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

Author: rickgrubin-noaa

configs/common/packages.yaml

@@ -171,6 +171,8 @@ packages:
   mapl:
     require: '@2.53 ~shared ~f2py'
     variants: '+pflogger'
+  # Note: Please check the sites/tier1/nas/packages_gcc.yaml if
+  #       this is changed, as it has a custom variant combination
   met:
     require:
     - '@12.0.1'

configs/sites/tier1/hercules/packages_oneapi.yaml

@@ -39,13 +39,13 @@ packages:
   gsibec:
     require::
     - '@1.2.1 ~mkl'
+  py-maturin:
+    require:
+    - '%gcc'
   py-numpy:
     require::
     - '@1.26'
     - '^openblas'
   py-scipy:
     require:
-      '%gcc'
-  zlib-ng:
-    require:
-    - '~shared'
+    - '%gcc'

configs/sites/tier1/jet/compilers.yaml

@@ -0,0 +1,49 @@
+# How to build spack-stack at NAS
+
+## Generic
+
+```
+git clone --recursive https://github.com/JCSDA/spack-stack.git -b release/1.9.0 spack-stack-1.9.1
+```
+
+## oneapi
+
+```
+cd spack-stack-1.9.1
+. setup.sh
+spack stack create env --name ue-oneapi-2024.2.0 --template unified-dev --site nas --compiler oneapi
+cd envs/ue-oneapi-2024.2.0
+spack env activate .
+spack concretize 2>&1 | tee log.concretize
+spack install --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install
+```
+
+NOTE: You might need to run the `spack install` command multiple times because sometimes
+it just fails. But then you run it more and more and it will eventually succeed.
+
+```
+spack module tcl refresh -y
+spack stack setup-meta-modules
+spack env deactivate
+```
+
+## gcc
+
+```
+cd spack-stack-1.9.1
+. setup.sh
+spack stack create env --name ue-gcc-12.3.0 --template unified-dev --site nas --compiler gcc
+cd envs/ue-gcc-12.3.0
+spack env activate .
+spack concretize 2>&1 | tee log.concretize
+spack install --verbose --fail-fast --show-log-on-error --no-check-signature 2>&1 | tee log.install
+```
+
+NOTE: You might need to run the `spack install` command multiple times because sometimes
+it just fails. But then you run it more and more and it will eventually succeed.
+
+```
+spack module tcl refresh -y
+spack stack setup-meta-modules
+spack env deactivate
+```

configs/sites/tier1/jet/packages_gcc.yaml

@@ -0,0 +1,57 @@
+compilers:
+- compiler:
+    spec: oneapi@=2024.2.0
+    paths:
+      cc: /nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/bin/icx
+      cxx: /nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/bin/icpx
+      f77: /nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/bin/ifort
+      fc: /nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/bin/ifort
+    flags: {}
+    operating_system: rhel8
+    target: x86_64
+    modules:
+    - comp-intel/2024.2.0-ifort
+    environment:
+      prepend_path:
+        PATH: '/nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin'
+        CPATH: '/nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/include'
+        LD_LIBRARY_PATH: '/nobackup/gmao_SIteam/intel/oneapi/compiler/2024.2/lib/:/nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/lib64'
+      set:
+        MPI_COLL_REPRODUCIBLE: 'yes'
+        MPI_MEMMAP_OFF: 'yes'
+        MPI_XPMEM_ENABLED: 'yes'
+        MPI_LAUNCH_TIMEOUT: '40'
+        MPI_COMM_MAX: '1024'
+        MPI_GROUP_MAX: '1024'
+        MPI_BUFS_PER_PROC: '256'
+      unset:
+        - MPI_NUM_MEMORY_REGIONS
+        - SUPPRESS_XPMEM_TRIM_THRESH
+        - PMI_RANK
+    extra_rpaths: []
+- compiler:
+    spec: gcc@=12.3.0
+    paths:
+      cc: /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin/gcc
+      cxx: /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin/g++
+      f77: /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin/gfortran
+      fc: /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/bin/gfortran
+    flags: {}
+    operating_system: rhel8
+    target: x86_64
+    modules:
+    - comp-gcc/12.3.0-TOSS4
+    environment:
+      set:
+        OMPI_MCA_mpi_preconnect_all: 1
+        OMPI_MCA_coll_tuned_bcast_algorithm: 7
+        OMPI_MCA_coll_tuned_scatter_algorithm: 2
+        OMPI_MCA_coll_tuned_reduce_scatter_algorithm: 3
+        OMPI_MCA_coll_tuned_allreduce_algorithm: 3
+        OMPI_MCA_coll_tuned_allgather_algorithm: 4
+        OMPI_MCA_coll_tuned_allgatherv_algorithm: 3
+        OMPI_MCA_coll_tuned_gather_algorithm: 1
+        OMPI_MCA_coll_tuned_barrier_algorithm: 0
+        OMPI_MCA_coll_tuned_use_dynamic_rules: 1
+        OMPI_MCA_sharedfp: '^lockedfile,individual'
+    extra_rpaths: []

configs/sites/tier1/jet/packages_intel.yaml

@@ -1,15 +1,15 @@
 mirrors:
   local-source:
     fetch:
-      url: file:///mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/source-cache
+      url: file:///nobackup/gmao_SIteam/spack-stack/source-cache
       access_pair:
       - null
       - null
       access_token: null
       profile: null
       endpoint_url: null
     push:
-      url: file:///mnt/lfs4/HFIP/hfv3gfs/role.epic/spack-stack/source-cache
+      url: file:///nobackup/gmao_SIteam/spack-stack/source-cache
       access_pair:
       - null
       - null

configs/sites/tier1/nas/README.md

@@ -0,0 +1,8 @@
+modules:
+  default:
+    enable::
+    - tcl
+    tcl:
+      include:
+      # List of packages for which we need modules that are blacklisted by default
+      - python