groff@1.23.0
+      prefix: /usr
+  libtool:
+    externals:
+    - spec: libtool@2.5.4
+      prefix: /usr
+  m4:
+    externals:
+    - spec: m4@1.4.21
+      prefix: /usr
+  perl:
+    externals:
+    - spec: perl@5.40.1~cpanm+opcode+open+shared+threads
+      prefix: /usr
+  pkgconf:
+    externals:
+    - spec: pkgconf@2.5.1
+      prefix: /usr
+  sed:
+    externals:
+    - spec: sed@4.9
+      prefix: /usr
+  tar:
+    buildable: false
+    externals:
+    - spec: tar@1.35
+      prefix: /usr
+  wget:
+    buildable: false
+    externals:
+    - spec: wget@1.25.0
+      prefix: /usr
+  # Not auto-detected (qmake is a qtchooser shim); apt qtbase5-dev. common requires qt@5.
+  qt:
+    buildable: false
+    externals:
+    - spec: qt@5.15.18
+      prefix: /usr

configs/sites/tier1/aws-ubuntu/packages_gcc.yaml

@@ -0,0 +1,13 @@
+packages:
+  gcc:
+    buildable: false
+    externals:
+    - spec: gcc@14.3.0 languages:='c,c++,fortran'
+      prefix: /usr
+      extra_attributes:
+        compilers:
+          c: /usr/bin/gcc-14
+          cxx: /usr/bin/g++-14
+          fortran: /usr/bin/gfortran-14
+  mpi:
+    require: ['openmpi@5.0.10']

configs/sites/tier2/aws-ubuntu2404/packages_oneapi.yaml → configs/sites/tier1/aws-ubuntu/packages_oneapi.yaml

@@ -1,9 +1,10 @@
 packages:
 
   # Compilers.
+  # Language preferences for oneAPI come from common/packages_oneapi.yaml. Don't
+  # add "all: prefer: ['%oneapi']": it acts as a dependency constraint and makes
+  # spack rebuild system externals.
   all:
-    prefer:
-    - '%oneapi'
     conflict:
     - '%c=oneapi %fortran=gcc'
     - '%c,cxx=oneapi %fortran=gcc'
@@ -13,8 +14,6 @@ packages:
     - '%fortran=oneapi %c,cxx=gcc'
     - '%fortran=gcc %c,cxx=oneapi'
     - '%fortran=gcc %c=oneapi'
-    providers:
-      mpi:: [intel-oneapi-mpi@2021.18]
 
   intel-oneapi-compilers:
     buildable: false
@@ -33,6 +32,13 @@ packages:
           fortran: /opt/intel/oneapi/compiler/2026.1/bin/ifx
           c: /opt/intel/oneapi/compiler/2026.1/bin/icx
           cxx: /opt/intel/oneapi/compiler/2026.1/bin/icpx
+        # Ubuntu 26.04's default gcc is 15. Left alone, icx/icpx pick the newest
+        # installed GCC for libstdc++ headers and libs, and ifx links its
+        # runtime. Pin them to gcc 14 so they match the gcc env.
+        flags:
+          cflags: --gcc-install-dir=/usr/lib/gcc/x86_64-linux-gnu/14
+          cxxflags: --gcc-install-dir=/usr/lib/gcc/x86_64-linux-gnu/14
+          fflags: -gcc-name=/usr/bin/gcc-14 -gxx-name=/usr/bin/g++-14
   openmpi:
     buildable: false
   mpich:
@@ -43,13 +49,13 @@ packages:
     - intel-oneapi-mpi@2021.18
   gcc:
     externals:
-    - spec: gcc@13.3.0 languages:='c,c++,fortran'
+    - spec: gcc@14.3.0 languages:='c,c++,fortran'
       prefix: /usr
       extra_attributes:
         compilers:
-          c: /usr/bin/gcc
-          cxx: /usr/bin/g++
-          fortran: /usr/bin/gfortran
+          c: /usr/bin/gcc-14
+          cxx: /usr/bin/g++-14
+          fortran: /usr/bin/gfortran-14
     buildable: false
   intel-oneapi-mkl:
     buildable: false
@@ -83,6 +89,15 @@ packages:
       - tbb/2023.1
 
   # Package constraints.
+  # Avoid duplicates. Unpinned, gmao-swell-env and py-pyresample pull two
+  # py-dask versions, which splits py-setuptools-scm (8 vs 9) and cascades into
+  # py-netcdf4, py-xarray, py-zarr and jedi-python-env. The gcc env settles on
+  # 2024.12.1 without a pin.
+  py-dask:
+    require: ['@2024.12.1']
+  # Unconstrained, one met concretizes ~graphics. Keep common's +shared-intel.
+  met:
+    require: ['+graphics +shared-intel']
   jedi-base-env:
     require: [+fftw, +hdf4]
   jedi-python-env:

configs/sites/tier1/container/Dockerfile.gcc

@@ -2,9 +2,9 @@
 # See the README.md for building instructions.
 
 ## ---------- build base container used by builder and runtime ----------
-FROM ubuntu:24.04 AS ubuntu_base
+FROM ubuntu:26.04 AS ubuntu_base
 
-ARG BUILD_JOBS=4
+ARG BUILD_JOBS=8
 ARG SPACK_STACK_TEMPLATE=unified-dev
 
 SHELL ["/bin/bash", "-c"]
@@ -22,14 +22,14 @@ RUN set -euo pipefail; \
     apt-get -yqq update && \
     apt-get -yqq upgrade && \
     apt-get -yqq install --no-install-recommends \
-        # Core build tools.
+        # Core build tools. build-essential pulls in the default gcc-15; we add
+        # gcc-14 alongside it, since spack-stack supports gcc up to 14.x.
         build-essential \
-        gcc-13 \
-        gcc++-13 \
-        gfortran-13 \
-        cpp-13 \
+        gcc-14 \
+        g++-14 \
+        gfortran-14 \
+        cpp-14 \
         make \
-        llvm-14 \
         autoconf \
         # External dependencies.
         libcurl4-openssl-dev \
@@ -55,10 +55,11 @@ RUN set -euo pipefail; \
         locales && \
     locale-gen en_US.UTF-8 && \
     # Update alternatives for compilers and tools
-    update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-13 100 && \
-    update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-13 100 && \
-    update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-13 100 && \
-    update-alternatives --install /usr/bin/llvm-config llvm-config /usr/bin/llvm-config-14 100 && \
+    # Make gcc-14 the default gcc/g++/gfortran for container users. Spack uses
+    # the -14 binaries by full path (see packages_gcc.yaml).
+    update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-14 100 && \
+    update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-14 100 && \
+    update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-14 100 && \
     rm -rf /var/lib/apt/lists/*
 
 
@@ -80,7 +81,8 @@ COPY --exclude=configs/sites/tier1/container/Dockerfile.oneapi \
 
 # Create spack-stack environment
 WORKDIR /opt/spack-stack
-RUN mkdir -p /tmp/spack-stack && \
+RUN set -o pipefail && \
+    mkdir -p /tmp/spack-stack && \
     source setup.sh && \
     spack stack create env \
         --site container \
@@ -93,7 +95,7 @@ RUN mkdir -p /tmp/spack-stack && \
     spack concretize 2>&1 | tee log.concretize
 
 # Build the spack environment.
-RUN  source setup.sh &&  cd ${SPACK_STACK_DIR}/envs/container && spack env activate . && \
+RUN  set -o pipefail && 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.
@@ -126,16 +128,19 @@ 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/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 stack-gcc/14.3.0" >> /etc/spack_container_rc.sh \
+    && echo "    module load stack-openmpi/5.0.10" >> /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 jedi-python-env" >> /etc/spack_container_rc.sh \
     && echo "    module load py-fortranformat" >> /etc/spack_container_rc.sh \
+    && echo "    module load py-matplotlib" >> /etc/spack_container_rc.sh \
+    && echo "    module load py-cartopy" >> /etc/spack_container_rc.sh \
+    && echo "    module load py-pyproj" >> /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 \
@@ -153,6 +158,14 @@ RUN useradd -U -k /etc/skel -s /bin/bash -d /home/nonroot -m nonroot --uid 43891
  && mkdir /home/nonroot/.pmix \
  && chown -R nonroot:nonroot /home/nonroot/.gitconfig /home/nonroot/.pmix
 
+# Fail the build if the stack meta-modules don't resolve to real compiler and
+# MPI modules (and nothing else) in the final image.
+RUN source /etc/spack_container_rc.sh && \
+    module load stack-gcc/14.3.0 stack-openmpi/5.0.10 && \
+    module is-loaded gcc/14.3.0 && module is-loaded openmpi/5.0.10 && \
+    ! module is-loaded ufs-weather-model-env && \
+    which mpicc mpif90 && mpif90 --version | grep -q " 14\.3\."
+
 # Ensure the container rc is run by non-login shells too.
 ENV BASH_ENV=/etc/spack_container_rc.sh