Update release/1.3.1 (starting from release/1.3.0) (#549)

* Update .gitmodules and submodule pointer for spack for code review and testing

* Update many versions in configs/common/packages.yaml and configs/templates/skylab-dev/spack.yaml, and remove ufs-weather-model~debug from configs/templates/unified-dev/spack.yaml and configs/templates/ufs-weather-model/spack.yaml

* Update containers for new versions in release 1.3.1

* Replace gsibec@1.1.1 with gsibec@1.1.2 (bug fix)

* Update submodule pointer for spack

* Missing updates for containers

* Update .gitmodules and container configs

* More documentation updates

* More documentation updates

* Add 'spack clean -a' to github CI workflows

* Add more 'spack clean -a' to github CI workflows

* Remove useless 'spack clean -a' from CI tests

* Update configs/containers/README.md

* Add missing jedi-mpas-env to configs/templates/unified-dev/spack.yaml

* Update .gitmodules and submodule pointer for spack

* Finalize container config and documentation

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

@@ -46,6 +46,7 @@ jobs:
       - name: create-env
         run: |
           source ./setup.sh
+
           # DH* 20230302 - to avoid using padded_length for build caches,
           # always build in the same environment so that the length of the
           # path doesn't change - see also other 'DH* 20230302' changes below

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

@@ -46,6 +46,7 @@ jobs:
       - name: create-env
         run: |
           source ./setup.sh
+
           # DH* 20230302 - to avoid using padded_length for build caches,
           # always build in the same environment so that the length of the
           # path doesn't change - see also other 'DH* 20230302' changes below

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "spack"]
   path = spack
   url = https://github.com/NOAA-EMC/spack
-  branch = spack-stack-1.3.0
+  branch = spack-stack-1.3.1
 [submodule "doc/CMakeModules"]
   path = doc/CMakeModules
   url = https://github.com/noaa-emc/cmakemodules

configs/common/packages.yaml

@@ -35,17 +35,17 @@
       version: [2.4.0]
       variants: +fix
     ecbuild:
-      version: [3.6.5]
+      version: [3.7.2]
     eccodes:
       version: [2.27.0]
     ecflow:
       version: [5.8.4]
       variants: +ui
     eckit:
-      version: [1.20.2]
+      version: [1.23.0]
       variants: linalg=eigen,lapack compression=lz4,bzip2
     ecmwf-atlas:
-      version: [0.32.1]
+      version: [0.33.0]
       variants: +fckit +trans
     ectrans:
       version: [1.2.0]
@@ -62,7 +62,7 @@
       version: [8.3.0b09]
       variants: ~xerces ~pnetcdf +pio snapshot=b09 ~shared
     fckit:
-      version: [0.10.0]
+      version: [0.10.1]
       variants: +eckit
     fftw:
       version: [3.3.10]
@@ -90,14 +90,14 @@
     grib-util:
       version: [1.2.3]
     gsibec:
-      version: [1.0.7]
+      version: [1.1.2]
     gsl-lite:
       version: [0.37.0]
     hdf:
       version: [4.2.15]
       variants: ~fortran ~netcdf
     hdf5:
-      version: [1.14.0]
+      version: [1.12.2]
       variants: +hl +fortran +mpi ~threadsafe +szip
     ip:
       version: [3.3.3]
@@ -155,7 +155,7 @@
     nlohmann-json-schema-validator:
       version: [2.1.0]
     odc:
-      version: [1.4.5]
+      version: [1.4.6]
       variants: ~fortran
     openblas:
       version: [0.3.19]
@@ -184,7 +184,7 @@
     py-eccodes:
       version: [1.4.2]
     py-h5py:
-      version: [3.7.0]
+      version: [3.6.0]
       variants: ~mpi
     # Comment out for now until build problems are solved
     # https://github.com/NOAA-EMC/spack-stack/issues/522

configs/containers/README.md

@@ -2,20 +2,20 @@
 
 To avoid hardcoding specs in the generic container recipes, we keep the specs list empty (`specs: []`) and manually add the specs for the particular spack-stack release and application as listed below, *after* running `spack stack create ctr`.
 
-### spack-stack-1.3.0 / skylab-4.0.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
+### spack-stack-1.3.1 / skylab-4.0.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
 ```
   specs: [base-env@1.0.0, jedi-base-env@1.0.0 ~fftw, jedi-ewok-env@1.0.0, jedi-fv3-env@1.0.0,
-    jedi-mpas-env@1.0.0, bacio@2.4.1, bison@3.8.2, bufr@11.7.1, ecbuild@3.6.5, eccodes@2.27.0, ecflow@5,
-    eckit@1.20.2, ecmwf-atlas@0.32.1 +trans ~fftw, ectrans@1.2.0 ~fftw, eigen@3.4.0,
-    fckit@0.10.0, fms@release-jcsda, g2@3.4.5, g2tmpl@1.10.0, gftl-shared@1.5.0,
-    gsibec@1.0.7, hdf@4.2.15, hdf5@1.14.0, ip@3.3.3, jasper@2.0.32, jedi-cmake@1.4.0,
+    jedi-mpas-env@1.0.0, bacio@2.4.1, bison@3.8.2, bufr@11.7.1, ecbuild@3.7.2, eccodes@2.27.0, ecflow@5,
+    eckit@1.23.0, ecmwf-atlas@0.33.0 +trans ~fftw, ectrans@1.2.0 ~fftw, eigen@3.4.0,
+    fckit@0.10.1, fms@release-jcsda, g2@3.4.5, g2tmpl@1.10.0, gftl-shared@1.5.0,
+    gsibec@1.1.2, hdf@4.2.15, hdf5@1.12.2, ip@3.3.3, jasper@2.0.32, jedi-cmake@1.4.0,
     libpng@1.6.37, nccmp@1.9.0.1, netcdf-c@4.9.2, netcdf-cxx4@4.3.1,
     netcdf-fortran@4.6.0, nlohmann-json@3.10.5, nlohmann-json-schema-validator@2.1.0,
     parallelio@2.5.9, parallel-netcdf@1.12.2, py-eccodes@1.4.2, py-f90nml@1.4.3,
-    py-gitpython@3.1.27, py-numpy@1.22.3,
+    py-gitpython@3.1.27, py-h5py@3.6.0, py-numpy@1.22.3,
     py-pandas@1.4.0, py-pip, py-pyyaml@6.0, py-scipy@1.9.3, py-shapely@1.8.0, py-xarray@2022.3.0,
     sp@2.3.3, udunits@2.2.28, w3nco@2.4.1, nco@5.0.6,
-    yafyaml@0.5.1, zlib@1.2.13, odc@1.4.5, crtm@v2.4-jedi.2, shumlib@macos_clang_linux_intel_port]
+    yafyaml@0.5.1, zlib@1.2.13, odc@1.4.6, crtm@v2.4.1-jedi, shumlib@macos_clang_linux_intel_port]
     # Don't build ESMF and MAPL for now:
     # https://github.com/JCSDA-internal/MPAS-Model/issues/38
     # https://github.com/NOAA-EMC/spack-stack/issues/326
@@ -25,9 +25,28 @@ To avoid hardcoding specs in the generic container recipes, we keep the specs li
     # py-mysql-connector-python@8.0.32, 
 ```
 
+### spack-stack-1.3.1 / ufs-weather-model-x.y.z containers for ufs-weather-model as of April 18, 2023
+
+**Note. This is not yet working correctly, some libraries are missing. Please do not use yet! Also, if using the clang-mpich container, need to disable openmp for fms, not clear how to do this cleanly.**
+
+```
+  specs: [base-env@1.0.0,
+    bacio@2.4.1, bison@3.8.2, bufr@11.7.1, ecbuild@3.7.2, eccodes@2.27.0, ecflow@5,
+    eckit@1.23.0, ecmwf-atlas@0.33.0 +trans ~fftw, ectrans@1.2.0 ~fftw, eigen@3.4.0,
+    fckit@0.10.1, fms@2022.04, g2@3.4.5, g2tmpl@1.10.0, gftl-shared@1.5.0,
+    gsibec@1.1.2, hdf@4.2.15, hdf5@1.12.2, ip@3.3.3, jasper@2.0.32, jedi-cmake@1.4.0,
+    libpng@1.6.37, nccmp@1.9.0.1, netcdf-c@4.9.2, netcdf-cxx4@4.3.1,
+    netcdf-fortran@4.6.0, nlohmann-json@3.10.5, nlohmann-json-schema-validator@2.1.0,
+    parallelio@2.5.9, parallel-netcdf@1.12.2, py-eccodes@1.4.2, py-f90nml@1.4.3,
+    py-gitpython@3.1.27, py-h5py@3.6.0, py-numpy@1.22.3, py-pandas@1.4.0,
+    py-pip, py-pyyaml@6.0, py-scipy@1.9.3, py-shapely@1.8.0, py-xarray@2022.3.0,
+    sp@2.3.3, udunits@2.2.28, w3emc@2.9.2, w3nco@2.4.1, nco@5.0.6, esmf@8.3.0b09, mapl@2.22.0,
+    yafyaml@0.5.1, zlib@1.2.13, odc@1.4.6, crtm@2.4.0, crtm-fix@2.4.0_emc]
+```
+
 ### Create an AMI on AWS EC2 to build docker containers
 
-AMI ami-0b5951b8be1fe5709 (dom-docker-builder-full-backup-20221221; JCSDA-NOAA account, us-east-1) was created following the instructions below
+AMI ami-0a934b7133c2b7102 (dom-docker-builder-full-backup-20230217; JCSDA-NOAA account, us-east-1) was created following the instructions below
 
 - See https://docs.docker.com/desktop/install/ubuntu/
 - Start with ami-052efd3df9dad4825

configs/containers/docker-ubuntu-clang-mpich.yaml

@@ -101,7 +101,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/noaa-emc/spack
-        ref: spack-stack-1.3.0
+        ref: spack-stack-1.3.1
         resolve_sha: false
 
     # Whether or not to strip binaries

configs/containers/docker-ubuntu-gcc-openmpi.yaml

@@ -88,7 +88,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/noaa-emc/spack
-        ref: spack-stack-1.3.0
+        ref: spack-stack-1.3.1
         resolve_sha: false
 
     # Whether or not to strip binaries

configs/containers/docker-ubuntu-intel-impi.yaml

@@ -106,7 +106,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/noaa-emc/spack
-        ref: spack-stack-1.3.0
+        ref: spack-stack-1.3.1
         resolve_sha: false
 
     # Whether or not to strip binaries

configs/templates/skylab-dev/spack.yaml

@@ -21,20 +21,20 @@ spack:
     - bufr@11.7.1
     - crtm@2.3.0
     - crtm@2.4.0
-    - crtm@v2.3-jedi.4
     - crtm@v2.4-jedi.2
+    - crtm@v2.4.1-jedi
     - crtm@v3.0.0-rc.1
-    - ecbuild@3.6.5
+    - ecbuild@3.7.2
     - eccodes@2.27.0
     - ecflow@5
-    - eckit@1.20.2
-    - ecmwf-atlas@0.32.1
+    - eckit@1.23.0
+    - ecmwf-atlas@0.33.0
     - ectrans@1.2.0
     - eigen@3.4.0
     - esmf@8.3.0b09
     # DH* fake version number
     #- ewok@0.0.1
-    - fckit@0.10.0
+    - fckit@0.10.1
     - fiat@1.1.0
     # Do not request specific version of flex - this leads to duplicate packages being built
     #- flex@2.6.4
@@ -46,9 +46,9 @@ spack:
     #- gdal@3.4.3
     #- geos@3.9.1
     - gftl-shared@1.5.0
-    - gsibec@1.0.7
+    - gsibec@1.1.2
     - hdf@4.2.15
-    - hdf5@1.14.0
+    - hdf5@1.12.2
     - ip@3.3.3
     - jasper@2.0.32
     - jedi-cmake@1.4.0
@@ -62,11 +62,12 @@ spack:
     - netcdf-fortran@4.6.0
     - nlohmann-json@3.10.5
     - nlohmann-json-schema-validator@2.1.0
-    - odc@1.4.5
+    - odc@1.4.6
     - parallelio@2.5.9
     - parallel-netcdf@1.12.2
     - py-eccodes@1.4.2
     - py-f90nml@1.4.3
+    - py-h5py@3.6.0
     - py-numpy@1.22.3
     - py-pandas@1.4.0
     - py-pyyaml@6.0

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

@@ -16,4 +16,3 @@ spack:
 
   specs:
     - ufs-weather-model-env~debug
-    - ufs-weather-model-env+debug

configs/templates/unified-dev/spack.yaml

@@ -12,15 +12,15 @@ spack:
       #- gsi-env@unified-dev
       - jedi-ewok-env@unified-dev
       - jedi-fv3-env@unified-dev
+      - jedi-mpas-env@unified-dev
       - jedi-tools-env@unified-dev
       - jedi-ufs-env@unified-dev
       - jedi-um-env@unified-dev
       #- nceplibs-env@unified-dev
       - soca-env@unified-dev
       - ufs-srw-app-env@unified-dev
       #- ufs-utils-env@unified-dev
-      - ufs-weather-model-env~debug@unified-dev
-      - ufs-weather-model-env+debug@unified-dev
+      - ufs-weather-model-env@unified-dev
       #- upp-env@unified-dev
       #- ww3-env@unified-dev