Update crtm-fix: link little endian and test files; run more tests for crtm and ufo; update NRL batch install to run tests

.gitmodules

@@ -4,5 +4,7 @@
   branch = spack-stack-dev
 [submodule "repos/builtin"]
   path = repos/builtin
-  url = https://github.com/jcsda/spack-packages
-  branch = spack-stack-dev
+  #url = https://github.com/jcsda/spack-packages
+  #branch = spack-stack-dev
+  url = https://github.com/climbfuji/spack-packages
+  branch = bugfix/crtm_fix_link_instead_of_flatten

configs/common/packages.yaml

@@ -87,6 +87,12 @@ packages:
     codee:
       require:
       - '@2025.4.7'
+    crtm_fix:
+      require:
+      - ~link-big-endian
+      - +link-little-endian
+      - +link-netcdf
+      - +link-testfiles
     # Attention - when updating also check the various jcsda-emc-bundles env packages
     crtm:
       require:

configs/sites/tier1/blueback/config.yaml

@@ -1,2 +1,2 @@
 config:
-  build_jobs: 8
+  build_jobs: 2

configs/sites/tier1/narwhal/config.yaml

@@ -1,2 +1,2 @@
 config:
-  build_jobs: 8
+  build_jobs: 2

configs/sites/tier1/nautilus/config.yaml

@@ -1,2 +1,2 @@
 config:
-  build_jobs: 8
+  build_jobs: 2

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

@@ -104,55 +104,38 @@ def setup_build_environment(self, env: EnvironmentModifications) -> None:
     def check(self):
         skipped_tests = None
         with when("@1.10.0.20250821"):
-            skipped_tests = [
-                "ufo_test_tier1_test_ufo_tropics_qc_filters",
-            ]
-            # Until issues with crtm fixed data organization are
-            # resolved, exclude any tests using crtm fixed data
-            skipped_tests += [
-                "_crtm",
-                "ufo_test_tier1_test_ufo_atms_skylab_filters",
-                "ufo_test_tier1_test_ufo_amsr2_qc",
-                "ufo_test_tier1_test_ufo_amsua_qc",
-                "ufo_test_tier1_test_ufo_amsua_allsky_gfs_gsi_qc",
-                "ufo_test_tier1_test_ufo_amsua_allsky_gsi_qc",
-                "ufo_test_tier1_test_ufo_amsua_qc_clwretmw",
-                "ufo_test_tier1_test_ufo_amsua_qc_filters",
-                "ufo_test_tier1_test_ufo_amsua_qc_filters_geos",
-                "ufo_test_tier1_test_ufo_amsua_qc_miss_val",
-                "ufo_test_tier1_test_ufo_atms_qc_filters",
-                "ufo_test_tier1_test_ufo_atms_n20_qc_filters_geos",
-                "ufo_test_tier1_test_ufo_cris_qc",
-                "ufo_test_tier1_test_ufo_cris_qc_land",
-                "ufo_test_tier1_test_ufo_amsr2_qc_filters",
-                "ufo_test_tier1_test_ufo_gmi_skylab_filters",
-                "ufo_test_tier1_test_ufo_gmi_qc_filters",
-                "ufo_test_tier1_test_ufo_gmi_qc_filters_geos",
-                "ufo_test_tier1_test_ufo_mhs_qc_filters_geos",
-                "ufo_test_tier1_test_ufo_qc_flags_true",
-                "ufo_test_tier1_test_ufo_gmi_clw_ret",
-                "ufo_test_tier1_test_ufo_ssmis_f17_gfs_backgroundcheck_bc",
-                "ufo_test_tier1_test_ufo_ssmis_f17_gfs_backgroundcheck_nbc",
-            ]
-            # Additional test failures with Intel oneAPI only
+            skipped_tests = []
             if self.spec.satisfies("%oneapi"):
                 skipped_tests += [
                     "ufo_test_tier1_test_ufo_obserrorcrossvarcorr",
                     "ufo_test_tier1_test_ufo_obserrorwithingroupcorr",
                     "ufo_test_tier1_test_ufo_obserrordiagonal",
+                    "ufo_test_tier1_test_ufo_gnssrobendmetoffice_qc",
                     "ufo_test_tier1_test_ufo_gnssrobendmetoffice_qc_profile",
+                    "ufo_test_tier1_test_ufo_gnssrobendmetoffice_obserror",
                     "ufo_test_tier1_test_ufo_gnssrorefmetoffice_qc",
                     "ufo_test_tier1_test_ufo_gnssrobndnbam_qc",
                     "ufo_test_tier1_test_ufo_gnssro_obs_error",
+                    "ufo_test_tier1_test_ufo_gnssro_super_refraction_check",
                     "ufo_test_tier1_test_ufo_qc_modelbestfitpressure",
                     "ufo_test_tier1_test_ufo_satwind_inversion_correction",
+                    "ufo_test_tier1_test_ufo_amsua_allsky_gfs_gsi_qc",
+                    "ufo_test_tier1_test_ufo_cris_qc",
+                    "ufo_test_tier1_test_ufo_cris_qc_land",
+                    "ufo_test_tier1_test_ufo_qc_flags_true",
                     "ufo_test_tier1_test_ufo_function_averagetemperaturebelow",
                     "ufo_test_tier1_test_ufo_function_assignvalueequalchannels",
                     "ufo_test_tier1_test_ufo_fov_amsua",
                     "ufo_test_tier1_test_ufo_sample_and_reduce_over_fov",
                     "ufo_test_tier1_test_ufo_opr_gnssrorefmetoffice",
                     "ufo_test_tier1_test_ufo_linopr_gnssrorefmetoffice",
+                    "ufo_test_tier1_test_ufo_opr_gnssrobendmetoffice",
+                    "ufo_test_tier1_test_ufo_linopr_gnssrobendmetoffice",
+                    "ufo_test_tier1_test_ufo_opr_gnssrobendmetoffice_nopseudo",
+                    "ufo_test_tier1_test_ufo_linopr_gnssrobendmetoffice_nopseudo",
                     "ufo_test_tier1_test_ufo_opr_gnssrobendmetoffice_profile",
+                    "ufo_test_tier1_test_ufo_opr_gnssrobendmetoffice_nosupercheck",
+                    "ufo_test_tier1_test_ufo_linopr_gnssrobendmetoffice_nosupercheck",
                     "ufo_test_tier1_test_ufo_opr_groundgnssmetoffice",
                     "ufo_test_tier1_test_ufo_linopr_groundgnssmetoffice",
                     "ufo_test_tier1_test_ufo_opr_logarithm",
@@ -162,15 +145,23 @@ def check(self):
                     "ufo_test_tier1_test_ufo_opr_seaicefrac",
                     "ufo_test_tier1_test_ufo_linopr_seaicefrac",
                     "ufo_test_tier1_test_ufo_opr_sfcpcorrected",
-                    "ufo_test_tier1_test_ufo_gnssrobendmetoffice_qc",
-                    "ufo_test_tier1_test_ufo_gnssrobendmetoffice_obserror",
-                    "ufo_test_tier1_test_ufo_gnssro_super_refraction_check",
-                    "ufo_test_tier1_test_ufo_opr_gnssrobendmetoffice",
-                    "ufo_test_tier1_test_ufo_linopr_gnssrobendmetoffice",
-                    "ufo_test_tier1_test_ufo_opr_gnssrobendmetoffice_nopseudo",
-                    "ufo_test_tier1_test_ufo_linopr_gnssrobendmetoffice_nopseudo",
-                    "ufo_test_tier1_test_ufo_opr_gnssrobendmetoffice_nosupercheck",
-                    "ufo_test_tier1_test_ufo_linopr_gnssrobendmetoffice_nosupercheck",
+                    "ufo_test_tier1_test_ufo_opr_abi_ahi_crtm",
+                    "ufo_test_tier1_test_ufo_linopr_abi_ahi_crtm",
+                    "ufo_test_tier1_test_ufo_opr_airs_crtm",
+                    "ufo_test_tier1_test_ufo_linopr_airs_crtm",
+                    "ufo_test_tier1_test_ufo_opr_crtm_vis_albedo",
+                    "ufo_test_tier1_test_ufo_opr_cris_crtm",
+                    "ufo_test_tier1_test_ufo_linopr_cris_crtm",
+                    "ufo_test_tier1_test_ufo_opr_cris_crtm_co2_options",
+                    "ufo_test_tier1_test_ufo_linopr_cris_crtm_co2_options",
+                    "ufo_test_tier1_test_ufo_opr_hirs4_crtm",
+                    "ufo_test_tier1_test_ufo_linopr_hirs4_crtm",
+                    "ufo_test_tier1_test_ufo_opr_iasi_crtm",
+                    "ufo_test_tier1_test_ufo_opr_seviri_crtm",
+                    "ufo_test_tier1_test_ufo_linopr_seviri_crtm",
+                    "ufo_test_tier1_test_ufo_opr_sndrd1-4_crtm",
+                    "ufo_test_tier1_test_ufo_linopr_sndrd1-4_crtm",
+                    "ufo_test_tier1_test_ufo_obsdiag_crtm_airs_optics",
                 ]
         ctest = Executable(self.spec["cmake"].prefix.bin.ctest)
         with working_dir(self.build_directory):

util/nrl/batch_install.sh

@@ -5,6 +5,19 @@ SPACK_STACK_DIR=$(dirname $(dirname ${SCRIPT_DIR}))
 
 set -e
 
+##################################################################################################
+# Packages for which to run tests when "-t" is specified; caveat: must be listed in order of     #
+# their respective dependencies (e.g. A depends on B --> B comes first)                          #
+##################################################################################################
+
+SPACK_STACK_PACKAGES_TO_TEST=(
+  "oops"
+  "ioda"
+  "ioda-converters"
+  "ropp-ufo"
+  "ufo"
+)
+
 ##################################################################################################
 # Options                                                                                        #
 ##################################################################################################
@@ -26,11 +39,13 @@ usage() {
   echo "      requires role 'dev' and mode 'build'"
   echo "  -e  Continue builds/install in existing environments;"
   echo "      by default, exit with an error if already exist"
+  echo "  -t  Run tests for specific thirdparty dependencies;"
+  echo "      these are currently hardcoded in batch_install.sh"
   echo "  -h  display this help"
   echo
 }
 
-while getopts r:m:d:c:uhe flag
+while getopts r:m:d:c:ueth flag
 do
   case "${flag}" in
     r)
@@ -51,6 +66,9 @@ do
     e)
       SPACK_STACK_IGNORE_ENV_EXIST="true"
       ;;
+    t)
+      SPACK_STACK_RUN_TESTS="true"
+      ;;
     *)
       usage
       exit 1
@@ -65,6 +83,7 @@ echo "  SPACK_STACK_ENVIRONMENT_DIRS:                ${SPACK_STACK_ENVIRONMENT_D
 echo "  SPACK_STACK_BUILDCACHE_DIR:                  ${SPACK_STACK_BUILDCACHE_DIR:-use default caches}"
 echo "  SPACK_STACK_UPDATE_DEV_CACHES:               ${SPACK_STACK_UPDATE_DEV_CACHES:-false}"
 echo "  SPACK_STACK_IGNORE_ENV_EXIST:                ${SPACK_STACK_IGNORE_ENV_EXIST:-false}"
+echo "  SPACK_STACK_RUN_TESTS:                       ${SPACK_STACK_RUN_TESTS:-false}"
 
 if [[ -z ${SPACK_STACK_ROLE} ]]; then
   echo "ERROR, SPACK_STACK_ROLE not defined. Provide -r ROLE as argument"
@@ -332,6 +351,12 @@ fi
 
 ignore_env_exist=${SPACK_STACK_IGNORE_ENV_EXIST:-false}
 
+if [[ "${SPACK_STACK_RUN_TESTS}" == "true" ]]; then
+  test_packages=("${SPACK_STACK_PACKAGES_TO_TEST[@]}")
+else
+  test_packages=()
+fi
+
 # Loop through all compilers and templates for this host
 first_pass="true"
 for compiler in "${SPACK_STACK_BATCH_COMPILERS[@]}"; do
@@ -607,10 +632,31 @@ for compiler in "${SPACK_STACK_BATCH_COMPILERS[@]}"; do
         exit 1
         ;;
     esac
-    spack install --verbose ${buildcache_install_flags} 2>&1 | tee log.install.${env_name}.001
 
-    # Run another spack install without redirects to catch build errors
-    spack install
+    # If no tests are required, install everything
+    if [[ ${#test_packages[@]} -eq 0 ]]; then
+      set -o pipefail
+      spack install --verbose ${buildcache_install_flags} 2>&1 | tee log.install.${env_name}.001
+      set +o pipefail
+    else
+      for (( idx=0; idx<${#test_packages[@]}; idx++ )); do
+        test_package=${test_packages[$idx]}
+        # First, check if this package is in this environment
+        set +e
+        grep -e "${test_package}@" log.concretize.${env_name}.001 || continue
+        set -e
+        idx_padded=$(printf "%03d" "$((idx+1))")
+        set -o pipefail
+        spack install --verbose ${buildcache_install_flags} --only=dependencies ${test_package} 2>&1 | tee log.install.${env_name}.${idx_padded}.${test_package}-dependencies
+        spack install --verbose --no-cache --test=root ${test_package} 2>&1 | tee log.install.${env_name}.${idx_padded}.${test_package}
+        set +o pipefail
+      done
+      # idx now equals the length of the array; install the rest
+      idx_padded=$(printf "%03d" "$((idx+1))")
+      set -o pipefail
+      spack install --verbose ${buildcache_install_flags} 2>&1 | tee log.install.${env_name}.${idx_padded}
+      set +o pipefail
+    fi
 
     # In build mode, update local binary cache
     if [[ "${update_build_cache}" == "true" ]]; then