[release/2.0] Fix MET segmentation faults in spack-packages, navy-aws site config updates round 2 (#1844)

- Fix MET segmentation faults (spack-packages submodule, see [release/2.0] Fix MET segfaults (fixup_rpath --> environment modification) spack-packages#29). This requires adding libpython3.* to the whitelist in util/ldd_check.py
- Site config updates for navy-aws tier1 site, add site config to NRL batch install script

Author: climbfuji

configs/sites/tier1/navy-aws/bootstrap.yaml

@@ -1,10 +1,10 @@
 config:
-  build_jobs: 6
+  build_jobs: 24
 
   # Overrides for spack build and staging areas to speed up builds
   # and avoid errors with hard links on the NFS filesystem /contrib
 
-  build_stage: ${HOME}/spack-stack-cache/build_stage
-  test_stage: ${HOME}/spack-stack-cache/test_stage
-  source_cache: ${HOME}/spack-stack-cache/source_cache
-  misc_cache: ${HOME}/spack-stack-cache/misc_cache
+  build_stage: /scratch/spack-stack-cache/build_stage
+  test_stage: /scratch/spack-stack-cache/test_stage
+  source_cache: /scratch/spack-stack-cache/source_cache
+  misc_cache: /scratch/spack-stack-cache/misc_cache

configs/sites/tier1/navy-aws/config.yaml

@@ -1,18 +1,4 @@
 mirrors:
-  local-source:
-    fetch:
-      url: file:///contrib/spack-stack/source-cache
-      access_pair:
-      - null
-      - null
-      access_token: null
-      profile: null
-      endpoint_url: null
-    push:
-      url: file:///contrib/spack-stack/source-cache
-      access_pair:
-      - null
-      - null
-      access_token: null
-      profile: null
-      endpoint_url: null
+  local-source: file:///project/spack-stack/source-cache
+  local-binary: file:///project/spack-stack/build-cache
+

configs/sites/tier1/navy-aws/mirrors.yaml

@@ -2,14 +2,6 @@ packages:
   # Modification of common packages
 
   # All other packages listed alphabetically
-  autoconf:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-  automake:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   bash:
     externals:
     - spec: [email protected]

configs/sites/tier1/navy-aws/packages.yaml

@@ -26,4 +26,7 @@ packages:
   openmpi:
     externals:
     - spec: [email protected]
-      prefix: /project/spack-stack/openmpi-4.1.8/gcc-13.3.1
+      #prefix: /project/spack-stack/openmpi-4.1.8/gcc-13.3.1
+      modules:
+      - openmpi/4.1.8
+

configs/sites/tier1/navy-aws/packages_gcc-13.3.1.yaml

@@ -1,11 +1,12 @@
 #!/usr/bin/env python3
 
 # Whitelist file patterns (checked with re.match()) that will be satisfied by
-# compiler & MPI modules (though arguably these should be added as extra
-# rpaths).
+# compiler, MPI, and Python modules (though arguably these should be added as
+# extra rpaths).
 whitelist = [
     "^libmkl.+",
     "^libifcore.so.*",
+    "^libpython3.*",
 ]
 
 ########

repos/builtin

@@ -103,6 +103,11 @@ fi
 SPACK_STACK_BATCH_HOST=$(echo ${HOSTNAME} | cut -d "." -f 1)
 SPACK_STACK_BATCH_HOST=${SPACK_STACK_BATCH_HOST//[0-9]/}
 
+# Workaround for ParallelWorks login nodes
+if [[ "${SPACK_STACK_BATCH_HOST}" == *"awsneptunecluster"* ]]; then
+  SPACK_STACK_BATCH_HOST="navy-aws"
+fi
+
 case ${SPACK_STACK_BATCH_HOST} in
   atlantis)
     SPACK_STACK_BATCH_COMPILERS=("oneapi@=2024.2.1" "oneapi@=2025.3.0" "gcc@=13.4.0" "clang@=21.1.0")
@@ -139,6 +144,13 @@ case ${SPACK_STACK_BATCH_HOST} in
     SPACK_STACK_BOOTSTRAP_MIRROR="/p/cwfs/projects/NEPTUNE/spack-stack/bootstrap-mirror"
     SPACK_STACK_CARGO_MIRROR="/p/cwfs/projects/NEPTUNE/spack-stack/cargo-mirror"
     ;;
+  navy-aws)
+    SPACK_STACK_BATCH_COMPILERS=("oneapi@=2025.3.0" "gcc@=13.3.1")
+    SPACK_STACK_BATCH_TEMPLATES=("neptune-dev" "cylc-dev")
+    SPACK_STACK_MODULE_CHOICE="tcl"
+    SPACK_STACK_BOOTSTRAP_MIRROR="/project/spack-stack/bootstrap-mirror"
+    SPACK_STACK_CARGO_MIRROR="/project/spack-stack/cargo-mirror"
+    ;;
   tusk)
     SPACK_STACK_BATCH_COMPILERS=("oneapi@=2024.2.0" "gcc@=12.1.0")
     SPACK_STACK_BATCH_TEMPLATES=("neptune-dev")
@@ -222,6 +234,13 @@ function fix_permissions() {
       fi
       nice -n 19 lfs find ${dir} -type f -print0 | xargs --null chmod a+r
       ;;
+    navy-aws)
+      nice -n 19 find ${dir} -type d -print0 | xargs --null chmod a+rx
+      if [[ ${executables} -eq 1 ]]; then
+        nice -n 19 find ${dir} -type f -executable -print0 | xargs --null chmod a+rx
+      fi
+      nice -n 19 find ${dir} -type f -print0 | xargs --null chmod a+r
+      ;;
     tusk)
       nice -n 19 lfs find ${dir} -type d -print0 | xargs --null chmod a+rx
       # In case the find command returns no executables
@@ -427,6 +446,15 @@ for compiler in "${SPACK_STACK_BATCH_COMPILERS[@]}"; do
         umask 0022
         module purge
         ;;
+      navy-aws)
+        umask 0022
+        module purge
+        case ${compiler} in
+          gcc-13.3.1)
+	    module use /project/spack-stack/openmpi-4.1.8/gcc-13.3.1/modulefiles
+	    ;;
+	esac
+        ;;
       tusk)
         umask 0022
         set +e