Merge branch 'release/1.9.0' into ashley/feature/discover_oneapi_conf

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

@@ -131,6 +131,16 @@ jobs:
               echo "jedi-ufs-env ..."
               spack install --fail-fast --source --no-check-signature jedi-ufs-env 2>&1 | tee log.install.gnu-11.4.0-buildcache.jedi-ufs-env
               spack buildcache create -u /home/ubuntu/spack-stack/build-cache/ jedi-ufs-env
+
+            elif [[ "${TEMPLATE}" == *"cylc-dev"* ]]; then
+              # Workaround for not being able to install rust from build-cache, see 
+              # https://github.com/spack/spack/issues/48971
+              echo "rust dependencies ..."
+              spack install --verbose --source --no-check-signature --only=dependencies rust 2>&1 | tee log.install.gnu-11.4.0-buildcache.${TEMPLATE}.001.rust-dependencies
+
+              # rust from source
+              echo "rust (from source) ..."
+              spack install --verbose --source --no-cache rust 2>&1 | tee log.install.gnu-11.4.0-buildcache.${TEMPLATE}.002.rust
             fi
 
             # the rest

configs/sites/tier1/acorn/compilers.yaml

@@ -21,7 +21,7 @@ compilers:
         CONFIG_SITE: ''
     extra_rpaths: []
 - compiler:
-    spec: intel@2022.0.2.262
+    spec: intel@2022.2.0.262
     paths:
       cc: cc
       cxx: CC

configs/sites/tier1/acorn/packages.yaml

@@ -41,3 +41,6 @@
       externals:
       - spec: [email protected]
         prefix: /usr
+    esmf:
+      require:
+      - '+python'

configs/sites/tier1/acorn/packages_intel.yaml

@@ -32,9 +32,7 @@
     py-numpy:
       require::
       - '^[virtuals=lapack,blas] openblas'
-      - '@:1.25'
-      - any_of: ['@:1.24']
-        when: '%[email protected]'
+      - '@1.26 %gcc'
     # *DH
     eckit:
       require:

configs/sites/tier1/hera/compilers.yaml

@@ -17,15 +17,32 @@ compilers:
         CPATH: '/apps/gnu/gcc-9.2.0/include'
     extra_rpaths: []
 - compiler:
-    spec: gcc@9.2.0
+    spec: gcc@13.2.0
     paths:
-      cc: /apps/gnu/gcc-9.2.0/bin/gcc
-      cxx: /apps/gnu/gcc-9.2.0/bin/g++
-      f77: /apps/gnu/gcc-9.2.0/bin/gfortran
-      fc:  /apps/gnu/gcc-9.2.0/bin/gfortran
+      cc: /apps/gnu/gcc-13.2.0/bin/gcc
+      cxx: /apps/gnu/gcc-13.2.0/bin/g++
+      f77: /apps/gnu/gcc-13.2.0/bin/gfortran
+      fc:  /apps/gnu/gcc-13.2.0/bin/gfortran
     flags: {}
     operating_system: rocky8
     modules:
-    - gnu/9.2.0
+    - gnu/13.2.0
     environment: {}
     extra_rpaths: []
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: /apps/oneapi/compiler/2024.2/bin/icx
+      cxx: /apps/oneapi/compiler/2024.2/bin/icpx
+      f77: /apps/oneapi/compiler/2024.2/bin/ifort
+      fc: /apps/oneapi/compiler/2024.2/bin/ifort
+    flags: {}
+    operating_system: rocky8
+    modules:
+    - intel/2024.2.1
+    environment:
+      prepend_path:
+        PATH: '/apps/gnu/gcc-13.2.0/bin'
+        LD_LIBRARY_PATH: '/apps/gnu/gcc-13.2.0/lib64'
+        CPATH: '/apps/gnu/gcc-13.2.0/include'
+    extra_rpaths: []

configs/sites/tier1/hera/mirrors.yaml

@@ -1,15 +1,15 @@
 mirrors:
   local-source:
     fetch:
-      url: file:///scratch1/NCEPDEV/nems/role.epic/spack-stack/source-cache
+      url: file:///scratch4/NCEPDEV/stmp/role.epic/spack-stack/mirror
       access_pair:
       - null
       - null
       access_token: null
       profile: null
       endpoint_url: null
     push:
-      url: file:///scratch1/NCEPDEV/nems/role.epic/spack-stack/source-cache
+      url: file:///scratch4/NCEPDEV/stmp/role.epic/spack-stack/mirror
       access_pair:
       - null
       - null

configs/sites/tier1/hera/packages_gcc.yaml

@@ -1,6 +1,6 @@
 packages:
   all:
-    compiler:: [gcc@9.2.0]
+    compiler:: [gcc@13.2.0]
     providers:
       mpi:: [[email protected]]
   mpi:
@@ -9,5 +9,5 @@ packages:
     externals:
     - spec: [email protected]~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-libevent~internal-pmix~java+legacylaunchers~lustre~memchecker~openshmem~orterunprefix+pmi+romio+rsh~singularity+static+vt+wrapper-rpath fabrics=ucx schedulers=slurm
       modules:
-      - gnu/9.2.0
-      - openmpi/4.1.6_gnu9.2.0
+      - gnu/13.2.0
+      - openmpi/4.1.6

configs/sites/tier1/hera/packages_oneapi.yaml

@@ -0,0 +1,43 @@
+packages:
+  all:
+    compiler:: [[email protected]]
+    providers:
+      mpi:: [[email protected]]
+      # Remove the next three lines to switch to intel-oneapi-mkl
+      blas:: [openblas]
+      fftw-api:: [fftw]
+      lapack:: [openblas]
+  mpi:
+    buildable: False
+  intel-oneapi-mpi:
+    buildable: False
+    externals:
+    - spec: [email protected]%[email protected]
+      modules:
+      - intel/2024.2.1
+      - impi/2024.2.1
+      prefix: /apps/oneapi
+  intel-oneapi-mkl:
+    # Remove buildable: False and uncomment externals section below to use intel-oneapi-mkl
+    buildable: False
+    #externals:
+    #- spec: [email protected]%[email protected]
+    #  prefix: /apps/oneapi
+  # DH* Remove this section to switch to intel-oneapi-mkl
+  ectrans:
+    require::
+    - '@1.2.0 ~mkl +fftw'
+  gsibec:
+    require::
+    - '@1.2.1 ~mkl'
+  py-numpy:
+    require::
+    - '@1.26'
+    - '^openblas'
+  # *DH
+  zlib-ng:
+    require:
+      - '~shared'
+  cdo:
+    require:
+      - '@2.3.0'

configs/sites/tier1/orion/packages.yaml

@@ -103,10 +103,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  qt:
-    externals:
-    - spec: [email protected]
-      prefix:  /apps/spack-managed/gcc-11.3.1/qt-5.15.8-d47tsna6f5dylcpblkfgw4gpn2cucihd
   sed:
     externals:
     - spec: [email protected]

configs/sites/tier1/s4/compilers.yaml

@@ -17,6 +17,27 @@ compilers:
         LD_LIBRARY_PATH: /opt/intel/oneapi/2023.2/compiler/2023.2.0/linux/compiler/lib/intel64_lin:/opt/gcc/10.2.0/lib64:/opt/gcc/10.2.0/lib
         CPATH: /opt/gcc/10.2.0/include
     extra_rpaths: []
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: /opt/intel/oneapi/2024/compiler/2024.2/bin/icx
+      cxx: /opt/intel/oneapi/2024/compiler/2024.2/bin/icpx
+      f77: /opt/intel/oneapi/2024/compiler/2024.2/bin/ifort
+      fc: /opt/intel/oneapi/2024/compiler/2024.2/bin/ifort
+    flags:
+      fflags: -diag-disable=10448
+    operating_system: rocky8
+    target: x86_64
+    modules:
+    - intel/2024.2
+    environment:
+      prepend_path:
+        PATH: /opt/gcc/10.2.0/bin
+        LD_LIBRARY_PATH: /opt/gcc/10.2.0/lib64:/opt/gcc/10.2.0/lib
+        CPATH: /opt/gcc/10.2.0/include
+      append_path:
+        PATH: /opt/intel/oneapi/2024/compiler/2024.2/opt/compiler/include/intel64
+    extra_rpaths: []
 - compiler:
     spec: gcc@=13.3.0
     paths:
@@ -58,3 +79,4 @@ compilers:
     modules: []
     environment: {}
     extra_rpaths: []
+

configs/sites/tier1/s4/packages.yaml

@@ -1,8 +1,10 @@
 packages:
   all:
-    compiler:: [[email protected],[email protected]]
+    compiler:: [[email protected],[email protected]]
+    #compiler:: [[email protected],[email protected]]
     providers:
-      mpi:: [[email protected]]
+      mpi:: [[email protected]]
+      # mpi:: [[email protected]]
       # Remove the next three lines to switch to intel-oneapi-mkl
       blas:: [openblas]
       fftw-api:: [fftw]
@@ -14,18 +16,24 @@ packages:
 ### MPI, Python, MKL
   mpi:
     buildable: False
+  #intel-oneapi-mpi:
+  #  externals:
+  #  - spec: [email protected]%[email protected] +classic-names
+  #    prefix: /opt/intel/oneapi/2024
+  #    modules:
+  #    - intel/2023.2
   intel-oneapi-mpi:
     externals:
-    - spec: intel-oneapi-mpi@2021.10.0%[email protected] +classic-names
-      prefix: /opt/intel/oneapi/2023.2
+    - spec: intel-oneapi-mpi@2021.13%[email protected]
+      prefix: /opt/intel/oneapi/2024
       modules:
-      - intel/2023.2
+      - intel/2024.2
   intel-oneapi-mkl:
     # Remove buildable: False and uncomment externals section below to use intel-oneapi-mkl
     buildable: False
     #externals:
     #- spec: [email protected]%[email protected]
-    #  prefix: /opt/intel/oneapi/2023.2
+    #  prefix: /opt/intel/oneapi/2024
     #  modules:
     #  - intel/2023.2
   # Remove this section to switch to intel-oneapi-mkl
@@ -80,7 +88,7 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  # OS curl/openssl cause problems 
+  # OS curl/openssl cause problems
   #curl:
   #  externals:
   #  - spec: [email protected]+gssapi+ldap+nghttp2
@@ -203,3 +211,4 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
+

configs/sites/tier1/wcoss2/compilers.yaml

@@ -0,0 +1,45 @@
+compilers:
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: cc
+      cxx: CC
+      f77: ftn
+      fc: ftn
+    flags: {}
+    operating_system: sles15
+    modules:
+    - PrgEnv-intel/8.3.3
+    - craype/2.7.17
+    - intel/19.1.3.304
+    - libfabric
+    environment:
+      set:
+        # OpenSUSE on WCOSS2 machines sets CONFIG_SITE so 
+        # Automake-based builds are installed in lib64 
+        # which confuses some packages.
+        CONFIG_SITE: ''
+      unset: [PYTHONPATH]
+    extra_rpaths: []
+- compiler:
+    spec: [email protected]
+    paths:
+      cc: cc
+      cxx: CC
+      f77: ftn
+      fc: ftn
+    flags: {}
+    operating_system: sles15
+    modules:
+    - PrgEnv-gnu/8.3.3
+    - craype/2.7.13
+    - gcc/10.2.0
+    - libfabric
+    environment:
+      set:
+        # OpenSUSE on WCOSS2 machines sets CONFIG_SITE so 
+        # Automake-based builds are installed in lib64 
+        # which confuses some packages.
+        CONFIG_SITE: ''
+      unset: [PYTHONPATH]
+    extra_rpaths: []

configs/sites/tier1/wcoss2/config.yaml

@@ -0,0 +1,5 @@
+config:
+  build_jobs: 6
+  template_dirs:
+  - $env/site/templates
+  - $spack/share/spack/templates

configs/sites/tier1/wcoss2/modules.yaml

@@ -0,0 +1,16 @@
+modules:
+  default:
+    enable::
+    - lmod
+    lmod:
+      include:
+      - python
+      hierarchy:
+      - mpi
+      - hdf5_virtual
+      - netcdf_c_virtual
+      - esmf_virtual
+      - python_virtual
+      boost:
+        suffixes:
+          '%gcc': gcc