release/1.5.0: site config and doc updates round 2 (S4, aws-pcluster,…

… Discover, Nautilus, JCSDA CI containers) (#775)

* Update S4 site config
* Update site config for aws-pcluster
* Update versions in configs/containers/README.md, cleanup unused parts
* Update discover site config
* Update nautilus site config
* Update to ip 4.3.0
* Update documentation
* [skip ci] Add python module to module includes on acorn

---------

Co-authored-by: Alex Richert <alexander.richert@noaa.gov>
Co-authored-by: Alex Richert <82525672+AlexanderRichert-NOAA@users.noreply.github.com>

configs/common/packages.yaml

@@ -18,7 +18,6 @@
       version: ['2.4.1']
     bison:
       version: ['3.8.2']
-    # 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

configs/containers/README.md

@@ -7,41 +7,23 @@ To avoid hardcoding specs in the generic container recipes, we keep the specs li
   specs: [base-env@1.0.0, jedi-base-env@1.0.0 ~fftw, 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@12.0.0, ecbuild@3.7.2, eccodes@2.27.0, ecflow@5,
     eckit@1.24.4, ecmwf-atlas@0.34.0 +trans ~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@1.10.0, gftl-shared@1.5.0,
-    gsibec@1.1.3, hdf@4.2.15, hdf5@1.14.1-2, ip@3.3.3, jasper@2.0.32, jedi-cmake@1.4.0,
+    fckit@0.11.0, fms@release-jcsda, g2@3.4.5, g2tmpl@1.10.2, gftl-shared@1.5.0,
+    gsibec@1.1.3, hdf@4.2.15, hdf5@1.14.0, ip@4.3.0, 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@4.6.0, nlohmann-json@3.10.5, nlohmann-json-schema-validator@2.1.0,
     parallelio@2.5.10, parallel-netcdf@1.12.2, py-eccodes@1.4.2, py-f90nml@1.4.3,
     py-gitpython@3.1.27, py-h5py@3.7.0, py-numpy@1.22.3,
-    py-pandas@1.4.0, py-pip, py-pyyaml@6.0, py-scipy@1.9.3, py-shapely@1.8.0, py-xarray@2022.3.0,
-    sp@2.3.3, udunits@2.2.28, w3nco@2.4.1, nco@5.0.6, esmf@8.4.2, mapl@2.35.2,
-    yafyaml@0.5.1, zlib@1.2.13, odc@1.4.6, shumlib@macos_clang_linux_intel_port]
+    py-pandas@1.5.3, py-pip, py-pyyaml@5.4.1, py-scipy@1.9.3, py-shapely@1.8.0, py-xarray@2022.3.0,
+    sp@2.3.3, udunits@2.2.28, w3nco@2.4.1, w3emc@2.10.0, nco@5.0.6, esmf@8.4.2, mapl@2.35.2,
+    yafyaml@0.5.1, zlib@1.2.13, zstd@1.5.2, odc@1.4.6, shumlib@macos_clang_linux_intel_port,
+    awscli@1.27.84, py-globus-cli@3.16.0]
     # Don't build CRTM by default so that it gets built in the JEDI bundles:
     # crtm@v2.4.1-jedi
     # Comment out for now until build problems are solved
     # https://github.com/jcsda/spack-stack/issues/522
     # py-mysql-connector-python@8.0.32
 ```
 
-### spack-stack-1.5.0 / ufs-weather-model-x.y.z containers for ufs-weather-model as of July 5, 2023
-
-**Note. This is not yet working correctly, some libraries are missing. Please do not use yet! Also, if using the clang-mpich container, need to disable openmp for fms, not clear how to do this cleanly.**
-
-```
-  specs: [base-env@1.0.0,
-    bacio@2.4.1, bison@3.8.2, bufr@12.0.0, ecbuild@3.7.2, eccodes@2.27.0, ecflow@5,
-    eckit@1.24.4, ecmwf-atlas@0.34.0 +trans ~fftw, fiat@1.2.0, ectrans@1.2.0 ~fftw, eigen@3.4.0,
-    fckit@0.11.0, fms@2023.01, g2@3.4.5, g2tmpl@1.10.0, gftl-shared@1.5.0,
-    gsibec@1.1.3, hdf@4.2.15, hdf5@1.14.1-2, ip@3.3.3, 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@4.6.0, nlohmann-json@3.10.5, nlohmann-json-schema-validator@2.1.0,
-    parallelio@2.5.10, parallel-netcdf@1.12.2, py-eccodes@1.4.2, py-f90nml@1.4.3,
-    py-gitpython@3.1.27, py-h5py@3.7.0, py-numpy@1.22.3, py-pandas@1.4.0,
-    py-pip, py-pyyaml@6.0, py-scipy@1.9.3, py-shapely@1.8.0, py-xarray@2022.3.0,
-    sp@2.3.3, udunits@2.2.28, w3emc@2.9.2, w3nco@2.4.1, nco@5.0.6, esmf@8.4.2, mapl@2.35.2,
-    yafyaml@0.5.1, zlib@1.2.13, odc@1.4.6, crtm@2.4.0, crtm-fix@2.4.0_emc]
-```
-
 ### Create an AMI on AWS EC2 to build docker containers
 
 AMI ami-0a934b7133c2b7102 (dom-docker-builder-full-backup-20230217; JCSDA-NOAA account, us-east-1) was created following the instructions below

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

@@ -235,8 +235,6 @@ spack:
         echo "export CXX=clang++" >> /root/.bashrc && \
         echo "export FC=gfortran" >> /root/.bashrc && \
         printf "[credential]\n    helper = cache --timeout=7200\n" >> /root/.gitconfig
-        # Source spack environment script for root
-        RUN echo "source /etc/profile.d/z10_spack_environment.sh\n" >> /root/.bashrc
 
     # Labels for the image
     labels:

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

@@ -184,8 +184,6 @@ spack:
         RUN echo "export OMPI_ALLOW_RUN_AS_ROOT=1" >> /root/.bashrc && \
         echo "export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1" >> /root/.bashrc && \
         echo "export OMPI_MCA_rmaps_base_oversubscribe=1" >> /root/.bashrc
-        # Source spack environment script for root
-        RUN echo "source /etc/profile.d/z10_spack_environment.sh\n" >> /root/.bashrc
 
     # Labels for the image
     labels:

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

@@ -211,8 +211,6 @@ spack:
         echo "source /opt/intel/oneapi/compiler/latest/env/vars.sh" >> /root/.bashrc && \
         echo "source /opt/intel/oneapi/mpi/latest/env/vars.sh" >> /root/.bashrc && \
         printf "[credential]\n    helper = cache --timeout=7200\n" >> /root/.gitconfig
-        # Source spack environment script for root
-        RUN echo "source /etc/profile.d/z10_spack_environment.sh\n" >> /root/.bashrc
 
     # Labels for the image
     labels:

configs/sites/acorn/modules.yaml

@@ -2,3 +2,6 @@ modules:
   default:
     enable::
     - lmod
+    lmod:
+      include:
+      - python

configs/sites/aws-pcluster/modules.yaml

@@ -4,7 +4,6 @@ modules:
     - lmod
     lmod:
       include:
-      # List of packages for which we need modules that are blacklisted by default
       - python
       exclude:
       - ecflow

configs/sites/aws-pcluster/packages.yaml

@@ -43,21 +43,11 @@ packages:
     externals:
     - spec: binutils@2.34
       prefix: /usr
-  bison:
-    externals:
-    - spec: bison@3.5.1
-      prefix: /usr
   boost:
     buildable: False
     externals:
     - spec: boost@1.71.0 +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
       prefix: /usr
-  # Don't use external cmake, this confuses the spack concretizer
-  # leading to duplicate packages being installed.
-  #cmake:
-  #  externals:
-  #  - spec: cmake@3.16.3
-  #    prefix: /usr
   coreutils:
     externals:
     - spec: coreutils@8.30
@@ -120,13 +110,6 @@ packages:
     externals:
     - spec: openssh@8.2p1
       prefix: /usr
-  # Don't use external openssl, this confuses the spack concretizer
-  # leading to duplicate packages (libarchive with different compression
-  # settings, somehow triggered by different cmake versions) being installed.
-  #openssl:
-  #  externals:
-  #  - spec: openssl@1.1.1f
-  #    prefix: /usr
   perl:
     externals:
     - spec: perl@5.30.0~cpanm+shared+threads

configs/sites/discover/modules.yaml

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

configs/sites/discover/packages.yaml

@@ -3,7 +3,6 @@ packages:
     compiler:: [intel@2022.0.1, gcc@10.1.0]
     providers:
       mpi:: [intel-oneapi-mpi@2021.5.0, openmpi@4.1.3]
-    target: [ivybridge]
 
 ### MPI, Python, MKL
   mpi:
@@ -20,20 +19,6 @@ packages:
       prefix: /discover/swdev/jcsda/spack-stack/openmpi-4.1.3/gcc-10.1.0
       modules:
       - openmpi/4.1.3-gcc-10.1.0
-  python:
-    buildable: False
-    externals:
-    - spec: python@3.9.7
-      prefix: /discover/swdev/jcsda/spack-stack/miniconda-3.9.7/
-      modules:
-      - miniconda/3.9.7
-  py-pip:
-    buildable: False
-    externals:
-    - spec: py-pip@21.2.4
-      prefix: /discover/swdev/jcsda/spack-stack/miniconda-3.9.7/
-      modules:
-      - miniconda/3.9.7
 
 ### Modification of common packages
 
@@ -57,25 +42,10 @@ packages:
     externals:
     - spec: berkeley-db@4.8.30
       prefix: /usr
-  # Don't use, leads to duplicate packages being built
-  #bison:
-  #  externals:
-  #  - spec: bison@2.7
-  #    prefix: /usr
   ccache:
     externals:
     - spec: ccache@3.1.9
       prefix: /usr
-  # Don't use external cmake, this confuses the spack concretizer
-  # leading to duplicate packages being installed.
-  #cmake:
-  #  externals:
-  #  - spec: cmake@3.5.2
-  #    prefix: /usr
-  #  - spec: cmake@3.21.0
-  #    prefix: /usr/local/other/cmake/3.21.0
-  #    modules:
-  #    - cmake/3.21.0
   cpio:
     externals:
     - spec: cpio@2.11
@@ -185,10 +155,6 @@ packages:
   # Old re2c on Discover unable to build newer versions of ninja
   ninja:
     version:: ['1.10.2']
-  openssl:
-    externals:
-    - spec: openssl@1.0.2j-fips
-      prefix: /usr
   perl:
     externals:
     - spec: perl@5.18.2~cpanm+shared+threads
@@ -213,10 +179,6 @@ packages:
     externals:
     - spec: sed@4.2.2
       prefix: /usr
-  sqlite:
-    externals:
-    - spec: sqlite@3.8.10.2~fts~functions+rtree
-      prefix: /usr
   texinfo:
     externals:
     - spec: texinfo@4.13

configs/sites/nautilus/compilers.yaml

@@ -34,7 +34,4 @@ compilers:
         PATH: '/opt/rh/gcc-toolset-11/root/usr/bin'
         CPATH: '/opt/rh/gcc-toolset-11/root/usr/include'
         LD_LIBRARY_PATH: '/opt/scyld/slurm/lib64:/opt/scyld/slurm/lib64/slurm:/p/app/compilers/intel/oneapi/compiler/2022.0.2/linux/compiler/lib/intel64_lin:/opt/rh/gcc-toolset-11/root/usr/lib64:/opt/rh/gcc-toolset-11/root/usr/lib'
-      # For intel-oneapi-mpi only
-      #set:
-      #  I_MPI_ROOT: '/p/app/compilers/intel/oneapi/mpi/2021.5.1'
     extra_rpaths: []

configs/sites/nautilus/packages.yaml

@@ -60,18 +60,10 @@ packages:
     externals:
     - spec: binutils@2.30.117
       prefix: /usr
-  bison:
-    externals:
-    - spec: bison@3.0.4
-      prefix: /usr
   coreutils:
     externals:
     - spec: coreutils@8.30
       prefix: /usr
-  #curl:
-  #  externals:
-  #  - spec: curl@7.61.1+gssapi+ldap+nghttp2
-  #    prefix: /usr
   diffutils:
     externals:
     - spec: diffutils@3.6
@@ -129,10 +121,6 @@ packages:
     externals:
     - spec: openssh@8.0p1
       prefix: /usr
-  openssl:
-    externals:
-    - spec: openssl@1.1.1k
-      prefix: /usr
   perl:
     externals:
     - spec: perl@5.26.3~cpanm+open+shared+threads

configs/sites/s4/modules.yaml

@@ -7,3 +7,4 @@ modules:
       - ecflow
       include:
       - mpich
+      - python

configs/sites/s4/packages.yaml

@@ -1,8 +1,12 @@
 packages:
   all:
-    compiler:: [intel@2021.5.0, gcc@9.3.0]
+    # Removing gcc/mpich for now, not working as expected
+    #compiler:: [intel@2021.5.0, gcc@9.3.0]
+    #providers:
+    #  mpi:: [intel-oneapi-mpi@2021.5.0, mpich@4.0.1]
+    compiler:: [intel@2021.5.0]
     providers:
-      mpi:: [intel-oneapi-mpi@2021.5.0, mpich@4.0.1]
+      mpi:: [intel-oneapi-mpi@2021.5.0]
 
 ### MPI, Python, MKL
   mpi:
@@ -11,31 +15,13 @@ packages:
     externals:
     - spec: intel-oneapi-mpi@2021.5.0%intel@2021.5.0
       prefix: /opt/intel/oneapi/2022.1
-      modules:
-      - intel/2022.1
-  mpich:
-    externals:
-    - spec: mpich@4.0.1%gcc@9.3.0 ~hydra device=ch4
-      prefix: /data/prod/hpc-stack/gnu-9.3.0/mpich/4.0.1
-      modules:
-      - mpich/4.0.1
-  python:
-    buildable: False
-    externals:
-    - spec: python@3.9.12
-      prefix: /data/prod/jedi/spack-stack/miniconda-3.9.12
-      modules:
-      - miniconda/3.9.12
-  py-pip:
-    buildable: False
-    externals:
-    - spec: py-pip@21.2.4
-      prefix: /data/prod/jedi/spack-stack/miniconda-3.9.12
-      modules:
-      - miniconda/3.9.12
-  # Versions 1.73+ don't compile on s4 (bootstrap.sh fails)
-  boost:
-    version:: ['1.72.0']
+  # Commenting this out for now, not working as expected
+  #mpich:
+  #  externals:
+  #  - spec: mpich@4.0.1%gcc@9.3.0 ~hydra device=ch4
+  #    prefix: /data/prod/hpc-stack/gnu-9.3.0/mpich/4.0.1
+  #    modules:
+  #    - mpich/4.0.1
 
 ### All other external packages listed alphabetically
   autoconf:
@@ -54,30 +40,14 @@ packages:
     externals:
     - spec: berkeley-db@5.3.21
       prefix: /usr
-  # Do not use, can lead to duplicate versions of nco being installed
-  #bison:
-  #  externals:
-  #  - spec: bison@3.0.4
-  #    prefix: /usr
   bzip2:
     externals:
     - spec: bzip2@1.0.6
       prefix: /usr
-  # Don't use external cmake, this confuses the spack concretizer
-  # leading to duplicate packages being installed
-  #cmake:
-  #  externals:
-  #  - spec: cmake@3.20.5
-  #    prefix: /usr
   cpio:
     externals:
     - spec: cpio@2.11
       prefix: /usr
-  # Don't use OS curl on S4, incomplete
-  #curl:
-  #  externals:
-  #  - spec: curl@7.29.0+ldap
-  #    prefix: /usr
   diffutils:
     externals:
     - spec: diffutils@3.3
@@ -178,10 +148,6 @@ packages:
     externals:
     - spec: openssh@7.4p1
       prefix: /usr
-  openssl:
-    externals:
-    - spec: openssl@1.0.2k-fips
-      prefix: /usr
   perl:
     externals:
     - spec: perl@5.16.3~cpanm+shared+threads
@@ -206,10 +172,6 @@ packages:
     externals:
     - spec: sed@4.2.2
       prefix: /usr
-  sqlite:
-    externals:
-    - spec: sqlite@3.7.17~fts~functions+rtree
-      prefix: /usr
   tar:
     externals:
     - spec: tar@1.26