release/1.7.0 - site config and doc updates (#1052)

* Bug fix in configs/sites/discover-scu17/compilers.yaml: remove duplicate env variable
* Documentation updates for release-1.7.0
* Update discover-scu16 intel config and documentation, and add note in doc/source/NewSiteConfigs.rst about problems of [email protected] with zlib-ng
* Update documentation for S4 and for problems of zlib-ng with [email protected] on some systems
* Update documentation for new Redhat 8 site configs
* Switch to tag spack-stack-1.7.0 for spack submodule
* Update doc/source/PreConfiguredSites.rst with information on mapl version/variant differences

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "spack"]
   path = spack
   url = https://github.com/jcsda/spack
-  branch = release/1.7.0
+  branch = spack-stack-1.7.0
 [submodule "doc/CMakeModules"]
   path = doc/CMakeModules
   url = https://github.com/noaa-emc/cmakemodules

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

@@ -115,7 +115,7 @@ spack:
       os: ubuntu:20.04
       spack:
         url: https://github.com/jcsda/spack
-        ref: release/1.7.0
+        ref: spack-stack-1.7.0
         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: release/1.7.0
+        ref: spack-stack-1.7.0
         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: release/1.7.0
+        ref: spack-stack-1.7.0
         resolve_sha: true
 
     # Whether or not to strip binaries

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, [email protected]]
+    compiler:: [intel@2021.6.0, [email protected]]
     providers:
-      mpi:: [intel-oneapi-mpi@2021.5.0, [email protected]]
+      mpi:: [intel-oneapi-mpi@2021.6.0, [email protected]]
 
 ### 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: [email protected]%[email protected] ~cuda~cxx~cxx_exceptions~java~memchecker+pmi~static~wrapper-rpath

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/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/s4/packages.yaml

@@ -7,6 +7,8 @@ packages:
     compiler:: [[email protected]]
     providers:
       mpi:: [[email protected]]
+      # https://github.com/JCSDA/spack-stack/issues/1055
+      zlib-api:: [zlib]
 
 ### MPI, Python, MKL
   mpi:

doc/source/NewSiteConfigs.rst

@@ -13,22 +13,25 @@ It is also instructive to peruse the GitHub actions scripts in ``.github/workflo
 +-------------------------------------------+----------------------------------------------------------------------+---------------------------+
 | Compiler                                  | Versions tested/in use in one or more site configs                   | Spack compiler identifier |
 +===========================================+======================================================================+===========================+
-| Intel classic (icc, icpc, ifort)          | 2021.3.0 to the latest available version in oneAPI 2023.1.0          | ``intel@``                |
+| Intel classic (icc, icpc, ifort)          | 2021.3.0 to the latest available version in oneAPI 2023.1.0 [#fn1]_  | ``intel@``                |
 +-------------------------------------------+----------------------------------------------------------------------+---------------------------+
 | Intel mixed (icx, icpx, ifort)            | all versions up to latest available version in oneAPI 2023.1.0       | ``intel@``                |
 +-------------------------------------------+----------------------------------------------------------------------+---------------------------+
 | GNU (gcc, g++, gfortran)                  | 9.2.0 to 12.2.0 (note: 13.x.y is **not** yet supported)              | ``gcc@``                  |
 +-------------------------------------------+----------------------------------------------------------------------+---------------------------+
-| Apple clang (clang, clang++, w/ gfortran) | 13.1.6 to 15.0.0 [#fn1]_                                             | ``apple-clang@``          |
+| Apple clang (clang, clang++, w/ gfortran) | 13.1.6 to 15.0.0 [#fn2]_                                             | ``apple-clang@``          |
 +-------------------------------------------+----------------------------------------------------------------------+---------------------------+
 | LLVM clang (clang, clang++, w/ gfortran)  | 10.0.0 to 14.0.3                                                     | ``clang@``                |
 +-------------------------------------------+----------------------------------------------------------------------+---------------------------+
 
 .. rubric:: Footnotes
 
 .. [#fn1]
-  Note that [email protected] compiler versions are fully supported, and [email protected] will work but requires the :ref:`workaround noted below<apple-clang-15-workaround>`.
-  Also, when using [email protected] you must use Command Line Tools version 15.1, and the Command Line Tools versions 15.3 and newer are not yet supported.
+  We have noted problems on some - not all - platforms with ``[email protected]`` when we switched from ``zlib`` to ``zlib-ng`` in spack-stack-1.7.0. These issues went away when using a different version of the compiler (anything between 2021.3.0 and 2021.11.0). It is therefore recommended to avoid using ``[email protected]`` unless it is the only option.
+
+.. [#fn2]
+  Note that ``[email protected]`` compiler versions are fully supported, and ``[email protected]`` will work but requires the :ref:`workaround noted below<apple-clang-15-workaround>`.
+  Also, when using ``[email protected]`` you must use Command Line Tools version 15.1, and the Command Line Tools versions 15.3 and newer are not yet supported.
 
 ..  _NewSiteConfigs_macOS:
 
@@ -384,6 +387,8 @@ The following instructions were used to prepare a basic Red Hat 8 system as it i
    yum -y install automake
    yum -y install xorg-x11-xauth
    yum -y install xterm
+   yum -y install perl-IPC-Cmd
+   yum -y install gettext-devel
    yum -y install texlive
    # Do not install qt@5 for now
 
@@ -511,8 +516,8 @@ It is recommended to increase the stacksize limit by using ``ulimit -S -s unlimi
    # JEDI-Skylab system (using R2D2 localhost)
    spack external find --scope system mysql
 
+   # Note - only needed for generating documentation
    spack external find --scope system texlive
-   spack external find --scope system sed
 
 5. Find compilers, add to site config's ``compilers.yaml``
 
@@ -535,10 +540,10 @@ It is recommended to increase the stacksize limit by using ``ulimit -S -s unlimi
    spack config add "packages:all:compiler:[gcc@YOUR-VERSION]"
 
    # Example for Red Hat 8 following the above instructions
-   spack config add "packages:all:providers:mpi:[openmpi@4.1.6]"
+   spack config add "packages:all:providers:mpi:[openmpi@5.0.1]"
 
    # Example for Ubuntu 20.04 or 22.04 following the above instructions
-   spack config add "packages:all:providers:mpi:[[email protected].1]"
+   spack config add "packages:all:providers:mpi:[[email protected].2]"
 
 .. warning::
    On some systems, the default compiler (e.g., ``gcc`` on Ubuntu 20) may not get used by spack if a newer version is found. Compare your entry to the output of the concretization step later and adjust the entry, if necessary.