[skip ci] Updates for spack v1 at NAS

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

@@ -112,7 +112,7 @@ jobs:
 
             # Concretize and check for duplicates
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
             # Add and update source cache
             spack mirror add local-source file://${SOURCE_CACHE_PATH}/
@@ -190,7 +190,7 @@ jobs:
 
           # Concretize and check for duplicates
           spack concretize --force 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
           # Add binary cache back in
           spack mirror add local-binary file://${BUILD_CACHE_PATH}/

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

@@ -128,7 +128,7 @@ jobs:
 
             # Concretize and check for duplicates
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
             # Add and update source cache
             spack mirror add local-source file://${SOURCE_CACHE_PATH}/
@@ -209,7 +209,7 @@ jobs:
 
           # Concretize and check for duplicates
           spack concretize --force 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
           # Add binary cache back in
           spack mirror add local-binary file://${BUILD_CACHE_PATH}/

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

@@ -128,7 +128,7 @@ jobs:
 
             # Concretize and check for duplicates
             spack concretize --force --fresh 2>&1 | tee log.concretize.${ENVNAME}
-            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+            ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
             # Add and update source cache
             spack mirror add local-source file://${SOURCE_CACHE_PATH}/
@@ -209,7 +209,7 @@ jobs:
 
           # Concretize and check for duplicates
           spack concretize --force 2>&1 | tee log.concretize.${ENVNAME}
-          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env
+          ${SPACK_STACK_DIR}/util/show_duplicate_packages.py -i fms -i crtm -i crtm-fix -i esmf -i mapl -i py-cython -i neptune-env -i fms
 
           # Add binary cache back in
           spack mirror add local-binary file://${BUILD_CACHE_PATH}/

configs/common/modules_lmod.yaml

@@ -144,8 +144,8 @@ modules:
           ^[email protected]+debug snapshot=none: 'esmf-8.9.0-debug'
       fms:
         suffixes:
-          constants=GFS: 'gfs_constants'
-          constants=GEOS: 'geos_constants'
+          constants=GFS: 'gfs-constants'
+          constants=GEOS: 'geos-constants'
       openmpi:
         environment:
           set:

configs/common/modules_tcl.yaml

@@ -163,8 +163,8 @@ modules:
           ^[email protected]+debug snapshot=none: 'esmf-8.9.0-debug'
       fms:
         suffixes:
-          constants=GFS: 'gfs_constants'
-          constants=GEOS: 'geos_constants'
+          constants=GFS: 'gfs-constants'
+          constants=GEOS: 'geos-constants'
       openmpi:
         environment:
           set:

configs/common/packages.yaml

@@ -107,9 +107,10 @@ packages:
     fms:
       require:
       - '@2024.02'
+      - precision=32,64 +quad_precision +openmp +pic build_type=Release +deprecated_io
       - any_of:
-        - precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io
-        - precision=32,64 +quad_precision ~gfs_phys +openmp +pic constants=GEOS build_type=Release +deprecated_io
+        - +gfs_phys constants=GFS
+        - ~gfs_phys constants=GEOS
     fontconfig:
       require:
       - +pic

configs/sites/tier1/nas/README.md

@@ -177,7 +177,7 @@ Then, once that package is built, you can go back to the compute node and run th
 ## Update module files and setup meta-modules
 
 ```
-spack module tcl refresh -y
+spack module tcl refresh -y --delete-tree
 spack stack setup-meta-modules
 ```
 

configs/sites/tier1/nas/packages_gcc-13.2.0.yaml

@@ -20,19 +20,6 @@ packages:
           c: /nobackup/gmao_SIteam/gcc/gcc-13.2.0/bin/gcc
           cxx: /nobackup/gmao_SIteam/gcc/gcc-13.2.0/bin/g++
           fortran: /nobackup/gmao_SIteam/gcc/gcc-13.2.0/bin/gfortran
-        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'
   openmpi:
     externals:
     - spec: [email protected] ~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath+lustre fabrics=ucx schedulers=tm %[email protected]

configs/sites/tier1/nas/packages_oneapi-2024.2.0.yaml

@@ -26,18 +26,6 @@ packages:
             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:
         - /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/lib64
         - /nobackup/gmao_SIteam/gcc/gcc-12.3.0-TOSS4/lib

configs/templates/unified-dev/spack.yaml

@@ -41,8 +41,8 @@ spack:
   - esmf@=8.9.0
 
   # Various fms builds
-  - fms@2024.02 precision=32,64 +quad_precision +gfs_phys +openmp +pic constants=GFS build_type=Release +deprecated_io
-  - fms@2024.02 precision=32,64 +quad_precision ~gfs_phys +openmp +pic constants=GEOS build_type=Release +deprecated_io
+  - fms +gfs_phys constants=GFS
+  - fms ~gfs_phys constants=GEOS
 
   # MADIS for WCOSS2 decoders.
   - [email protected]

repos/spack_stack/spack_repo/spack_stack/packages/gmao_swell_env/package.py

@@ -25,7 +25,7 @@ class GmaoSwellEnv(BundlePackage):
     depends_on("crtm", type="run")
 
     # Additional dependencies for JEDI used by swell
-    depends_on("fms", type="run")
+    depends_on("fms +gfs_phys constants=GFS", type="run")
     depends_on("nco", type="run")
 
     # GEOS

repos/spack_stack/spack_repo/spack_stack/packages/jedi_fv3_env/package.py

@@ -18,6 +18,6 @@ class JediFv3Env(BundlePackage):
     version("1.0.0")
 
     depends_on("jedi-base-env", type="run")
-    depends_on("fms", type="run")
+    depends_on("fms +gfs_phys constants=GFS", type="run")
 
     # There is no need for install() since there is no code.

repos/spack_stack/spack_repo/spack_stack/packages/jedi_ufs_env/package.py

@@ -18,7 +18,7 @@ class JediUfsEnv(BundlePackage):
     version("1.0.0")
 
     depends_on("jedi-base-env", type="run")
-    depends_on("fms", type="run")
+    depends_on("fms +gfs_phys constants=GFS", type="run")
 
     depends_on("bacio", type="run")
     depends_on("g2", type="run")

repos/spack_stack/spack_repo/spack_stack/packages/ufs_srw_app_env/package.py

@@ -26,7 +26,7 @@ class UfsSrwAppEnv(BundlePackage):
     depends_on("netcdf-fortran")
     depends_on("parallelio")
     depends_on("esmf")
-    depends_on("fms")
+    depends_on("fms +gfs_phys constants=GFS")
     depends_on("bacio")
     depends_on("crtm")
     depends_on("g2")

repos/spack_stack/spack_repo/spack_stack/packages/ufs_weather_model_env/package.py

@@ -27,7 +27,7 @@ class UfsWeatherModelEnv(BundlePackage):
     depends_on("base-env", type="run")
     depends_on("ufs-pyenv", type="run", when="+python")
 
-    depends_on("fms", type="run")
+    depends_on("fms +gfs_phys constants=GFS", type="run")
     depends_on("bacio", type="run")
     depends_on("crtm", type="run")
     depends_on("g2", type="run")