Merge remote-tracking branch 'upstream/develop' into develop

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

@@ -20,7 +20,9 @@ jobs:
         run: |
           pwd
           ls -lart
+          set +e
           find ./* -type d -exec chmod u+xw {} \;
+          set -e
           rm -fr *
 
       - name: checkout

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

@@ -8,7 +8,7 @@ on:
   #    - '**.md'
   #    - '.github/ISSUE_TEMPLATE/*'
   #    - '.gitignore'
-  # 
+  #
   schedule:
     - cron: '0 8 * * *'
   workflow_dispatch:

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

@@ -20,7 +20,9 @@ jobs:
         run: |
           pwd
           ls -lart
+          set +e
           find ./* -type d -exec chmod u+xw {} \;
+          set -e
           rm -fr *
 
       - name: checkout

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

@@ -20,7 +20,9 @@ jobs:
         run: |
           pwd
           ls -lart
+          set +e
           find ./* -type d -exec chmod u+xw {} \;
+          set -e
           rm -fr *
 
       - name: checkout

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

@@ -20,7 +20,9 @@ jobs:
         run: |
           pwd
           ls -lart
+          set +e
           find ./* -type d -exec chmod u+xw {} \;
+          set -e
           rm -fr *
 
       - name: checkout

configs/common/packages.yaml

@@ -54,7 +54,7 @@ packages:
   # Also, check the acorn and derecho site configs which have esmf modifications.
   esmf:
     require:
-      - '~xerces ~pnetcdf +shared +external-parallelio'
+      - '~xerces ~pnetcdf +shared +external-parallelio +python'
       - any_of: ['@=8.6.1 snapshot=none', '@=8.7.0b11 snapshot=b11']
       - any_of: ['fflags="-fp-model precise" cxxflags="-fp-model precise"']
         when: "%intel"
@@ -75,8 +75,9 @@ packages:
     # Pin version to avoid duplicates
     require: '@2.6.4'
   fms:
-    require: '@2024.02'
-    variants: 'precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io'
+    require:
+    - '@2024.02'
+    - 'precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io'
   fontconfig:
     require: '+pic'
   freetype:
@@ -214,6 +215,9 @@ packages:
   ## To avoid duplicate packages
   #py-jinja2:
   #  require: '@3.1.2'
+  # https://github.com/JCSDA/spack-stack/issues/1276
+  py-matplotlib:
+     require: '@3.7.4'
   py-meson-python:
      require: '@0.15.0'
   # Comment out for now until build problems are solved
@@ -226,13 +230,17 @@ packages:
     require: '@1.5.8 ~mpi'
   # [email protected] causes many build problems with older Python packages
   # also check Nautilus site config when making changes here
+  # https://github.com/JCSDA/spack-stack/issues/1276
   py-numpy:
     require:
-    - '@:1.25'
+    - '@:1.23.5'
   py-pandas:
     require: '+excel'
   py-pybind11:
     require: '@2.11.0'
+  # To avoid duplicate packages
+  py-ruamel-yaml:
+    require: '@0.17.16'
   # Pin the py-setuptools version to avoid duplicate Python packages
   py-setuptools:
     require: '@63.4.3'
@@ -270,7 +278,8 @@ packages:
   w3nco:
     require: '@2.4.1'
   wgrib2:
-    require: '@3.1.1'
+    require:
+    - '@3.1.1'
   wrf-io:
     require: '@1.2.0'
   zstd:

configs/common/packages_aocc.yaml

@@ -0,0 +1,15 @@
+packages:
+  all:
+    providers:
+      blas: [openblas]
+      fftw-api: [fftw]
+      lapack: [openblas]
+  ectrans:
+    require:
+    - '~mkl +fftw'
+  gsibec:
+    require:
+    - '~mkl'
+  py-numpy:
+    require:
+    - '^openblas'

configs/containers/docker-ubuntu-clang-mpich.yaml

@@ -42,12 +42,6 @@ spack:
       externals:
       - spec: [email protected]
         prefix: /usr
-    g2:
-      # https://github.com/NOAA-EMC/NCEPLIBS-g2/issues/745
-      require:
-        - any_of: ['fflags="-fno-range-check"']
-          when: "@3.5.1 %clang"
-          message: "Extra g2 compile options for version 3.5.1 with clang"
     g2tmpl:
       # https://github.com/JCSDA/spack-stack/issues/525
       require:

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

@@ -45,12 +45,6 @@ spack:
       externals:
       - spec: [email protected]
         prefix: /usr
-    g2:
-      # https://github.com/NOAA-EMC/NCEPLIBS-g2/issues/745
-      require:
-      - any_of: ['fflags="-fno-range-check"']
-        when: "@3.5.1 %gcc"
-        message: "Extra g2 compile options for version 3.5.1 with gcc/gfortran"
     diffutils:
       buildable: false
       externals:

configs/containers/specs/jedi-ci.yaml

@@ -38,7 +38,7 @@
     [email protected],
     [email protected],
     [email protected],
-    py-numpy@1.25.2,
+    py-numpy@1.23.5,
     [email protected],
     py-pip,
     [email protected],

configs/sites/tier1/acorn/compilers.yaml

@@ -6,18 +6,17 @@ compilers:
       cxx: CC
       f77: ftn
       fc: ftn
-    flags: {}
+    flags:
+      cflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
+      cxxflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
+      fflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
     operating_system: sles15
     modules:
-    - PrgEnv-intel/8.3.3
-    - craype/2.7.13
+    - PrgEnv-intel/8.5.0
+    - craype/2.7.17
     - intel/19.1.3.304
     - libfabric
     environment:
-      prepend_path:
-        PATH: /opt/cray/pe/gcc/10.2.0/bin
-        LD_LIBRARY_PATH: /opt/cray/pe/gcc/10.2.0/snos/lib64
-        CPATH: /opt/cray/pe/gcc/10.2.0/snos/include
       set:
         # OpenSUSE on WCOSS2 machines sets CONFIG_SITE so 
         # Automake-based builds are installed in lib64 
@@ -31,11 +30,14 @@ compilers:
       cxx: CC
       f77: ftn
       fc: ftn
-    flags: {}
+    flags:
+      cflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
+      cxxflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
+      fflags: -static-libgcc -static-libstdc++ -Bstatic -lstdc++ -Bdynamic -lm -lpthread
     operating_system: sles15
     modules:
-    - PrgEnv-intel/8.3.3
-    - craype/2.7.13
+    - PrgEnv-intel/8.5.0
+    - craype/2.7.17
     - intel-classic/2022.2.0.262
     - libfabric
     environment:

configs/sites/tier1/acorn/packages.yaml

@@ -9,11 +9,6 @@
       externals:
       - spec: [email protected]
         modules: [git-lfs/2.11.0]
-    perl:
-      buildable: false
-      externals:
-      - spec: [email protected]~cpanm+shared+threads
-        prefix: /usr
     mysql:
       buildable: false
       externals:
@@ -38,6 +33,7 @@
     gdal:
       variants: ~curl
     flex:
+      buildable: false
       externals:
       - spec: [email protected]+lex
         prefix: /usr

configs/sites/tier1/acorn/packages_intel.yaml

@@ -31,21 +31,29 @@
       - '@1.2.1 ~mkl'
     py-numpy:
       require::
-      - '@:1.25 ^openblas'
+      - '^[virtuals=lapack,blas] openblas'
+      - '@:1.25'
+      - any_of: ['@:1.24']
+        when: '%[email protected]'
     # *DH
     eckit:
       require:
       - any_of: ["@1.23.1"]
         when: "%[email protected]"
     eccodes:
       require:
-      - any_of: ["@2.27.0"]
+      - any_of: ["@2.25.0"]
         when: "%[email protected]"
+        message: "2.25.0 is the last version to use C++11 (as opposed to C++17)"
     py-scipy:
       require:
       - any_of: ["@1.10.1"]
         when: "%[email protected]"
     cdo:
       require:
+      - any_of: ["@2.3.0"]
+        when: "%[email protected]"
+        message: "2.3.0 is the last version to use C++17"
       - any_of: ["@2.0.5"]
         when: "%[email protected]"
+        message: "2.0.5 is the last version to use C++14"

configs/sites/tier1/atlantis/compilers.yaml

@@ -54,4 +54,3 @@ compilers:
       append_path:
         CPATH: /cm/shared/apps/intel/oneapi-2024.2.1/compiler/2024.2/opt/compiler/include/intel64/
     extra_rpaths: []
-# Todo: Define gcc compiler (default for Atlantis) for Intel (ecflow)

configs/sites/tier1/atlantis/modules.yaml

@@ -6,5 +6,3 @@ modules:
       include:
       # List of packages for which we need modules that are blacklisted by default
       - python
-      exclude:
-      - ecflow

configs/sites/tier1/atlantis/packages_oneapi.yaml

@@ -2,12 +2,12 @@ packages:
   all:
     compiler:: [[email protected],[email protected]]
     providers:
-      mpi:: [[email protected].0]
+      mpi:: [[email protected]]
   mpi:
     buildable: False
   intel-oneapi-mpi:
     externals:
-    - spec: [email protected]%2024.2.1
+    - spec: [email protected]%oneapi@2024.2.1
       prefix: /cm/shared/apps/intel/oneapi-2024.2.1
       modules:
       - mpi/2021.13