release/1.5.1: add [email protected], 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, [email protected]) * Update doc/source/PreConfiguredSites.rst for casper, hera, gaea-c4, jet * Add [email protected] 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
JCSDA · Nov 7, 2023 · 883ebcb · 883ebcb
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diff --git a/.gitmodules b/.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

diff --git a/configs/common/packages.yaml b/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

diff --git a/configs/containers/README.md b/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: [[email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected], [email protected], [email protected], [email protected], ecflow@5,
     [email protected], [email protected] +fckit +ectrans +tesselation +fftw, [email protected], [email protected] +fftw,
-    [email protected], [email protected], fms@release-jcsda, [email protected], [email protected], gftl-shared@1.5.0,
+    [email protected], [email protected], fms@release-jcsda, [email protected], [email protected], gftl-shared@1.6.1,
     [email protected], [email protected], [email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected], [email protected],
     [email protected], [email protected], [email protected],
     [email protected], py-pip, [email protected], [email protected], [email protected], [email protected],
-    [email protected], [email protected], [email protected], [email protected], [email protected], esmf@8.4.2, mapl@2.35.2,
-    [email protected], [email protected], [email protected], [email protected], shumlib@macos_clang_linux_intel_port,
+    [email protected], [email protected], [email protected], [email protected], [email protected], esmf@8.5.0, mapl@2.40.3,
+    [email protected], [email protected], [email protected], shumlib@macos_clang_linux_intel_port,
     [email protected], [email protected]]
     # Notes:
-    # 1. Remove [email protected] 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
     #    [email protected]
 ```

diff --git a/configs/containers/docker-ubuntu-clang-mpich.yaml b/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

diff --git a/configs/containers/docker-ubuntu-gcc-openmpi.yaml b/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

diff --git a/configs/containers/docker-ubuntu-intel-impi.yaml b/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

diff --git a/configs/sites/casper/compilers.yaml b/configs/sites/casper/compilers.yaml
@@ -1,24 +1,15 @@
 compilers::
   - compiler:
-      spec: [email protected]
+      spec: [email protected]
       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: '[email protected]'
-          LM_LICENSE_FILE: '[email protected]'
-          I_MPI_ROOT: '/glade/u/apps/opt/intel/2022.1/mpi/2021.5.1'
-
+      - gcc/12.2.0
+      environment: {}
       extra_rpaths: []
diff --git a/configs/sites/casper/packages.yaml b/configs/sites/casper/packages.yaml
@@ -1,45 +1,53 @@
 packages:
   all:
-    compiler:: [[email protected]]
+    compiler:: [[email protected]]
     providers:
-      mpi:: [[email protected]]
+      mpi:: [[email protected]]
 
 ### MPI, Python, MKL
   mpi:
     buildable: False
-  intel-oneapi-mpi:
+  openmpi:
     externals:
-    - spec: [email protected]%[email protected]
-      prefix: /glade/u/apps/opt/intel/2022.1
+    - spec: [email protected]%[email protected]+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 [email protected]
-  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: [email protected]
+    - spec: [email protected]
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: [email protected]
       prefix: /usr
   berkeley-db:
     externals:
     - spec: [email protected]
       prefix: /usr
   binutils:
     externals:
-    - spec: binutils@2.27.43
+    - spec: binutils@2.41.0
       prefix: /usr
   bzip2:
     externals:
     - spec: [email protected]
       prefix: /usr
+  coreutils:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
   cmake:
     externals:
     - spec: [email protected]
@@ -53,19 +61,21 @@ packages:
       prefix: /usr
   cvs:
     externals:
-    - spec: cvs@1.11.23
+    - spec: cvs@1.12.13
       prefix: /usr
   curl:
     externals:
-    - spec: [email protected]+gssapi+ldap+nghttp2
+    - spec: [email protected]+nghttp2
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: [email protected]+gssapi+ldap+nghttp2
       prefix: /usr
   diffutils:
     externals:
     - spec: [email protected]
       prefix: /usr
   doxygen:
     externals:
-    - spec: [email protected]+graphviz~mscgen
+    - spec: [email protected]
       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: [email protected]
-      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: [email protected]
-      modules:
-      - git/2.33.1
+    - spec: [email protected]~tcltk
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: [email protected]+tcltk
+      prefix: /usr
   git-lfs:
     externals:
-    - spec: [email protected]
-      modules:
-      - git/2.33.1
+    - spec: [email protected]
+      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: [email protected].2
+    - spec: [email protected].4
       prefix: /usr
   krb5:
     buildable: False
@@ -131,15 +137,13 @@ packages:
     variants: ~gssapi
   libtool:
     externals:
-    - spec: [email protected]
-      prefix: /usr
-  libxpm:
-    externals:
-    - spec: [email protected]
+    - spec: [email protected]
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: [email protected]
       prefix: /usr
   m4:
     externals:
-    - spec: [email protected].16
+    - spec: [email protected].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: [email protected]~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: [email protected]
@@ -192,19 +193,17 @@ packages:
       prefix: /usr
   subversion:
     externals:
-    - spec: [email protected]
-      prefix: /usr
-  swig:
-    externals:
-    - spec: [email protected]
+    - spec: [email protected]
       prefix: /usr
   tar:
     externals:
-    - spec: tar@1.26
+    - spec: tar@1.34
       prefix: /usr
   texinfo:
     externals:
-    - spec: [email protected]
+    - spec: [email protected]
+      prefix: /glade/u/apps/casper/23.10/opt/view
+    - spec: [email protected]
       prefix: /usr
   texlive:
     externals:

diff --git a/configs/sites/hercules/compilers.yaml b/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: [email protected]
-#    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: []