add ghci container

E3SM-Project · Sep 11, 2024 · 917af3f · 917af3f
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diff --git a/.github/workflows/ghci.yaml b/.github/workflows/ghci.yaml
@@ -0,0 +1,80 @@
+name: ghci
+
+on:
+  pull_request:
+    branches: [ main ]
+    paths:
+      - 'ghci/**'
+      - '.github/workflows/ghci.yaml'
+  push:
+    branches: [ main ]
+    paths:
+      - 'ghci/**'
+      - '.github/workflows/ghci.yaml'
+    tags:
+      - 'ghci-*'
+
+env:
+  GCC_VERSION: "11.4.0"
+  MPICH_VERSION: "3.4.3"
+  SZIP_VERSION: "2.1.1"
+  HDF5_VERSION: "1.12.3"
+  NETCDFC_VERSION: "4.9.2"
+  NETCDFCXX_VERSION: "4.2"
+  NETCDFFORTRAN_VERSION: "4.6.1"
+  PNETCDF_VERSION: "1.12.1"
+
+jobs:
+  ocis:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    steps:
+      - 
+        name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          show-progress: false
+          persist-credentials: false
+      -
+        name: GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      -
+        name: Meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ghcr.io/${{ github.repository }}-ghci
+      -
+        name: QEMU
+        uses: docker/setup-qemu-action@v3
+      -
+        name: Buildx
+        uses: docker/setup-buildx-action@v3
+      -
+        name: Push
+        uses: docker/build-push-action@v6
+        with:
+          context: ghci/
+          file: ghci/Dockerfile
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          build-args: |
+            GCC_VERSION=${{ env.GCC_VERSION }}
+            MPICH_VERSION=${{ env.MPICH_VERSION }}
+            SZIP_VERSION=${{ env.SZIP_VERSION }}
+            HDF5_VERSION=${{ env.HDF5_VERSION }}
+            NETCDFC_VERSION=${{ env.NETCDFC_VERSION }}
+            NETCDFCXX_VERSION=${{ env.NETCDFCXX_VERSION }}
+            NETCDFFORTRAN_VERSION=${{ env.NETCDFFORTRAN_VERSION }}
+            PNETCDF_VERSION=${{ env.PNETCDF_VERSION }}
diff --git a/ghci/Dockerfile b/ghci/Dockerfile
@@ -0,0 +1,131 @@
+FROM spack/ubuntu-jammy:0.22.1
+
+ARG GCC_VERSION=11.4.0
+ARG MPICH_VERSION=3.4.3
+ARG SZIP_VERSION=2.1.1
+ARG HDF5_VERSION=1.12.3
+ARG NETCDFC_VERSION=4.9.2
+ARG NETCDFCXX_VERSION=4.2
+ARG NETCDFFORTRAN_VERSION=4.6.1
+ARG PNETCDF_VERSION=1.12.1
+
+ENV GCC_VERSION=${GCC_VERSION}
+ENV MPICH_VERSION=${MPICH_VERSION}
+ENV SZIP_VERSION=${SZIP_VERSION}
+ENV HDF5_VERSION=${HDF5_VERSION}
+ENV NETCDFC_VERSION=${NETCDFC_VERSION}
+ENV NETCDFCXX_VERSION=${NETCDFCXX_VERSION}
+ENV NETCDFFORTRAN_VERSION=${NETCDFFORTRAN_VERSION}
+ENV PNETCDF_VERSION=${PNETCDF_VERSION}
+
+RUN apt-get update
+RUN apt-get -y upgrade
+RUN apt-get -y remove cmake
+RUN apt-get -y install software-properties-common
+RUN add-apt-repository universe
+RUN apt-get update && apt-get -y install \
+    locales csh m4 libcurl4-openssl-dev \
+    libz-dev gcc g++ gfortran liblapack-dev make git \
+    git wget subversion libxml2-dev libxml2-utils libxml-libxml-perl \
+    libswitch-perl build-essential checkinstall zlib1g-dev libssl-dev python3-distutils
+
+# TODO: move to env file (spack.yaml)?
+RUN mkdir -p /opt/spack-environment \
+&&  (echo "spack:" \
+&&   echo " " \
+&&   echo "  definitions:" \
+&&   echo "    - compilers: [gcc@${GCC_VERSION}]" \
+&&   echo "    - mpis: [mpich@${MPICH_VERSION}]" \
+&&   echo "    - mpipkgs:"  \
+&&   echo "      - hdf5@${HDF5_VERSION}" \
+&&   echo "      - netcdf-c@${NETCDFC_VERSION}" \
+&&   echo "      - netcdf-cxx@${NETCDFCXX_VERSION}" \
+&&   echo "      - netcdf-fortran@${NETCDFFORTRAN_VERSION}" \
+&&   echo "      - parallel-netcdf@${PNETCDF_VERSION}" \
+&&   echo "    - othpkgs:" \
+&&   echo "      - cmake" \
+&&   echo "      - cprnc" \
+&&   echo " " \
+&&   echo "  specs:" \
+&&   echo "    - szip" \
+&&   echo "    - matrix:" \
+&&   echo "      - [\$mpis]" \
+&&   echo "      - [\$%compilers]" \
+&&   echo "    - matrix:" \
+&&   echo "      - [\$othpkgs]" \
+&&   echo "      - [\$%compilers]" \
+&&   echo "    - matrix:" \
+&&   echo "      - [\$mpipkgs]" \
+&&   echo "      - [\$^mpis]" \
+&&   echo "      - [\$%compilers]" \
+&&   echo " " \
+&&   echo "  concretizer:" \
+&&   echo "    unify: true" \
+&&   echo " " \
+&&   echo "  config:" \
+&&   echo "    install_tree: /opt/software" \
+&&   echo " " \
+&&   echo "  view: /usr/local/packages" \
+&&   echo "") > /opt/spack-environment/spack.yaml
+
+# TODO: do these intervene with each other?
+# https://cache.spack.io/tag/v0.22.1/
+RUN spack mirror add v0.22.1 https://binaries.spack.io/v0.22.1
+RUN spack buildcache keys --install --trust
+# https://cache.spack.io/tag/v0.22.1/?stack=e4s
+RUN spack mirror add v0.22.1-e4s https://binaries.spack.io/v0.22.1/e4s
+RUN spack buildcache keys --install --trust
+# https://cache.spack.io/tag/v0.22.1/?stack=root#
+RUN spack mirror add v0.22.1-root https://binaries.spack.io/v0.22.1/root
+RUN spack buildcache keys --install --trust
+# https://oaciss.uoregon.edu/e4s/inventory.html
+RUN spack mirror add E4S-24.0 https://cache.e4s.io/24.0
+RUN spack buildcache keys -it
+RUN spack mirror add E4S https://cache.e4s.io
+RUN spack buildcache keys -it
+
+RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
+
+RUN cd /opt/spack-environment && \
+    spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
+
+ENV INPUT_DATA_DIR=/projects/e3sm/inputdata
+RUN mkdir -p $INPUT_DATA_DIR
+
+RUN mkdir -p /projects/e3sm/inputdata/atm/cam/physprops/
+RUN wget https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/p3_lookup_table_1.dat-v4.1.2
+RUN mv p3_lookup_table_1.dat-v4.1.2 /projects/e3sm/inputdata/atm/cam/physprops/
+
+ENV USER=ghciocitester
+
+RUN git config --global user.email "${USER}@${USER}.${USER}"
+RUN git config --global user.name "${USER}"
+
+ARG DEBIAN_FRONTEND=noninteractive
+ENV TZ=America/Los_Angeles
+
+ENV LANGUAGE=en_US:en \
+    LANG=en_US.UTF-8
+
+# TODO: move this to a separate image (i.e., above is "base", below is "full")?
+RUN mkdir -p /app/ \
+&& (echo "" \
+&&  echo "cat /app/files.txt | while read -r line; do" \
+&&  echo "    file_url=\$line" \
+&&  echo "    file_loc=\${line//https\:\/\/web\.lcrc\.anl\.gov\/public\/e3sm\/inputdata/${INPUT_DATA_DIR}}" \
+&&  echo "    mkdir -p \$( dirname -- \"\$file_loc\")" \
+&&  echo "    touch \"\$file_loc\"" \
+&&  echo "    echo \"downloading from \$file_url\"" \
+&&  echo "    echo \"downloading to \$file_loc\"" \
+&&  echo "    wget -q -O \"\$file_loc\" \"\$file_url\"" \
+&&  echo "done" \
+&&  echo "") > /app/download.sh
+
+RUN chmod +x /app/download.sh
+
+COPY files.txt /app/files.txt
+RUN /app/download.sh
+
+# TODO: maybe add a test here or in the workflow?
+
+ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
diff --git a/ghci/files.txt b/ghci/files.txt
@@ -0,0 +1,117 @@
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/dvel/regrid_vegetation.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/ocn/docn7/domain.ocn.1x1.111007.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/ndepdata/fndep_elm_cbgc_exp_simyr1849-2101_1.9x2.5_c190103.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/sulfate_rrtmg_c080918.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/dust_aeronet_rrtmg_c141106.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/paramdata/clm_params_c211124.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/emissions-cmip6_e3sm_SOAG0_surf_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/waccm/gw/newmfspectra40_dc25.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/scream/init/rrtmgp-data-lw-g128-210809.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_CH3CHO_surface_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/solar/Solar_2010control_input4MIPS_c20181017.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/ocn/docn7/SSTDATA/sst_ice_CMIP6_DECK_E3SM_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/waccm/phot/temp_prs_GT200nm_JPL10_c130206.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_NO_surface_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/surfdata_map/surfdata_ne4pg2_simyr2000_c190620_with_TOP.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_CH3COCH3_surface_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/phot/o2src.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_CH2O_surface_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so4_a2_surf_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/phot/exo_coldens.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/ub/clim_p_trop.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/paramdata/clm_params_c180301.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/pdepdata/fpdep_clm_hist_simyr2000_1.9x2.5_c150929.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/ssam_rrtmg_c100508.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/F_nwvl200_mu20_lam50_res64_t298_c080428.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DMSflux.2010.1deg_latlon_conserv.POPmonthlyClimFromACES4BGC_c20190220.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/share/domains/domain.ocn.oQU480.151209.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/rof/mosart/US_reservoir_8th_NLDAS3_c20161220_updated_20170314.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/iceoptics_c080917.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a1_surf_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/waccm/phot/RSF_GT200nm_v3.0_c080811.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so2_elev_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/bcpho_rrtmg_c100508.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so2_surf_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so4_a1_surf_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/rof/mosart/MOSART_Global_2deg_antarctica_flowing_to_north_c09162020.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/ocphi_rrtmg_c100508.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/paramdata/CNP_parameters_c131108.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/firedata/elmforc.ssp5_hdm_0.5x0.5_simyr1850-2100_c190109.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_so4_a1_elev_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/methane/ch4_oxid_1.9x2.5_L26_1990-1999clim.c090804.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/cpl/gridmaps/oQU480/map_oQU480_to_ne4pg2_mono.200527.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_bc_a4_surf_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mam/atmsrf_ne4pg2_200527.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/mam4_mode3_rrtmg_aeronetdust_c141106.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/ice/mpas-seaice/general/snicar_drdt_bst_fit_60_c04262019.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/cpl/gridmaps/ne4pg2/map_ne4pg2_to_oQU480_mono.200527.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/scream/init/rrtmgp-data-sw-g112-210809.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_MTERP_surface_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/scream/init/vertical_coordinates_L72_20220927.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_ISOP_surface_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/ub/ubvals_b40.20th.track1_1996-2005_c110315.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/mam5_mode5_rrtmg_sig1.2_dgnl.40_c03072023.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/snicardata/snicar_optics_5bnd_mam_c160322.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/dvel/clim_soilw.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/emissions-cmip6_e3sm_SOAG0_elev_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/cpl/cpl6/map_r2_to_oQU480_nn.210211.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/mam4_mode2_rrtmg_c130628.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/dvel/season_wes.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a1_elev_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/waccm/sulf/SAD_SULF_1950-2011_1.9x2.5_c130102.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/ub/Linoz_Chlorine_Loading_CMIP6_0003-2017_c20171114.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/scream/init/screami_ne4np4L72_20220823.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/oxid/oxid_1.9x2.5_L26_1850-2015_c20181106.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart/ub/linv3_1849-2017_CMIP6_Hist_10deg_58km_c20230705.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_C3H8_surface_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_pom_a4_surf_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_NO2_aircraft_vertical_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/cpl/gridmaps/ne4pg2/map_r2_to_ne4pg2_mono.210211.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/share/domains/domain.lnd.ne4pg2_oQU480.200527.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/ice/mpas-seaice/general/snicar_optics_5bnd_snow_and_aerosols.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/chem_gases/2degrees/emissions-cmip6_e3sm_C2H6_surface_2010_clim_1.9x2.5_c20230213.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/ocn/mpas-o/oQU480/ocean.QU.480km.151209.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/waccm/sulf/sulfate.ar5_camchem_c130304.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/datm7/NASA_LIS/clmforc.Li_2012_climo1995-2011.T62.lnfm_Total_c140423.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a4_elev_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/waccm/phot/wasolar_ave.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/scream/init/rrtmgp-cloud-optics-coeffs-lw.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/chem/trop_mozart_aero/emis/DECK_ne30/cmip6_mam4_num_a2_elev_1x1_2010_clim_c20190821.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/cpl/gridmaps/ne4pg2/map_ne4pg2_to_oQU480_bilin.200527.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/lnd/clm2/paramdata/CNP_parameters_c180529.nc
+https://web.lcrc.anl.gov/public/e3sm/inputdata/atm/cam/physprops/mam4_mode4_rrtmg_c130628.nc
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