[feature/update_to_spack_v1] [email protected], bug fix netcdf-c+mpi, bug fix setup-meta-modules, Nautilus gcc stack update

configs/common/modules_lmod.yaml

@@ -142,6 +142,8 @@ modules:
           ^[email protected]+debug snapshot=none: 'esmf-8.8.0-debug'
           ^[email protected]~debug snapshot=none: 'esmf-8.9.0'
           ^[email protected]+debug snapshot=none: 'esmf-8.9.0-debug'
+          ^[email protected]~debug snapshot=none: 'esmf-8.9.1'
+          ^[email protected]+debug snapshot=none: 'esmf-8.9.1-debug'
       openmpi:
         environment:
           set:

configs/common/modules_tcl.yaml

@@ -161,6 +161,8 @@ modules:
           ^[email protected]+debug snapshot=none: 'esmf-8.8.0-debug'
           ^[email protected]~debug snapshot=none: 'esmf-8.9.0'
           ^[email protected]+debug snapshot=none: 'esmf-8.9.0-debug'
+          ^[email protected]~debug snapshot=none: 'esmf-8.9.1'
+          ^[email protected]+debug snapshot=none: 'esmf-8.9.1-debug'
       openmpi:
         environment:
           set:

configs/common/packages.yaml

@@ -84,7 +84,7 @@ packages:
     esmf:
       require:
       - ~xerces ~pnetcdf +shared +external-parallelio
-      - any_of: ['@=8.6.1 snapshot=none', '@=8.8.0 snapshot=none', '@=8.9.0 snapshot=none']
+      - any_of: ['@=8.6.1 snapshot=none', '@=8.8.0 snapshot=none', '@=8.9.0 snapshot=none', '@=8.9.1 snapshot=none']
       - any_of: ['fflags="-fp-model precise" cxxflags="-fp-model precise"']
         when: '%intel'
         message: Extra ESMF compile options for Intel

configs/sites/tier1/nautilus/packages_gcc-13.3.1.yaml

@@ -2,7 +2,7 @@ packages:
   mpi:
     buildable: False
     require:
-    - openmpi@4.1.8
+    - openmpi@5.0.8
   gcc-runtime:
     buildable: False
     externals:
@@ -23,8 +23,14 @@ packages:
   openmpi:
     buildable: False
     externals:
-    - spec: openmpi@4.1.8
-      prefix: /p/app/penguin/openmpi/4.1.8/gcc-13.3.1
+    - spec: openmpi@5.0.8
+      prefix: /p/app/penguin/openmpi/5.0.8/gcc-13.3.1
       modules:
-      - penguin/openmpi/4.1.8/gcc-13.3.1
+      - penguin/openmpi/5.0.8/gcc-13.3.1
       - slurm
+      extra_attributes:
+        environment:
+          set:
+            OMPI_MCA_coll: "^hcoll,cuda"
+            OMPI_MCA_pml: "ucx"
+

configs/templates/neptune-dev/spack.yaml

@@ -8,10 +8,10 @@ spack:
   include: []
 
   specs:
-  - neptune-env ~debug +espc ^esmf@=8.9.0
-  - neptune-env +debug +espc ^esmf@=8.9.0
-  - neptune-python-env    ^neptune-env ~debug +espc ^esmf@=8.9.0
-  - jedi-neptune-env +adp ^neptune-env ~debug +espc ^esmf@=8.9.0
+  - neptune-env ~debug +espc ^esmf@=8.9.1
+  - neptune-env +debug +espc ^esmf@=8.9.1
+  - neptune-python-env    ^neptune-env ~debug +espc ^esmf@=8.9.1
+  - jedi-neptune-env +adp ^neptune-env ~debug +espc ^esmf@=8.9.1
   - [email protected]
   - [email protected]
 

configs/templates/neptune-ops/spack.yaml

@@ -8,7 +8,7 @@ spack:
   include: []
 
   specs:
-  - neptune-env ~debug +espc ^esmf@=8.9.0
+  - neptune-env ~debug +espc ^esmf@=8.9.1
 
   packages:
     # Turn off python variant for esmf

configs/templates/skylab-dev/spack.yaml

@@ -14,12 +14,12 @@ spack:
   - jedi-fv3-env
   - jedi-geos-env         ^esmf@=8.6.1
   - jedi-mpas-env
-  - jedi-neptune-env      ^esmf@=8.9.0
+  - jedi-neptune-env      ^esmf@=8.9.1
   - jedi-tools-env
   - jedi-ufs-env          ^esmf@=8.8.0
   #- jedi-um-env
-  - neptune-env           ^esmf@=8.9.0
-  - neptune-python-env    ^esmf@=8.9.0
+  - neptune-env           ^esmf@=8.9.1
+  - neptune-python-env    ^esmf@=8.9.1
   - soca-env
 
   # Various crtm tags (list all to avoid duplicate packages)
@@ -33,7 +33,7 @@ spack:
   # Various esmf tags (list all to avoid duplicate packages)
   - esmf@=8.6.1
   - esmf@=8.8.0
-  - esmf@=8.9.0
+  - esmf@=8.9.1
 
   packages:
     # Turn on python variant for esmf

configs/templates/unified-dev/spack.yaml

@@ -17,12 +17,12 @@ spack:
   - jedi-fv3-env
   - jedi-geos-env         ^esmf@=8.6.1
   - jedi-mpas-env
-  - jedi-neptune-env      ^esmf@=8.9.0
+  - jedi-neptune-env      ^esmf@=8.9.1
   #- jedi-tools-env
   - jedi-ufs-env          ^esmf@=8.8.0
   #- jedi-um-env
-  - neptune-env           ^esmf@=8.9.0
-  - neptune-python-env    ^esmf@=8.9.0
+  - neptune-env           ^esmf@=8.9.1
+  - neptune-python-env    ^esmf@=8.9.1
   - soca-env
   - ufs-srw-app-env       ^esmf@=8.8.0 ^crtm@=3.1.2
   - ufs-weather-model-env ^esmf@=8.8.0 ^crtm@=3.1.2
@@ -38,7 +38,7 @@ spack:
   # Various esmf tags (list all to avoid duplicate packages)
   - esmf@=8.6.1
   - esmf@=8.8.0
-  - esmf@=8.9.0
+  - esmf@=8.9.1
 
   # MADIS for WCOSS2 decoders.
   - [email protected]

spack-ext/lib/jcsda-emc/spack-stack/stack/meta_modules.py

@@ -373,6 +373,12 @@ def custom_sort_key(entry):
         raise Exception(f"Expected no or one MPI provider, but got {mpi_providers}")
     logging.info(f"  ... mpi_providers: {mpi_providers}")
 
+    # To catch errors (invalid compilers, etc) we check that the number of written
+    # stack-* meta modules matches what we expect: One module for the preferred
+    # compiler, and (if applicable) one for each (currently one) MPI provider.
+    number_of_meta_modules_expected = 1 + len(mpi_providers)
+    number_of_meta_modules_written = 0
+
     # Prepare meta module directory
     logging.info("Preparing meta module directory ...")
     meta_module_dir = os.path.join(module_dir, "Core")
@@ -508,6 +514,7 @@ def custom_sort_key(entry):
         with open(compiler_module_file, "w") as f:
             f.write(module_content)
         logging.info("  ... writing {}".format(compiler_module_file))
+        number_of_meta_modules_written += 1
 
         # If this is the last compiler in the list (i.e. the preferred compiler),
         # then save the substitutes for later when building the MPI meta module
@@ -520,13 +527,15 @@ def custom_sort_key(entry):
     # Create mpi modules - currently, only one mpi provider is allowed
     for mpi_provider in mpi_providers:
 
+        if module_choice == "lmod":
+            mpi_alias = mpi_provider.name
+        else:
+            mpi_alias = ALIASES[mpi_provider.name]
+
         # For tcl, append modulepath for external specs and for specs without
         # compiler dependencies; remove the compiler/mpi prefices from the moduless
         if module_choice == "tcl":
 
-            # Module paths are short names for tcl modules
-            mpi_alias = ALIASES[mpi_provider.name]
-
             modulepath_save = os.path.join(module_dir, mpi_alias, str(mpi_provider.version), "none", "none")
             if not os.path.isdir(modulepath_save):
                 os.makedirs(modulepath_save)
@@ -548,7 +557,7 @@ def custom_sort_key(entry):
 
             # Module paths are short names for tcl modules
             if module_choice == "lmod":
-                mpi_alias = compiler.name
+                compiler_alias = compiler.name
             else:
                 compiler_alias = ALIASES[compiler.name]
 
@@ -654,10 +663,10 @@ def custom_sort_key(entry):
             substitutes["FC"]  = COMPILER_SUBSTITUTES_SAVE["FC"]
 
             # Environment variables
-            if "environment" in compiler.extra_attributes.keys():
-                for action in compiler.extra_attributes["environment"].keys():
-                    for env_name in compiler.extra_attributes["environment"][action]:
-                        env_values = compiler.extra_attributes["environment"][action][env_name]
+            if "environment" in mpi_provider.extra_attributes.keys():
+                for action in mpi_provider.extra_attributes["environment"].keys():
+                    for env_name in mpi_provider.extra_attributes["environment"][action]:
+                        env_values = mpi_provider.extra_attributes["environment"][action][env_name]
                         substitutes["ENVVARS"] += envmod_command(
                             module_choice,
                             action,
@@ -689,5 +698,10 @@ def custom_sort_key(entry):
             with open(mpi_module_file, "w") as f:
                 f.write(module_content)
             logging.info("  ... writing {}".format(mpi_module_file))
+            number_of_meta_modules_written += 1
 
-    logging.info("Metamodule generation completed successfully in {}".format(meta_module_dir))
+
+    if number_of_meta_modules_written == number_of_meta_modules_expected:
+        logging.info("Metamodule generation completed successfully in {}".format(meta_module_dir))
+    else:
+        raise Exception("Metamodule generation NOT successful, check output (invalid compiler?)")