Feature/blueback tds cole

.gitmodules

@@ -1,8 +1,8 @@
 [submodule "spack"]
   path = spack
-  url = https://github.com/jcsda/spack
-  branch = spack-stack-dev
+  url = https://github.nrlmry.navy.mil/jcsda/spack
+  branch = release/neptune-1.5
 [submodule "doc/CMakeModules"]
   path = doc/CMakeModules
-  url = https://github.com/noaa-emc/cmakemodules
-  branch = v1.3.0
+  url = https://github.nrlmry.navy.mil/jcsda/cmakemodules
+  branch = release/neptune-1.5

configs/common/packages.yaml

@@ -240,10 +240,10 @@ packages:
   # https://github.com/JCSDA/spack-stack/issues/1276
   py-matplotlib:
     require: '@3.7.4'
-  # Variant ~mpi not working for latest py-netcdf4
-  # https://github.com/spack/spack/issues/47652
+  # https://github.com/Unidata/netcdf4-python/issues/1389
+  # https://github.com/Unidata/netcdf4-python/issues/1389#issuecomment-2599760051
   py-netcdf4:
-    require: '@1.7.1 +mpi'
+    require: '@1.7.1 ~mpi'
   # To avoid duplicate packages
   py-numpy:
     require:

configs/sites/tier2/cole/compilers.yaml

@@ -0,0 +1,43 @@
+compilers::
+  - compiler:
+      spec: [email protected]
+      paths:
+        cc: cc
+        cxx: CC
+        f77: ftn
+        fc: ftn
+      flags: {}
+      operating_system: sles15
+      modules:
+      - PrgEnv-intel/8.5.0
+      - intel/2024.2.1
+      - cray-libsci/24.03.0
+      - libfabric/1.20.1
+      environment:
+        prepend_path:
+          LD_LIBRARY_PATH: '/opt/cray/libfabric/1.20.1/lib64:/opt/cray/pe/libsci/24.03.0/INTEL/2023.2/x86_64/lib'
+        set:
+          CONFIG_SITE: ''
+          CRAY_CPU_TARGET: x86-genoa
+      extra_rpaths: []
+  - compiler:
+      spec: [email protected]
+      paths:
+        cc: cc
+        cxx: CC
+        f77: ftn
+        fc: ftn
+      flags: {}
+      operating_system: sles15
+      modules:
+      - PrgEnv-gnu/8.5.0
+      - gcc-native/12.3
+      - cray-libsci/24.03.0
+      - libfabric/1.20.1
+      environment:
+        prepend_path:
+          LD_LIBRARY_PATH: '/opt/cray/libfabric/1.20.1/lib64:/opt/cray/pe/libsci/24.03.0/GNU/12.3/x86_64/lib'
+        set:
+          CONFIG_SITE: ''
+          CRAY_CPU_TARGET: x86-genoa
+      extra_rpaths: []

configs/sites/tier2/cole/mirrors.yaml

@@ -0,0 +1,3 @@
+mirrors:
+  local-source: file:///p/work1/heinzell/spack-stack/source-cache
+  local-binary: file:///p/work1/heinzell/spack-stack/build-cache

configs/sites/tier2/cole/packages.yaml

@@ -0,0 +1,148 @@
+packages:
+
+# Modification of common packages
+  # Use system zlib instead of spack-built zlib-ng
+  all:
+    providers:
+      zlib-api:: [zlib]
+  zlib-api:
+    buildable: False
+  zlib:
+    buildable: False
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+
+# All other packages listed alphabetically
+  autoconf:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  automake:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  binutils:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  cmake:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  coreutils:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  curl:
+    externals:
+    - spec: [email protected]+gssapi+ldap+nghttp2
+      prefix: /usr
+  cvs:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  diffutils:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  findutils:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  flex:
+    externals:
+    - spec: [email protected]+lex
+      prefix: /usr
+  gawk:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  gettext:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  git:
+    externals:
+    - spec: [email protected]+tcltk
+      prefix: /usr
+  git-lfs:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  gmake:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  grep:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  groff:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  libtool:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  m4:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  mysql:
+    buildable: False
+    externals:
+    - spec: [email protected]
+      prefix: /p/app/projects/NEPTUNE/spack-stack/mysql-8.0.31
+      modules:
+      - mysql/8.0.31
+  openssh:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+    - spec: [email protected]
+      prefix: /usr/local/krb5
+  openssl:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  perl:
+    externals:
+    - spec: [email protected]~cpanm+opcode+open+shared+threads
+      prefix: /usr
+  pkg-config:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  qt:
+    buildable: False
+    externals:
+    - spec: [email protected]
+      prefix: /p/app/projects/NEPTUNE/spack-stack/qt-5.15.2/5.15.2/gcc_64
+      modules:
+      - qt/5.15.2
+  sed:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  subversion:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  swig:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  tar:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  texinfo:
+    externals:
+    - spec: [email protected]
+      prefix: /usr
+  wget:
+    externals:
+    - spec: [email protected]
+      prefix: /usr

configs/sites/tier2/cole/packages_gcc.yaml

@@ -0,0 +1,13 @@
+packages:
+  all:
+    compiler:: [[email protected]]
+    providers:
+      mpi:: [[email protected]]
+  mpi:
+    buildable: False
+  cray-mpich:
+    externals:
+    - spec: [email protected]%[email protected] ~wrappers
+      modules:
+      - cray-mpich/8.1.29
+      - craype-network-ofi

configs/sites/tier2/cole/packages_oneapi.yaml

@@ -0,0 +1,25 @@
+packages:
+  all:
+    compiler:: [[email protected],[email protected]]
+    providers:
+      mpi:: [[email protected]]
+  mpi:
+    buildable: False
+  cray-mpich:
+    externals:
+    - spec: [email protected]%[email protected] ~wrappers
+      modules:
+      - cray-mpich/8.1.29
+      - craype-network-ofi
+  intel-oneapi-mkl:
+    externals:
+    - spec: [email protected]%[email protected]
+      prefix: /p/work1/heinzell/spack-stack/oneapi-2024.2.1
+  intel-oneapi-tbb:
+    externals:
+    - spec: [email protected]%[email protected]
+      prefix: /p/work1/heinzell/spack-stack/oneapi-2024.2.1
+  intel-oneapi-runtime:
+    externals:
+    - spec: [email protected]%[email protected]
+      prefix: /p/work1/heinzell/spack-stack/oneapi-2024.2.1

configs/sites/tier2/tusk/config.yaml

@@ -0,0 +1,2 @@
+config:
+  build_jobs: 8

configs/sites/tier2/tusk/mirrors.yaml

@@ -0,0 +1,3 @@
+mirrors:
+  local-source: file:///p/work1/heinzell/spack-stack/source-cache
+  local-binary: file:///p/work1/heinzell/spack-stack/build-cache

configs/sites/tier2/tusk/modules.yaml

@@ -0,0 +1,7 @@
+modules:
+  default:
+    enable::
+    - tcl
+    tcl:
+      include:
+      - python

configs/sites/tier1/blueback/packages.yaml → configs/sites/tier2/tusk/packages.yaml

@@ -1,4 +1,5 @@
 packages:
+
 # Modification of common packages
   # Use system zlib instead of spack-built zlib-ng
   all:
@@ -9,12 +10,8 @@ packages:
   zlib:
     buildable: False
     externals:
-    # For TDS tusk
     - spec: [email protected]
       prefix: /usr
-    # For TDS cole
-    #- spec: [email protected]
-    #  prefix: /usr
 
 # All other packages listed alphabetically
   autoconf:

configs/templates/neptune-dev/spack.yaml

@@ -9,6 +9,7 @@ spack:
   - compilers: ['%aocc', '%apple-clang', '%gcc', '%intel', '%oneapi']
   - packages:
       - neptune-env +espc                           ^esmf@=8.8.0
+      # Comment out for Cole and Tusk or any other air-gapped system:
       - neptune-python-env +xnrl ^neptune-env +espc ^esmf@=8.8.0
 
   specs:

doc/source/PreConfiguredSites.rst

@@ -70,7 +70,7 @@ Pre-configured sites (tier 1)
 |                     +-----------------------+--------------------+--------------------------------------------------------+-----------------+
 | U.S. Navy (HPCMP)   | Nautilus              | GCC, Intel, oneAPI | ``/p/app/projects/NEPTUNE/spack-stack/``               | NRL             |
 |                     +-----------------------+--------------------+--------------------------------------------------------+-----------------+
-|                     | Blueback (earlyaccess)| GCC, oneAPI        | (experimental only, no project directories yet         | NRL             |
+|                     | Blueback (earlyaccess)| GCC, oneAPI        | (experimental only)                                    | NRL             |
 +---------------------+-----------------------+--------------------+--------------------------------------------------------+-----------------+
 | Univ. of Wisconsin  | S4                    | Intel              | ``/data/prod/jedi/spack-stack/``                       | SSEC            |
 +---------------------+-----------------------+--------------------+--------------------------------------------------------+-----------------+
@@ -257,46 +257,12 @@ The following is required for building new spack environments with Intel oneAPI
 .. code-block:: console
 
    umask 0022
-   module unload PrgEnv-cray
-   module load PrgEnv-intel/8.4.0
-   module unload intel
-   module load intel/2024.2
-   module unload cray-mpich
-   module unload craype-network-ofi
-   # Warning. Do not load craype-network-ucx
-   # or cray-mpich-ucx/8.1.21!
-   # There is a bug in the modulefile that prevents
-   # spack from setting the environment for its
-   # build steps when the module is already
-   # loaded. Instead, let spack load it when the
-   # package requires it.
-   #module load craype-network-ucx
-   #module load cray-mpich-ucx/8.1.21
-   module load libfabric/1.12.1.2.2.1
-   module unload cray-libsci
-   module load cray-libsci/23.05.1.4
+   # This section will be updated when Blueback becomes available.
 
 The following is required for building new spack environments with GNU on this platform.. Don't use ``module purge`` on Blueback!
 
    umask 0022
-   module unload PrgEnv-cray
-   module load PrgEnv-gnu/8.4.0
-   module unload gcc
-   module load gcc/12.1.0
-   module unload cray-mpich
-   module unload craype-network-ofi
-   # Warning. Do not load craype-network-ucx
-   # or cray-mpich-ucx/8.1.21!
-   # There is a bug in the modulefile that prevents
-   # spack from setting the environment for its
-   # build steps when the module is already
-   # loaded. Instead, let spack load it when the
-   # package requires it.
-   #module load craype-network-ucx
-   #module load cray-mpich-ucx/8.1.21
-   module load libfabric/1.12.1.2.2.1
-   module unload cray-libsci
-   module load cray-libsci/23.05.1.4
+   # This section will be updated when Blueback becomes available.
 
 
 .. _Preconfigured_Sites_Derecho: