Update develop from release/1.7.0 and rename spack fork branch

.gitmodules

@@ -1,9 +1,7 @@
 [submodule "spack"]
   path = spack
-  #url = https://github.com/spack/spack
-  #branch = develop
   url = https://github.com/jcsda/spack
-  branch = jcsda_emc_spack_stack
+  branch = spack-stack-dev
 [submodule "doc/CMakeModules"]
   path = doc/CMakeModules
   url = https://github.com/noaa-emc/cmakemodules

configs/common/modules_lmod.yaml

@@ -189,7 +189,6 @@ modules:
             'TOCGRIB': '{prefix}/bin/tocgrib'
             'TOCGRIB2': '{prefix}/bin/tocgrib2'
             'TOCGRIB2SUPER': '{prefix}/bin/tocgrib2super'
-            'WGRIB2': '{prefix}/bin/wgrib2'
       landsfcutil:
         environment:
           set:

configs/common/modules_tcl.yaml

@@ -191,7 +191,6 @@ modules:
             'TOCGRIB': '{prefix}/bin/tocgrib'
             'TOCGRIB2': '{prefix}/bin/tocgrib2'
             'TOCGRIB2SUPER': '{prefix}/bin/tocgrib2super'
-            'WGRIB2': '{prefix}/bin/wgrib2'
       landsfcutil:
         environment:
           set:

configs/common/packages.yaml

@@ -82,7 +82,7 @@
     freetype:
       variants: +pic
     g2:
-      version: ['3.4.5']
+      version: ['3.4.9']
     g2c:
       version: ['1.6.4']
     g2tmpl:
@@ -100,7 +100,7 @@
       # the container builds.
       #version: ['2.11.0']
     grib-util:
-      version: ['1.3.0']
+      version: ['1.4.0']
     gsibec:
       version: ['1.2.1']
     gsi-ncdiag:
@@ -114,7 +114,7 @@
       version: ['1.14.3']
       variants: +hl +fortran +mpi ~threadsafe ~szip
     ip:
-      version: ['4.3.0']
+      version: ['5.0.0']
       variants: precision=4,d,8
     ip2:
       version: ['1.1.2']
@@ -259,6 +259,8 @@
       variants: precision=4,d,8
     udunits:
       version: ['2.2.28']
+    ufs-utils:
+      version: ['1.13.0']
     # Note - we can remove upp from stack at some point?
     upp:
       version: ['10.0.10']

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

@@ -115,7 +115,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/jcsda/spack
-        ref: jcsda_emc_spack_stack
+        ref: spack-stack-dev
         resolve_sha: true
 
     # Whether or not to strip binaries

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

@@ -96,7 +96,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/jcsda/spack
-        ref: jcsda_emc_spack_stack
+        ref: spack-stack-dev
         resolve_sha: true
 
     # Whether or not to strip binaries

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

@@ -115,7 +115,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/jcsda/spack
-        ref: jcsda_emc_spack_stack
+        ref: spack-stack-dev
         resolve_sha: true
 
     # Whether or not to strip binaries

configs/containers/specs/jedi-ci.yaml

@@ -2,15 +2,15 @@
   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@12.0.1, ecbuild@3.7.2, eccodes@2.33.0, ecflow@5,
     eckit@1.24.5, ecmwf-atlas@0.36.0 +fckit +trans +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@1.10.2, gftl-shared@1.6.1,
-    gsibec@1.2.1, hdf@4.2.15, hdf5@1.14.3, ip@4.3.0, jasper@2.0.32, jedi-cmake@1.4.0,
+    eigen@3.4.0, fckit@0.11.0, fms@release-jcsda, g2@3.4.9, g2tmpl@1.10.2, gftl-shared@1.6.1,
+    gsibec@1.2.1, hdf@4.2.15, hdf5@1.14.3, ip@5.0.0, 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@4.6.1, nlohmann-json@3.10.5, nlohmann-json-schema-validator@2.1.0,
     parallelio@2.6.2, parallel-netcdf@1.12.3, py-eccodes@1.5.0, py-f90nml@1.4.3,
     py-gitpython@3.1.40, py-h5py@3.8.0, py-numpy@1.22.3,
     py-pandas@1.5.3, py-pip, py-pyyaml@6.0, py-scipy@1.11.4, py-shapely@1.8.0, py-xarray@2023.7.0,
     sp@2.5.0, udunits@2.2.28, w3emc@2.10.0, nco@5.1.6, esmf@8.6.0, mapl@2.40.3,
-    zlib@1.2.13, zstd@1.5.2, odc@1.4.6, shumlib@macos_clang_linux_intel_port,
+    zlib-ng@2.1.5, zstd@1.5.2, odc@1.4.6, shumlib@macos_clang_linux_intel_port,
     awscli-v2@2.13.22, py-globus-cli@3.16.0]
     # Notes:
     # 1. Don't build CRTM by default so that it gets built in the JEDI bundles

configs/sites/derecho/compilers.yaml

@@ -25,7 +25,7 @@ compilers::
         FI_CXI_RX_MATCH_MODE: 'hybrid'
         # https://github.com/JCSDA/spack-stack/issues/1012
         I_MPI_EXTRA_FILESYSTEM: 'ON'
-      extra_rpaths: []
+    extra_rpaths: []
 - compiler:
     spec: gcc@12.2.0
     paths:

configs/sites/discover-scu16/compilers.yaml

@@ -1,24 +1,24 @@
 compilers:
 - compiler:
-    spec: intel@=2021.5.0
+    spec: intel@=2021.6.0
     paths:
-      cc: /usr/local/intel/oneapi/2021/compiler/2022.0.1/linux/bin/intel64/icc
-      cxx: /usr/local/intel/oneapi/2021/compiler/2022.0.1/linux/bin/intel64/icpc
-      f77: /usr/local/intel/oneapi/2021/compiler/2022.0.1/linux/bin/intel64/ifort
-      fc: /usr/local/intel/oneapi/2021/compiler/2022.0.1/linux/bin/intel64/ifort
+      cc: /usr/local/intel/oneapi/2021/compiler/2022.1.0/linux/bin/intel64/icc
+      cxx: /usr/local/intel/oneapi/2021/compiler/2022.1.0/linux/bin/intel64/icpc
+      f77: /usr/local/intel/oneapi/2021/compiler/2022.1.0/linux/bin/intel64/ifort
+      fc: /usr/local/intel/oneapi/2021/compiler/2022.1.0/linux/bin/intel64/ifort
     flags:
       ldflags: '-L/usr/local/other/gcc/11.2.0/lib64'
     operating_system: sles12
     target: x86_64
     modules:
-    - comp/intel/2021.5.0
+    - comp/intel/2021.6.0
     environment:
       prepend_path:
         PATH: '/usr/local/other/gcc/11.2.0/bin'
         CPATH: '/usr/local/other/gcc/11.2.0/include'
-        LD_LIBRARY_PATH: '/usr/local/intel/oneapi/2021/compiler/2022.0.1/linux/compiler/lib/intel64_lin:/usr/local/other/gcc/11.2.0/lib64'
+        LD_LIBRARY_PATH: '/usr/local/intel/oneapi/2021/compiler/2022.1.0/linux/compiler/lib/intel64_lin:/usr/local/other/gcc/11.2.0/lib64'
       set:
-        I_MPI_ROOT: '/usr/local/intel/oneapi/2021/mpi/2021.5.0'
+        I_MPI_ROOT: '/usr/local/intel/oneapi/2021/mpi/2021.6.0'
     extra_rpaths: []
 - compiler:
     spec: gcc@=12.1.0

configs/sites/discover-scu16/packages.yaml

@@ -1,18 +1,18 @@
 packages:
   all:
-    compiler:: [intel@2021.5.0, gcc@12.1.0]
+    compiler:: [intel@2021.6.0, gcc@12.1.0]
     providers:
-      mpi:: [intel-oneapi-mpi@2021.5.0, openmpi@4.1.3]
+      mpi:: [intel-oneapi-mpi@2021.6.0, openmpi@4.1.3]
 
 ### MPI, Python, MKL
   mpi:
     buildable: False
   intel-oneapi-mpi:
     externals:
-    - spec: intel-oneapi-mpi@2021.5.0%intel@2021.5.0
+    - spec: intel-oneapi-mpi@2021.6.0%intel@2021.6.0
       prefix: /usr/local/intel/oneapi/2021
       modules:
-      - mpi/impi/2021.5.0
+      - mpi/impi/2021.6.0
   openmpi::
     externals:
     - spec: openmpi@4.1.3%gcc@12.1.0 ~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath
@@ -26,8 +26,12 @@ packages:
   # Problems building shared hdf-eos2 with Intel, not needed
   hdf-eos2:
     variants: ~shared
+  # Explicitly requested by GMAO collaborators
   met:
     variants: +python +grib2 +graphics +lidar2nc +modis
+  # xnnpack option doesn't build on this system
+  py-torch:
+    variants: ~xnnpack
 
 ### All other external packages listed alphabetically
   autoconf:

configs/sites/discover-scu17/compilers.yaml

@@ -20,11 +20,10 @@ compilers:
         CPATH: '/usr/local/other/gcc/11.4.0/include'
         LD_LIBRARY_PATH: '/usr/local/intel/oneapi/2021/compiler/2023.2.1/linux/compiler/lib/intel64_lin:/usr/local/other/gcc/11.4.0/lib64'
       set:
-        # https://github.com/JCSDA/spack-stack/issues/1012
-        I_MPI_EXTRA_FILESYSTEM: 'ON'
         # https://github.com/JCSDA/spack-stack/issues/1011
         I_MPI_SHM_HEAP_VSIZE: '512'
         PSM2_MEMORY: 'large'
+        # https://github.com/JCSDA/spack-stack/issues/1012
         I_MPI_EXTRA_FILESYSTEM: '1'
         I_MPI_EXTRA_FILESYSTEM_FORCE: 'gpfs'
         I_MPI_FABRICS: 'ofi'

configs/sites/hera/compilers.yaml

@@ -7,7 +7,7 @@ compilers:
       f77: /apps/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort
       fc: /apps/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort
     flags: {}
-    operating_system: centos7
+    operating_system: rocky8
     modules:
     - intel/2022.1.2
     environment:
@@ -24,7 +24,7 @@ compilers:
       f77: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/ifort
       fc: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/ifort
     flags: {}
-    operating_system: centos7
+    operating_system: rocky8
     modules:
     - intel/18.0.5.274
 - compiler:
@@ -35,7 +35,7 @@ compilers:
       f77: /apps/gnu/gcc-9.2.0/bin/gfortran
       fc:  /apps/gnu/gcc-9.2.0/bin/gfortran
     flags: {}
-    operating_system: centos7
+    operating_system: rocky8
     modules:
     - gnu/9.2.0
     environment: {}

configs/sites/hera/packages.yaml

@@ -3,7 +3,7 @@ packages:
     compiler:: [intel@2021.5.0, gcc@9.2.0]
     #compiler:: [intel@18.0.5.274]
     providers:
-      mpi:: [intel-oneapi-mpi@2021.5.1, openmpi@4.1.5]
+      mpi:: [intel-oneapi-mpi@2021.5.1, openmpi@4.1.6]
       #mpi:: [intel-mpi@2018.0.4]
     # To support hecflow01
     target: [haswell]
@@ -22,11 +22,14 @@ packages:
       prefix: /apps/oneapi
   openmpi:
     externals:
-    - spec: openmpi@4.1.5~cuda~cxx~cxx_exceptions~java+lustre~memchecker+pmi~static~wrapper-rpath schedulers=slurm
-      prefix: /scratch1/NCEPDEV/jcsda/jedipara/spack-stack/openmpi-4.1.5
+    - spec: openmpi@4.1.6~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-libevent~internal-pmix~java+legacylaunchers~lustre~memchecker~openshmem~orterunprefix+pmi+romio+rsh~singularity+static+vt+wrapper-rpath fabrics=ucx schedulers=slurm
       modules:
       - gnu/9.2.0
-      - openmpi/4.1.5
+      - openmpi/4.1.6_gnu9.2.0
+  zlib-ng:
+    require:
+      - any_of: ['~shared']
+        when: "%intel"
 
 ### All other external packages listed alphabetically
   autoconf:

configs/sites/jet/compilers.yaml

@@ -7,14 +7,14 @@ compilers:
       f77: /apps/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort
       fc: /apps/oneapi/compiler/2022.0.2/linux/bin/intel64/ifort
     flags: {}
-    operating_system: centos7
+    operating_system: rocky8
     modules:
     - intel/2022.1.2
     environment:
       prepend_path:
-        PATH: '/apps/gnu/gcc-9.2.0/bin'
-        LD_LIBRARY_PATH: '/apps/gnu/gcc-9.2.0/lib64'
-        CPATH: '/apps/gnu/gcc-9.2.0/include'
+        PATH: '/apps/gnu/gcc-9.2.0b/bin'
+        LD_LIBRARY_PATH: '/apps/gnu/gcc-9.2.0b/lib64'
+        CPATH: '/apps/gnu/gcc-9.2.0b/include'
     extra_rpaths: []
 - compiler:
     spec: intel@18.0.5.274
@@ -24,19 +24,19 @@ compilers:
       f77: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/ifort
       fc: /apps/intel/parallel_studio_xe_2018.4.057/compilers_and_libraries_2018/linux/bin/intel64/ifort
     flags: {}
-    operating_system: centos7
+    operating_system: rocky8
     modules:
     - intel/18.0.5.274
 - compiler:
     spec: gcc@9.2.0
     paths:
-      cc: /apps/gnu/gcc-9.2.0/bin/gcc
-      cxx: /apps/gnu/gcc-9.2.0/bin/g++
-      f77: /apps/gnu/gcc-9.2.0/bin/gfortran
-      fc:  /apps/gnu/gcc-9.2.0/bin/gfortran
+      cc: /apps/gnu/gcc-9.2.0b/bin/gcc
+      cxx: /apps/gnu/gcc-9.2.0b/bin/g++
+      f77: /apps/gnu/gcc-9.2.0b/bin/gfortran
+      fc:  /apps/gnu/gcc-9.2.0b/bin/gfortran
     flags: {}
-    operating_system: centos7
+    operating_system: rocky8
     modules:
-    - gnu/9.2.0
+    - gnu/9.2.0b
     environment: {}
     extra_rpaths: []

configs/sites/jet/packages.yaml

@@ -3,7 +3,7 @@ packages:
     compiler:: [intel@2021.5.0, gcc@9.2.0]
     #compiler:: [intel@18.0.5.274]
     providers:
-      mpi:: [intel-oneapi-mpi@2021.5.1, openmpi@3.1.4]
+      mpi:: [intel-oneapi-mpi@2021.5.1, openmpi@4.1.6]
       #mpi:: [intel-mpi@2018.4.274]
     # To support all generations of jet
     target: [core2]
@@ -23,11 +23,15 @@ packages:
       - impi/2022.1.2
   openmpi:
     externals:
-    - spec: openmpi@3.1.4%gcc@9.2.0~cuda+cxx+cxx_exceptions~java~memchecker+pmi+static~wrapper-rpath schedulers=slurm
-      prefix: /apps/openmpi/3.1.4/gnu/gcc-9.2.0
+    - spec: openmpi@4.1.6%gcc@9.2.0
+      prefix: /apps/openmpi/4.1.6/gnu9.2.0/
       modules:
-      - gnu/9.2.0
-      - openmpi/3.1.4
+      - gnu/9.2.0b
+      - openmpi/4.1.6_gnu9.2.0
+  zlib-ng:
+    require:
+      - any_of: ['~shared']
+        when: "%intel"
 
 ### All other external packages listed alphabetically
   autoconf:
@@ -148,12 +152,6 @@ packages:
       prefix: /lfs4/HFIP/hfv3gfs/role.epic/apps/mysql-8.0.31
       modules:
       - mysql/8.0.31
-  ncurses:
-    externals:
-    - spec: ncurses@6.3.20211021+termlib abi=6
-      prefix: /lfs4/HFIP/hfv3gfs/Kyle.Gerheiser/miniconda/miniconda-3.9.7
-    - spec: ncurses@5.9.20130511+termlib abi=5
-      prefix: /usr
   perl:
     externals:
     - spec: perl@5.16.3~cpanm+shared+threads
@@ -186,10 +184,6 @@ packages:
     externals:
     - spec: wget@1.14
       prefix: /usr
-  xz:
-    externals:
-    - spec: xz@5.2.5
-      prefix: /lfs4/HFIP/hfv3gfs/Kyle.Gerheiser/miniconda/miniconda-3.9.7
   zip:
     externals:
     - spec: zip@3.0

configs/sites/noaa-gcloud/README.md

@@ -26,6 +26,9 @@ mkdir -p /contrib/admin
 cat <<EOF > /contrib/admin/basic_setup.sh
 #!/bin/bash
 
+yum-config-manager --disable intel-clck-2019-repo
+yum-config-manager --disable intel-hpc-platform
+yum-config-manager --disable intelpython
 chmod 777 /contrib
 yum install -y qt5-qtbase-devel
 yum install -y qt5-qtsvg-devel

configs/sites/orion/compilers.yaml

@@ -17,24 +17,6 @@ compilers:
         LD_LIBRARY_PATH: '/apps/gcc-10.2.0/gcc-10.2.0/lib64:/apps/gcc-10.2.0/gcc-10.2.0/contrib/lib'
         CPATH: '/apps/gcc-10.2.0/gcc-10.2.0/include'
     extra_rpaths: []
-- compiler:
-    spec: intel@18.0.5
-    paths:
-      cc: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/icc
-      cxx: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/icpc
-      f77: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/ifort
-      fc: /apps/intel-2018/intel-2018.u4/compilers_and_libraries_2018.5.274/linux/bin/intel64/ifort
-    flags: {}
-    operating_system: centos7
-    target: x86_64
-    modules:
-    - intel/2018.4
-    environment:
-      prepend_path:
-        PATH: '/apps/gcc-8/gcc-8.3.0/bin'
-        LD_LIBRARY_PATH: '/apps/gcc-8/gcc-8.3.0/lib64:/apps/gcc-8/gcc-8.3.0//lib:/apps/gcc-8/gcc-8.3.0/mpfr-4.0.2/lib:/apps/gcc-8/gcc-8.3.0/mpc-1.1.0/lib:/apps/gcc-8/gcc-8.3.0/gmp-6.1.2/lib'
-        CPATH: '/apps/gcc-8/gcc-8.3.0/include'
-    extra_rpaths: []
 - compiler:
     spec: gcc@10.2.0
     paths: