release/1.5.1: add fms@2023.03, site config updates round 3 (#855)

* Update site configs for NOAA Parallel Works
* Update casper site config and build documentation
* Update container specs in configs/containers/README.md
* Update Hercules site config (gnu@12, mvapich2@2.3.7)
* Update  doc/source/PreConfiguredSites.rst for casper, hera, gaea-c4, jet
* Add fms@2023.03 in spack submodule, add to unified-dev and skylab-dev templates
* Update configs/containers after tagging spack submodule as spack-stack-1.5.1
* Update documentation for AWS AMI release 1.5.1
* Update macOS section in doc/source/NewSiteConfigs.rst to match Linux section

Author: climbfuji

.gitmodules

@@ -3,7 +3,7 @@
   #url = https://github.com/spack/spack
   #branch = develop
   url = https://github.com/jcsda/spack
-  branch = release/1.5.1
+  branch = spack-stack-1.5.1
 [submodule "doc/CMakeModules"]
   path = doc/CMakeModules
   url = https://github.com/noaa-emc/cmakemodules

configs/common/packages.yaml

@@ -28,6 +28,7 @@
       variants: +pic
     # Newer versions of CDO require the C++-17 standard, which doesn't
     # work with all compilers that are currently in use in spack-stack
+    # When making changes here, also check Hercules/Casper site configs
     cdo:
       version: ['2.0.5']
       variants: ~openmp

configs/containers/README.md

@@ -2,25 +2,24 @@
 
 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-1.5.0 / skylab-6.0.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
+### spack-stack-1.5.1 / skylab-6.1.0 containers for fv3-jedi and mpas-jedi (but not for ufs-jedi)
 ```
   specs: [base-env@1.0.0, jedi-base-env@1.0.0, 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@12.0.0, ecbuild@3.7.2, eccodes@2.27.0, ecflow@5,
     eckit@1.24.4, ecmwf-atlas@0.35.0 +fckit +ectrans +tesselation +fftw, fiat@1.2.0, ectrans@1.2.0 +fftw,
-    eigen@3.4.0, fckit@0.11.0, fms@release-jcsda, g2@3.4.5, g2tmpl@1.10.0, gftl-shared@1.5.0,
+    eigen@3.4.0, fckit@0.11.0, fms@release-jcsda, g2@3.4.5, g2tmpl@1.10.0, gftl-shared@1.6.1,
     gsibec@1.1.3, hdf@4.2.15, hdf5@1.14.0, ip@4.3.0, 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@2.5.10, parallel-netcdf@1.12.2, py-eccodes@1.4.2, py-f90nml@1.4.3,
     py-gitpython@3.1.27, py-h5py@3.7.0, py-numpy@1.22.3,
     py-pandas@1.5.3, py-pip, py-pyyaml@5.4.1, 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, w3emc@2.10.0, nco@5.0.6, esmf@8.4.2, mapl@2.35.2,
-    yafyaml@0.5.1, zlib@1.2.13, zstd@1.5.2, odc@1.4.6, shumlib@macos_clang_linux_intel_port,
+    sp@2.3.3, udunits@2.2.28, w3nco@2.4.1, w3emc@2.10.0, nco@5.0.6, esmf@8.5.0, mapl@2.40.3,
+    zlib@1.2.13, zstd@1.5.2, odc@1.4.6, shumlib@macos_clang_linux_intel_port,
     awscli@1.27.84, py-globus-cli@3.16.0]
     # Notes:
-    # 1. Remove mapl@2.35.2 from clang/mpich container, because mapl doesn't work with mpich@4
-    # 2. Don't build CRTM by default so that it gets built in the JEDI bundles
-    # 3. Comment out for now until build problems are solved
+    # 1. Don't build CRTM by default so that it gets built in the JEDI bundles
+    # 2. Comment out for now until build problems are solved
     #    https://github.com/jcsda/spack-stack/issues/522
     #    py-mysql-connector-python@8.0.32
 ```

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

@@ -110,7 +110,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/jcsda/spack
-        ref: release/1.5.1
+        ref: spack-stack-1.5.1
         resolve_sha: false
 
     # Whether or not to strip binaries

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

@@ -98,7 +98,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/jcsda/spack
-        ref: release/1.5.1
+        ref: spack-stack-1.5.1
         resolve_sha: false
 
     # Whether or not to strip binaries

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

@@ -116,7 +116,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/jcsda/spack
-        ref: release/1.5.1
+        ref: spack-stack-1.5.1
         resolve_sha: false
 
     # Whether or not to strip binaries

configs/sites/casper/compilers.yaml

@@ -1,24 +1,15 @@
 compilers::
   - compiler:
-      spec: intel@2022.0.2
+      spec: gcc@12.2.0
       paths:
-        cc: /glade/u/apps/opt/intel/2022.1/compiler/2022.0.2/linux/bin/intel64/icc
-        cxx: /glade/u/apps/opt/intel/2022.1/compiler/2022.0.2/linux/bin/intel64/icpc
-        f77: /glade/u/apps/opt/intel/2022.1/compiler/2022.0.2/linux/bin/intel64/ifort
-        fc: /glade/u/apps/opt/intel/2022.1/compiler/2022.0.2/linux/bin/intel64/ifort
+        cc: /glade/u/apps/casper/23.10/spack/opt/spack/gcc/12.2.0/pucl/bin/gcc
+        cxx: /glade/u/apps/casper/23.10/spack/opt/spack/gcc/12.2.0/pucl/bin/g++
+        f77: /glade/u/apps/casper/23.10/spack/opt/spack/gcc/12.2.0/pucl/bin/gfortran
+        fc: /glade/u/apps/casper/23.10/spack/opt/spack/gcc/12.2.0/pucl/bin/gfortran
       flags: {}
-      operating_system: centos7
+      operating_system: opensuse15
       target: x86_64
       modules:
-      - intel/2022.1
-      environment:
-        prepend_path:
-          PATH: '/glade/work/epicufsrt/contrib/spack-stack/casper/gcc-10.1.0/bin'
-          CPATH: '/glade/work/epicufsrt/contrib/spack-stack/casper/gcc-10.1.0/include'
-          LD_LIBRARY_PATH: '/glade/u/apps/opt/intel/2022.1/compiler/latest/linux/compiler/lib/intel64_lin:/glade/u/apps/opt/intel/2022.1/mpi/2021.5.1/libfabric/lib:/glade/work/epicufsrt/contrib/spack-stack/casper/gcc-10.1.0/lib64'
-        set:
-          INTEL_LICENSE_FILE: '28518@128.117.177.41'
-          LM_LICENSE_FILE: '28518@128.117.177.41'
-          I_MPI_ROOT: '/glade/u/apps/opt/intel/2022.1/mpi/2021.5.1'
-
+      - gcc/12.2.0
+      environment: {}
       extra_rpaths: []

configs/sites/casper/packages.yaml

@@ -1,45 +1,53 @@
 packages:
   all:
-    compiler:: [intel@2022.0.2]
+    compiler:: [gcc@12.2.0]
     providers:
-      mpi:: [intel-oneapi-mpi@2021.5.1]
+      mpi:: [openmpi@4.1.6]
 
 ### MPI, Python, MKL
   mpi:
     buildable: False
-  intel-oneapi-mpi:
+  openmpi:
     externals:
-    - spec: intel-oneapi-mpi@2021.5.1%intel@2022.0.2
-      prefix: /glade/u/apps/opt/intel/2022.1
+    - spec: openmpi@4.1.6%gcc@12.2.0+cuda~cxx~cxx_exceptions~java+lustre~memchecker+pmi+static~wrapper-rpath fabrics=ucx schedulers=tm
+      prefix: /glade/u/apps/casper/23.10/spack/opt/spack/openmpi/4.1.6/gcc/12.2.0/yia4
       modules:
-      - intel-oneapi-mpi/2021.5.1.lua
+      - openmpi/4.1.6
+      - ucx/1.14.1
+      - cuda/12.2.1
 
-### Modification of common packages
-  # Default gdal (3.7.0) doesn't build on Casper with intel@2022.0.2
-  gdal:
-    version:: ['3.6.3']
+### Modifications of common packages
+  # Version 2.0.5 doesn't compile on Hercules with gcc
+  cdo
+    version:: ['2.2.0']
 
 ### All other external packages listed alphabetically
   autoconf:
     externals:
-    - spec: autoconf@2.69
-      prefix: /usr
+    - spec: autoconf@2.71
+      prefix: /glade/u/apps/casper/23.10/opt/view
   automake:
     externals:
-    - spec: automake@1.13.4
+    - spec: automake@1.16.5
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: automake@1.15.1
       prefix: /usr
   berkeley-db:
     externals:
     - spec: berkeley-db@4.7.25
       prefix: /usr
   binutils:
     externals:
-    - spec: binutils@2.27.43
+    - spec: binutils@2.41.0
       prefix: /usr
   bzip2:
     externals:
     - spec: bzip2@1.0.6
       prefix: /usr
+  coreutils:
+    externals:
+    - spec: coreutils@8.32
+      prefix: /usr
   cmake:
     externals:
     - spec: cmake@3.16.8
@@ -53,19 +61,21 @@ packages:
       prefix: /usr
   cvs:
     externals:
-    - spec: cvs@1.11.23
+    - spec: cvs@1.12.13
       prefix: /usr
   curl:
     externals:
-    - spec: curl@7.29.0+gssapi+ldap+nghttp2
+    - spec: curl@8.1.2+nghttp2
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: curl@8.0.1+gssapi+ldap+nghttp2
       prefix: /usr
   diffutils:
     externals:
     - spec: diffutils@3.3
       prefix: /usr
   doxygen:
     externals:
-    - spec: doxygen@1.8.5+graphviz~mscgen
+    - spec: diffutils@3.6
       prefix: /usr
   ecflow:
     buildable: False
@@ -74,23 +84,19 @@ packages:
       prefix: /glade/work/epicufsrt/contrib/spack-stack/casper/ecflow-5.8.4
       modules:
       - ecflow/5.8.4
-  file:
-    externals:
-    - spec: file@5.11
-      prefix: /usr
   findutils:
     externals:
-    - spec: findutils@4.5.11
+    - spec: findutils@4.8.0
       prefix: /usr
   flex:
     # Must set buildable: false to avoid duplicate packages
-    buildable: false
+    #buildable: false
     externals:
-    - spec: flex@2.5.37+lex
-      prefix: /usr
+    - spec: flex@2.6.4+lex
+      prefix: /glade/u/apps/casper/23.10/opt/view
   gawk:
     externals:
-    - spec: gawk@4.0.2
+    - spec: gawk@4.2.1
       prefix: /usr
   gettext:
     externals:
@@ -102,21 +108,21 @@ packages:
       prefix: /usr
   git:
     externals:
-    - spec: git@2.33.1
-      modules:
-      - git/2.33.1
+    - spec: git@2.41.0~tcltk
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: git@2.35.3+tcltk
+      prefix: /usr
   git-lfs:
     externals:
-    - spec: git-lfs@3.0.2
-      modules:
-      - git/2.33.1
+    - spec: git-lfs@3.3.0
+      prefix: /glade/u/apps/casper/23.10/opt/view
   gmake:
     externals:
-    - spec: gmake@3.82
+    - spec: gmake@4.2.1
       prefix: /usr
   groff:
     externals:
-    - spec: groff@1.22.2
+    - spec: groff@1.22.4
       prefix: /usr
   krb5:
     buildable: False
@@ -131,15 +137,13 @@ packages:
     variants: ~gssapi
   libtool:
     externals:
-    - spec: libtool@2.4.2
-      prefix: /usr
-  libxpm:
-    externals:
-    - spec: libxpm@4.11.0
+    - spec: libtool@2.4.7
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: libtool@2.4.6
       prefix: /usr
   m4:
     externals:
-    - spec: m4@1.4.16
+    - spec: m4@1.4.18
       prefix: /usr
   mysql:
     buildable: False
@@ -150,34 +154,31 @@ packages:
       - mysql/8.0.31
   ncurses:
     externals:
-    - spec: ncurses@5.9.20130511+termlib abi=5
-      prefix: /usr
+    - spec: ncurses@6.4.20221231+termlib abi=6
+      prefix: /glade/u/apps/casper/23.10/opt/view
   # Old re2c on Casper unable to build newer versions of ninja
   ninja:
     version:: ['1.10.2']
   openssh:
     externals:
-    - spec: openssh@7.4p1
+    - spec: openssh@8.4p1
       prefix: /usr
   openssl:
     externals:
-    - spec: openssl@1.0.2k-fips
+    - spec: openssl@1.1.1l
       prefix: /usr
-  # Pin patchelf to 0.15.0 for Intel compiler (no C++-17 features)
-  #patchelf:
-  #  version:: ['0.15.0']
   perl:
     externals:
     - spec: perl@5.16.3~cpanm+shared+threads
       prefix: /usr
   pkg-config:
     externals:
-    - spec: pkg-config@0.27.1
+    - spec: pkg-config@0.29.2
       prefix: /usr
   qt:
     externals:
-    - spec: qt@5.15.2
-      prefix: /glade/work/epicufsrt/contrib/spack-stack/casper/qt-5.15.2
+    - spec: qt@5.14.2
+      prefix: /glade/u/apps/casper/23.10/opt/view
   rsync:
     externals:
     - spec: rsync@3.1.2
@@ -192,19 +193,17 @@ packages:
       prefix: /usr
   subversion:
     externals:
-    - spec: subversion@1.7.14
-      prefix: /usr
-  swig:
-    externals:
-    - spec: swig@2.0.10
+    - spec: subversion@1.14.1
       prefix: /usr
   tar:
     externals:
-    - spec: tar@1.26
+    - spec: tar@1.34
       prefix: /usr
   texinfo:
     externals:
-    - spec: texinfo@5.1
+    - spec: texinfo@7.0.3
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: texinfo@6.5
       prefix: /usr
   texlive:
     externals:

configs/sites/hercules/compilers.yaml

@@ -13,34 +13,17 @@ compilers:
     - intel-oneapi-compilers/2023.1.0
     environment: {}
     extra_rpaths: []
-# Spack gets confused if both intel and oneapi are present
-#- compiler:
-#    spec: oneapi@2022.2.1
-#    paths:
-#      cc: /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2022.2.1-z2sjni66fcyqcsamnoccgb7c77mn37qj/compiler/2022.2.1/linux/bin/icx
-#      cxx: /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2022.2.1-z2sjni66fcyqcsamnoccgb7c77mn37qj/compiler/2022.2.1/linux/bin/icpx
-#      # For now ...
-#      f77: /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2022.2.1-z2sjni66fcyqcsamnoccgb7c77mn37qj/compiler/2022.2.1/linux/bin/intel64/ifort
-#      fc: /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2022.2.1-z2sjni66fcyqcsamnoccgb7c77mn37qj/compiler/2022.2.1/linux/bin/intel64/ifort
-#      #f77: /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2022.2.1-z2sjni66fcyqcsamnoccgb7c77mn37qj/compiler/2022.2.1/linux/bin/ifx
-#      #fc: /apps/spack-managed/gcc-11.3.1/intel-oneapi-compilers-2022.2.1-z2sjni66fcyqcsamnoccgb7c77mn37qj/compiler/2022.2.1/linux/bin/ifx
-#    flags: {}
-#    operating_system: rocky9
-#    target: x86_64
-#    modules:
-#    - intel-oneapi-compilers/2022.2.1
-#    environment: {}
-#    extra_rpaths: []
 - compiler:
-    spec: gcc@11.3.1
+    spec: gcc@12.2.0
     paths:
-      cc: /usr/bin/gcc
-      cxx: /usr/bin/g++
-      f77: /usr/bin/gfortran
-      fc: /usr/bin/gfortran
+      cc: /apps/spack-managed/gcc-11.3.1/gcc-12.2.0-7cu3qahzhsxpauy4jlnsbcqmlbkxbbbo/bin/gcc
+      cxx: /apps/spack-managed/gcc-11.3.1/gcc-12.2.0-7cu3qahzhsxpauy4jlnsbcqmlbkxbbbo/bin/g++
+      f77: /apps/spack-managed/gcc-11.3.1/gcc-12.2.0-7cu3qahzhsxpauy4jlnsbcqmlbkxbbbo/bin/gfortran
+      fc: /apps/spack-managed/gcc-11.3.1/gcc-12.2.0-7cu3qahzhsxpauy4jlnsbcqmlbkxbbbo/bin/gfortran
     flags: {}
     operating_system: rocky9
     target: x86_64
-    modules: []
+    modules:
+    - gcc/12.2.0
     environment: {}
     extra_rpaths: []