release/1.5.0: site updates part 1 (Orion, Hercules, Narwhal)

.github/workflows/macos-ci-aarch64.yaml

@@ -111,6 +111,12 @@ jobs:
           echo "Packages in combined spack build caches:"
           spack buildcache list
 
+          # Workaround for limited disk space on macOS arm instance
+          spack config add "config:build_stage:/Users/ec2-user/spack-stack/spack-cache/build_stage"
+          spack config add "config:test_stage:/Users/ec2-user/spack-stack/spack-cache/test_stage"
+          spack config add "config:source_cache:/Users/ec2-user/spack-stack/spack-cache/source_cache"
+          spack config add "config:misc_cache:/Users/ec2-user/spack-stack/spack-cache/misc_cache"
+
           # Break installation up in pieces and create build caches in between
           # This allows us to "spin up" builds that altogether take longer than
           # six hours, and/or fail later in the build process.

configs/common/packages.yaml

@@ -11,13 +11,14 @@
         lapack: [openblas]
         yacc: [bison]
     #
+    # This version of awscli goes with [email protected]
     awscli:
-      version: ['1.29.41']
-    bacio:  
+      version: ['1.27.84']
+    bacio:
       version: ['2.4.1']
     bison:
       version: ['3.8.2']
-    # Attention - when updating also check orion site config
+    # Attention - when updating also check S4 site config
     boost:
       version: ['1.78.0']
       variants: ~atomic +chrono +date_time +exception +filesystem ~graph ~iostreams ~locale ~log ~math ~mpi ~numpy +pic +program_options +python ~random +regex +serialization ~signals +system +test +thread +timer ~wave cxxstd=17 visibility=hidden
@@ -137,8 +138,12 @@
       version: ['0.2.5']
     mapl:
       # 2.35.2 goes with [email protected], 2.40.3 goes with [email protected]
+      # turn off ~pflogger and extdata2g to avoid compilation
+      # errors with [email protected]+, see
+      # https://github.com/JCSDA/spack-stack/issues/769
+      # also: ... extdata2g segfault UFS?
       version: ['2.35.2']
-      variants: ~shared
+      variants: ~shared ~extdata2g ~pflogger
     # If making changes here, also check the Discover site config and the CI workflows
     met:
       version: ['11.1.0']
@@ -260,8 +265,9 @@
       # Versions earlier than 0.11.0 don't compile on macOS with llvm-clang/13.0.0 and Python/3.9,
       # and 0.11.0 leads to downstream errors in py-scipy with the Intel compilers
       version: ['0.12.2']
+    # This version of py-pyyaml goes with [email protected]
     py-pyyaml:
-      version: ['6.0']
+      version: ['5.4.1']
     py-scipy:
       version: ['1.9.3']
     # Pin the py-setuptools version to avoid duplicate Python packages

configs/sites/hercules/modules.yaml

@@ -5,3 +5,5 @@ modules:
     lmod:
       exclude:
       - ecflow
+      include:
+      - python

configs/sites/hercules/packages.yaml

@@ -20,11 +20,6 @@ packages:
       prefix: /work/noaa/epic/role-epic/spack-stack/hercules/openmpi-4.1.5/gcc-11.3.1
       modules:
       - openmpi/4.1.5
-  python:
-    buildable: False
-    externals:
-    - spec: [email protected] #+bz2+crypt+ctypes+dbm+lzma~nis+pyexpat~pythoncmd+readline+sqlite3+ssl~tix~tkinter+uuid+zlib
-      prefix: /usr
 
 ### Modifications of common packages
   # Version 2.0.8 doesn't compile on Hercules
@@ -44,15 +39,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  bison:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
-  # Do not use!
-  #cmake:
-  #  externals:
-  #  - spec: [email protected]
-  #    prefix: /usr
   coreutils:
     externals:
     - spec: [email protected]
@@ -121,17 +107,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  # Do not use, can lead to duplicate packages being built
-  #openssl:
-  #  buildable: False
-  #  externals:
-  #  - spec: [email protected]
-  #    prefix: /usr
-  # Do not use, incomplete package (missing FindBin for example)
-  #perl:
-  #  externals:
-  #  - spec: [email protected]~cpanm+shared+threads
-  #    prefix: /usr
   pkgconf:
     externals:
     - spec: [email protected]
@@ -146,11 +121,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  # Do not use, problems on compute nodes with Intel
-  #tar:
-  #  externals:
-  #  - spec: [email protected]
-  #    prefix: /usr
   texinfo:
     externals:
     - spec: [email protected]
@@ -159,10 +129,3 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  # Do not use external zlib; causes issues with tar due to qt/zlib dependencies
-  # zlib:
-  #   externals:
-  #   - spec: [email protected]
-  #     prefix: /apps/spack-managed/gcc-11.3.1/zlib-1.2.13-ltp4c3zzde3zi3gf7x4b7c7nj5ww4i4g
-  #     modules:
-  #     - zlib/1.2.13

configs/sites/narwhal/mirrors.yaml

@@ -1,15 +1,15 @@
 mirrors:
   local-source:
     fetch:
-      url: file:///p/app/projects/NEPTUNE/spack-stack/spack-stack-v1/source-cache
+      url: file:///p/app/projects/NEPTUNE/spack-stack/source-cache
       access_pair:
       - null
       - null
       access_token: null
       profile: null
       endpoint_url: null
     push:
-      url: file:///p/app/projects/NEPTUNE/spack-stack/spack-stack-v1/source-cache
+      url: file:///p/app/projects/NEPTUNE/spack-stack/source-cache
       access_pair:
       - null
       - null

configs/sites/narwhal/modules.yaml

@@ -5,3 +5,5 @@ modules:
     tcl:
       exclude:
       - ecflow
+      include:
+      - python

configs/sites/narwhal/packages.yaml

@@ -27,20 +27,6 @@ packages:
   #    prefix: /opt/intel/oneapi_2021.3.0.3219
   #    modules:
   #    - intel/2021.3.0
-  python:
-    buildable: False
-    externals:
-    - spec: [email protected]+bz2+ctypes+dbm+lzma+nis+pyexpat+pythoncmd+readline+sqlite3+ssl+tix+tkinter+uuid+zlib
-      prefix: /opt/cray/pe/python/3.9.7.1
-      modules:
-      - cray-python/3.9.7.1
-  py-pip:
-    buildable: False
-    externals:
-    - spec: [email protected]
-      prefix: /opt/cray/pe/python/3.9.7.1
-      modules:
-      - cray-python/3.9.7.1
 
 ### All other external packages listed alphabetically
   autoconf:
@@ -55,10 +41,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  bison:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   curl:
     externals:
     - spec: [email protected]+gssapi+ldap+nghttp2

configs/sites/orion/modules.yaml

@@ -5,3 +5,5 @@ modules:
     lmod:
       exclude:
       - ecflow
+      include:
+      - python

configs/sites/orion/packages.yaml

@@ -28,25 +28,8 @@ packages:
       prefix: /apps/gcc-10.2.0/openmpi-4.0.4/openmpi-4.0.4
       modules:
       - openmpi/4.0.4
-  python:
-    buildable: False
-    externals:
-    - spec: [email protected]
-      prefix: /work/noaa/da/jedipara/spack-stack/miniconda-3.9.7
-      modules:
-      - miniconda/3.9.7
-  py-pip:
-    buildable: False
-    externals:
-    - spec: [email protected]
-      prefix: /work/noaa/da/jedipara/spack-stack/miniconda-3.9.7
-      modules:
-      - miniconda/3.9.7
 
 ### Modifications of common packages
-  # Versions 1.73+ don't compile on orion (bootstrap.sh fails)
-  boost:
-    version:: ['1.72.0']
 
 ### All other external packages listed alphabetically
   autoconf:
@@ -65,11 +48,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  # Do not use, can lead to duplicate versions of nco being installed
-  #bison:
-  #  externals:
-  #  - spec: [email protected]
-  #    prefix: /usr
   bzip2:
     externals:
     - spec: [email protected]
@@ -78,7 +56,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  # Don't use OS curl, doesn't support secure transfers
   diffutils:
     externals:
     - spec: [email protected]
@@ -91,7 +68,7 @@ packages:
     buildable: False
     externals:
     - spec: [email protected]+ui+static_boost
-      prefix: /work/noaa/da/role-da/spack-stack/ecflow-5.8.4
+      prefix: /work/noaa/epic/role-epic/spack-stack/orion/ecflow-5.8.4
       modules:
       - ecflow/5.8.4
   file:
@@ -168,7 +145,7 @@ packages:
     buildable: False
     externals:
     - spec: [email protected]
-      prefix: /work/noaa/da/role-da/spack-stack/mysql-8.0.31
+      prefix: /work/noaa/epic/role-epic/spack-stack/orion/mysql-8.0.31
       modules:
       - mysql/8.0.31
   ncurses:
@@ -179,10 +156,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  openssl:
-    externals:
-    - spec: [email protected]
-      prefix: /usr
   perl:
     externals:
     - spec: [email protected]+cpanm+shared+threads
@@ -207,10 +180,6 @@ packages:
     externals:
     - spec: [email protected]
       prefix: /usr
-  sqlite:
-    externals:
-    - spec: [email protected]~fts~functions+rtree
-      prefix: /usr
   tar:
     externals:
     - spec: [email protected]

doc/source/MaintainersSection.rst

@@ -227,22 +227,18 @@ MSU Orion
 
 On Orion, it is necessary to change the default ``umask`` from ``0027`` to ``0022`` so that users not in the group of the role account can still see and use the software stack. This can be done by running ``umask 022`` after logging into the role account.
 
-miniconda
-   Follow the instructions in :numref:`Section %s <MaintainersSection_Miniconda>` to create a basic ``miniconda`` installation and associated modulefile for working with spack. Don't forget to log off and back on to forget about the conda environment.
-
 ecflow
   ``ecFlow`` must be built manually using the GNU compilers and linked against a static ``boost`` library. After installing `miniconda`, and loading the following modules, follow the instructions in :numref:`Section %s <MaintainersSection_ecFlow>`. Note that the default/system ``qt@5`` can be used on Orion.
 
 .. code-block:: console
 
    module purge
-   module use /work/noaa/da/jedipara/spack-stack/modulefiles
-   module load miniconda/3.9.7
+   module load python/3.9.2
    module load cmake/3.22.1
    module load gcc/10.2.0
 
 mysql
-  ``mysql`` must be installed separately from ``spack`` using a binary tarball provided by the MySQL community. Follow the instructions in :numref:`Section %s <MaintainersSection_MySQL>` to install ``mysql`` in ``/work/noaa/da/role-da/spack-stack/mysql-8.0.31``.
+  ``mysql`` must be installed separately from ``spack`` using a binary tarball provided by the MySQL community. Follow the instructions in :numref:`Section %s <MaintainersSection_MySQL>`.
 
 .. _MaintainersSection_Hercules: