Merge branch 'develop' into package_check_util

.github/workflows/macos-ci-aarch64.yaml

@@ -56,7 +56,9 @@ jobs:
           export SPACK_SYSTEM_CONFIG_PATH="${ENVDIR}/site"
 
           # Find external packages
-          spack external find --scope system --exclude bison --exclude openssl
+          spack external find --scope system \
+              --exclude bison --exclude openssl \
+              --exclude python
           spack external find --scope system perl
           spack external find --scope system wget
           PATH="/opt/homebrew/opt/curl/bin:$PATH" \
@@ -77,7 +79,7 @@ jobs:
           # *DH
 
           # Set compiler and MPI
-          spack config add "packages:all:providers:mpi:[openmpi@4.1.6]"
+          spack config add "packages:all:providers:mpi:[openmpi@5.0.1]"
           spack config add "packages:all:compiler:[[email protected]]"
           sed -i '' "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%apple-clang'\]/g" $ENVDIR/spack.yaml
 
@@ -136,7 +138,7 @@ jobs:
 
           module use ${ENVDIR}/install/modulefiles/Core
           module load stack-apple-clang/14.0.3
-          module load stack-openmpi/4.1.6
+          module load stack-openmpi/5.0.1
           module load stack-python/3.10.13
           module available
 

.github/workflows/macos-ci-x86_64.yaml

@@ -49,7 +49,11 @@ jobs:
           export SPACK_SYSTEM_CONFIG_PATH="${ENVDIR}/site"
 
           # Find external packages
-          spack external find --scope system --exclude bison --exclude openssl
+          spack external find --scope system \
+              --exclude bison --exclude openssl  \
+              --exclude python --exclude gettext
+          # Need to find gettext outside of default (presumed to be a system) path for krb5
+          spack external find --path=/usr/local/Cellar/gettext/0.21.1 gettext
           spack external find --scope system perl
           spack external find --scope system wget
           PATH="/usr/local/opt/curl/bin:$PATH" \
@@ -70,7 +74,7 @@ jobs:
           # *DH
 
           # Set compiler and MPI
-          spack config add "packages:all:providers:mpi:[openmpi@4.1.6]"
+          spack config add "packages:all:providers:mpi:[openmpi@5.0.1]"
           spack config add "packages:all:compiler:[[email protected]]"
           sed -i '' "s/\['\%aocc', '\%apple-clang', '\%gcc', '\%intel'\]/\['\%apple-clang'\]/g" $ENVDIR/spack.yaml
 
@@ -127,7 +131,7 @@ jobs:
 
           module use ${ENVDIR}/install/modulefiles/Core
           module load stack-apple-clang/14.0.0
-          module load stack-openmpi/4.1.6
+          module load stack-openmpi/5.0.1
           module load stack-python/3.10.13
           module available
 

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

@@ -49,7 +49,9 @@ jobs:
           export SPACK_SYSTEM_CONFIG_PATH="${ENVDIR}/site"
 
           # Find external packages
-          spack external find --scope system --exclude bison --exclude openssl
+          spack external find --scope system \
+              --exclude bison --exclude openssl \
+              --exclude python
           spack external find --scope system sed
           spack external find --scope system perl
           spack external find --scope system wget

configs/common/modules_lmod.yaml

@@ -285,5 +285,3 @@ modules:
       - PKG_CONFIG_PATH
       lib64/pkgconfig:
       - PKG_CONFIG_PATH
-      '':
-      - CMAKE_PREFIX_PATH

configs/common/modules_tcl.yaml

@@ -284,5 +284,3 @@ modules:
       - PKG_CONFIG_PATH
       lib64/pkgconfig:
       - PKG_CONFIG_PATH
-      '':
-      - CMAKE_PREFIX_PATH

configs/common/packages.yaml

@@ -40,7 +40,7 @@
     ecbuild:
       version: ['3.7.2']
     eccodes:
-      version: ['2.32.0']
+      version: ['2.33.0']
       variants: +png
     ecflow:
       version: ['5.11.4']
@@ -49,7 +49,7 @@
       version: ['1.24.5']
       variants: linalg=eigen,lapack compression=lz4,bzip2
     ecmwf-atlas:
-      version: ['0.35.1']
+      version: ['0.36.0']
       variants: +fckit +trans +tesselation +fftw
     ectrans:
       version: ['1.2.0']
@@ -113,8 +113,8 @@
       version: ['4.2.15']
       variants: +external-xdr ~fortran ~netcdf
     hdf5:
-      version: ['1.14.0']
-      variants: +hl +fortran +mpi ~threadsafe +szip
+      version: ['1.14.3']
+      variants: +hl +fortran +mpi ~threadsafe ~szip
     ip:
       version: ['4.3.0']
       variants: precision=4,d,8
@@ -124,8 +124,6 @@
       version: ['2.0.32']
     jedi-cmake:
       version: ['1.4.0']
-    jpeg:
-      version: ['9.1.0']
     landsfcutil:
       version: ['2.4.1']
     libjpeg-turbo:
@@ -148,10 +146,8 @@
       require: "+int64 +real64"
     mpich:
       variants: ~hwloc +two_level_namespace
-    mysql:
-      variants: +download_boost
     nco:
-      version: ['5.0.6']
+      version: ['5.1.6']
       variants: ~doc
     # ncview - when adding information here, also check Orion
     # and Discover site configs
@@ -166,7 +162,7 @@
     netcdf-c:
       version: ['4.9.2']
       # If using 4.9.1, turn off byterange variant to fix compile error: ~byterange
-      variants: +dap +mpi ~parallel-netcdf
+      variants: +dap +mpi ~parallel-netcdf ~szip
     netcdf-cxx4:
       version: ['4.3.1']
     netcdf-fortran:
@@ -183,17 +179,17 @@
       version: ['0.3.24']
       variants: +noavx512
     openmpi:
-      variants: +internal-hwloc +two_level_namespace
+      variants: ~internal-hwloc +two_level_namespace
     # Pin openssl to avoid duplicate packages being built
     openssl:
       variants: +shared
     p4est:
       version: ['2.8']
     parallelio:
-      version: ['2.5.10']
+      version: ['2.6.2']
       variants: +pnetcdf
     parallel-netcdf:
-      version: ['1.12.2']
+      version: ['1.12.3']
     pflogger:
       version: ['1.12.0']
       variants: +mpi
@@ -221,6 +217,9 @@
     # to avoid duplicate packages being built (cylc dependencies soft-want @3:)
     py-cython:
       require: "@0.29.36"
+    ## https://github.com/JCSDA/spack-stack/issues/980
+    #py-gitpython:
+    #  require: "@3.1.27"
     py-h5py:
       version: ['3.7.0']
       variants: ~mpi
@@ -237,9 +236,6 @@
       require: ['@1.22.3']
     py-pandas:
       variants: +excel
-    # To avoid pip._vendor.pep517.wrappers.BackendInvalid errors with newer
-    # versions of py-poetry-core when using external/homebrew Python as
-    # we do at the moment in spack-stack.
     # Pin the py-setuptools version to avoid duplicate Python packages
     py-setuptools:
       require: ['@63.4.3']
@@ -263,6 +259,7 @@
       variants: precision=4,d,8
     udunits:
       version: ['2.2.28']
+    # Note - we can remove upp from stack at some point?
     upp:
       version: ['10.0.10']
     w3emc:
@@ -278,7 +275,7 @@
     wrf-io:
       version: ['1.2.0']
     yafyaml:
-      version: ['0.5.1']
+      version: ['1.2.0']
     zlib:
       version: ['1.2.13']
     zstd:

configs/sites/derecho/compilers.yaml

@@ -17,6 +17,9 @@ compilers::
           PATH: '/opt/cray/pe/gcc/12.2.0/bin'
           CPATH: '/opt/cray/pe/gcc/12.2.0/snos/include'
           LD_LIBRARY_PATH: '/glade/u/apps/common/23.08/spack/opt/spack/intel-oneapi-compilers/2023.2.1/compiler/2023.2.1/linux/compiler/lib/intel64_lin:/opt/cray/pe/gcc/12.2.0/snos/lib:/opt/cray/pe/gcc/12.2.0/lib64'
+        set:
+          # https://github.com/JCSDA/spack-stack/issues/957
+          FI_CXI_RX_MATCH_MODE: 'hybrid'
       extra_rpaths: []
   - compiler:
       spec: [email protected]
@@ -33,6 +36,7 @@ compilers::
       - gcc/12.2.0
       environment:
         set:
-          CRAYPE_LINK_TYPE: 'dynamic'
+          # https://github.com/JCSDA/spack-stack/issues/957
+          FI_CXI_RX_MATCH_MODE: 'hybrid'
       extra_rpaths: []
 

configs/templates/skylab-dev/spack.yaml

@@ -11,6 +11,7 @@ spack:
       - ewok-env +ecflow +cylc
       - geos-gcm-env
       - jedi-fv3-env
+      - jedi-geos-env
       - jedi-mpas-env
       - jedi-neptune-env
       - jedi-ufs-env

configs/templates/ufs-weather-model-static/spack.yaml

@@ -26,13 +26,13 @@ spack:
   - [email protected]
   - [email protected]
   - [email protected]
-  - [email protected]+hl+mpi~shared~tools
+  - [email protected]+hl+mpi~shared~tools~szip
   - [email protected]
   - [email protected]~shared
   - libjpeg-turbo~shared
   - [email protected] libs=static
   - [email protected]~shared~pflogger~fargparse~extdata2g
-  - [email protected]~parallel-netcdf+mpi~shared~dap
+  - [email protected]~parallel-netcdf+mpi~shared~dap~szip
   - [email protected]~shared
   - [email protected]~shared
   - [email protected]+fortran~pnetcdf~shared

configs/templates/unified-dev/spack.yaml

@@ -14,6 +14,7 @@ spack:
       - gmao-swell-env
       - gsi-env
       - jedi-fv3-env
+      - jedi-geos-env
       - jedi-mpas-env
       - jedi-neptune-env
       - jedi-tools-env

doc/source/MaintainersSection.rst

@@ -557,7 +557,7 @@ NOAA RDHPCS Gaea C5
 On Gaea C5, ``miniconda``, ``qt``, ``ecflow``, and ``mysql`` need to be installed as a one-off before spack can be used.
 
 qt (qt@5)
-   The default ``qt@5`` in ``/usr`` is incomplete and thus insufficient for building ``ecflow``. After loading/unloading the modules as shown below, refer to :numref:`Section %s <MaintainersSection_Qt5>` to install ``[email protected]`` in ``/lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/qt-5.15.2``. :numref:`Section %s <MaintainersSection_Qt5>` describes how to export the X windows environment in order to install ``qt@5`` using the role account.
+   The default ``qt@5`` in ``/usr`` is incomplete and thus insufficient for building ``ecflow``. After loading/unloading the modules as shown below, refer to :numref:`Section %s <MaintainersSection_Qt5>` to install ``[email protected]`` in ``/ncrc/proj/epic/spack-stack/qt-5.15.2``. :numref:`Section %s <MaintainersSection_Qt5>` describes how to export the X windows environment in order to install ``qt@5`` using the role account.
 
 .. code-block:: console
 
@@ -566,22 +566,21 @@ qt (qt@5)
    module load PrgEnv-gnu/8.3.3
 
 ecflow
-  ``ecFlow`` must be built manually using the GNU compilers and linked against a static ``boost`` library. After installing `qt5` and loading the following modules, follow the instructions in :numref:`Section %s <MaintainersSection_ecFlow>`. Because of the dependency on ``miniconda``, that module must be loaded automatically in the ``ecflow`` module (similar to ``[email protected]``).  Ensure to follow the extra instructions in that section for Gaea C5 in ``/lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/ecflow-5.8.4``.
+  ``ecFlow`` must be built manually using the GNU compilers and linked against a static ``boost`` library. After installing `qt5` and loading the following modules, follow the instructions in :numref:`Section %s <MaintainersSection_ecFlow>`. Because of the dependency on ``miniconda``, that module must be loaded automatically in the ``ecflow`` module (similar to ``[email protected]``).  Ensure to follow the extra instructions in that section for Gaea C5 in ``/ncrc/proj/epic/spack-stack/ecflow-5.8.4``.
 
    Ensure to follow the extra instructions in that section for Gaea.
 
 .. code-block:: console
 
-   module unload intel-classic cray-mpich PrgEnv-intel
-   module load gcc/10.3.0
    module load PrgEnv-gnu/8.3.3
+   module use /ncrc/proj/epic/spack-stack/modulefiles/
+   module load qt/5.15.2
    module load python/3.9.12
+   module load cmake/3.23.1
 
-   module use /lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/modulefiles
-   module load qt/5.15.2
 
 mysql
-  ``mysql`` must be installed separately from ``spack`` using a binary tarball provided by the MySQL community. Follow the instructions in :numref:`Section %s <MaintainersSection_MySQL>` to install ``mysql`` in ``/lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/mysql-8.0.31``.
+  ``mysql`` must be installed separately from ``spack`` using a binary tarball provided by the MySQL community. Follow the instructions in :numref:`Section %s <MaintainersSection_MySQL>` to install ``mysql`` in ``/ncrc/proj/epic/spack-stack/mysql-8.0.36``.
 
 .. _MaintainersSection_Hera:
 

doc/source/NewSiteConfigs.rst

@@ -206,7 +206,9 @@ Remember to activate the ``lua`` module environment and have MacTeX in your sear
 
 .. code-block:: console
 
-   spack external find --scope system --exclude bison --exclude openssl
+   spack external find --scope system \
+       --exclude bison --exclude openssl \
+       --exclude python
    spack external find --scope system libiconv
    spack external find --scope system perl
    spack external find --scope system wget
@@ -249,7 +251,7 @@ Remember to activate the ``lua`` module environment and have MacTeX in your sear
    # Check your clang version then add it to your site compiler config.
    clang --version
    spack config add "packages:all:compiler:[apple-clang@YOUR-VERSION]"
-   spack config add "packages:all:providers:mpi:[openmpi@4.1.6]"
+   spack config add "packages:all:providers:mpi:[openmpi@5.0.1]"
 
 8. If applicable (depends on the environment), edit the main config file for the environment and adjust the compiler matrix to match the compilers for macOS, as above:
 
@@ -449,7 +451,7 @@ It is recommended to increase the stacksize limit by using ``ulimit -S -s unlimi
    spack external find --scope system \
        --exclude bison --exclude cmake \
        --exclude curl --exclude openssl \
-       --exclude openssh
+       --exclude openssh --exclude python
    spack external find --scope system wget
    spack external find --scope system mysql
    spack external find --scope system texlive

doc/source/PreConfiguredSites.rst

@@ -32,7 +32,7 @@ Ready-to-use spack-stack 1.6.0 installations are available on the following, ful
 +---------------------+----------------------------------+-----------------+---------------------------------------------------------------------------------------------------------+-------------------------------+
 | NOAA (NCEP)         | Acorn                            | Intel           | ``/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.6.0/envs/unified-env-intel{19,2022}``          | Hang Lei / Alex Richert       |
 +---------------------+----------------------------------+-----------------+---------------------------------------------------------------------------------------------------------+-------------------------------+
-|                     | Gaea C5                          | Intel           | ``/lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/spack-stack-1.6.0/envs/unified-env``              | Cam Book / Dom Heinzeller     |
+|                     | Gaea C5                          | Intel           | ``/ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env``                                      | Cam Book / Dom Heinzeller     |
 |                     +----------------------------------+-----------------+---------------------------------------------------------------------------------------------------------+-------------------------------+
 | NOAA (RDHPCS)       | Hera                             | GCC, Intel      | ``/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env``                     | Mark Potts / Dom Heinzeller   |
 |                     +----------------------------------+-----------------+---------------------------------------------------------------------------------------------------------+-------------------------------+
@@ -454,15 +454,15 @@ The following is required for building new spack environments and for using spac
    module load cray-mpich/8.1.25
    module load python/3.9.12
 
-   module use /lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/modulefiles
+   module use /ncrc/proj/epic/spack-stack/modulefiles
    module load ecflow/5.8.4
-   module load mysql/8.0.31
+   module load mysql/8.0.36
 
 For ``spack-stack-1.6.0`` with Intel, load the following modules after loading miniconda and ecflow:
 
 .. code-block:: console
 
-   module use /lustre/f2/dev/wpo/role.epic/contrib/spack-stack/c5/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core
+   module use /ncrc/proj/epic/spack-stack/spack-stack-1.6.0/envs/unified-env/install/modulefiles/Core
    module load stack-intel/2023.1.0
    module load stack-cray-mpich/8.1.25
    module load stack-python/3.10.13

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

@@ -213,7 +213,7 @@ def write(self):
         # Activate environment
         env = ev.Environment(manifest_dir=env_dir)
         ev.activate(env)
-        env_scope = env.env_file_config_scope_name()
+        env_scope = env.scope_name
 
         # Save original data in spack.yaml because it has higest precedence.
         # spack.config.add will overwrite as it goes.
@@ -271,7 +271,7 @@ def write(self):
             os.makedirs(env_pkgs_path, exist_ok=False)
             with open(os.path.join(env_repo_path, "repo.yaml"), "w") as f:
                 f.write("repo:\n  namespace: envrepo")
-            repo_paths = spack.config.get("repos", scope=spack.config.default_list_scope())
+            repo_paths = spack.config.get("repos")
             repo_paths = [p.replace("$spack/", spack.paths.spack_root + "/") for p in repo_paths]
             for pkg_name in self.modifypkg:
                 pkg_found = False

spack-ext/lib/jcsda-emc/spack-stack/tests/test_setup_meta_modules.py

@@ -49,7 +49,7 @@ def test_setup_meta_modules():
 
     # Setup env and pretend that a build exists
     # by creating the module directory structure.
-    scope = env.env_file_config_scope_name()
+    scope = env.scope_name
     spack.config.add("packages:all:compiler:[{}]".format(comp), scope=scope)
     spack.config.add("packages:all:providers:mpi:[{}]".format(mpi), scope=scope)
     spack.config.add("packages:openmpi:version:[{}]".format(mpi_ver))

spack-ext/repos/spack-stack/packages/jedi-mpas-env/package.py

@@ -18,5 +18,6 @@ class JediMpasEnv(BundlePackage):
 
     depends_on("jedi-base-env", type="run")
     depends_on("metis", type="run")
+    depends_on("jasper", type="run")
 
     # There is no need for install() since there is no code.