Update CTM to be in line with GEOSgcm 10.19.5

.github/workflows/release-tarball.yml

@@ -0,0 +1,38 @@
+name: Create Complete Release Tarball
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  release:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+        with:
+          path: ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
+
+      - name: Checkout mepo
+        uses: actions/checkout@v2
+        with:
+          repository: GEOS-ESM/mepo
+          path: mepo
+
+      - name: Run mepo
+        run : |
+          cd ${GITHUB_WORKSPACE}/${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
+          ${GITHUB_WORKSPACE}/mepo/mepo clone
+
+      - name: Create tarball
+        run: |
+          tar --exclude-vcs --exclude=.mepo -cf ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}.COMPLETE.tar ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}
+          xz -T6 ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}.COMPLETE.tar
+
+      - name: Upload tarball
+        run: |
+          gh release upload ${{ github.event.release.tag_name }} ${{ github.event.repository.name }}-${{ github.event.release.tag_name }}.COMPLETE.tar.xz -R ${{ github.repository_owner }}/${{ github.event.repository.name }}
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+

.github/workflows/workflow.yml

@@ -6,6 +6,7 @@ on:
     # Do not run if the only files changed cannot affect the build
     paths-ignore:
       - "**.md"
+      - "**.json"
       - "parallel_build.csh"
       - ".github/CODEOWNERS"
       - ".codebuild/**"
@@ -17,7 +18,7 @@ jobs:
     if: "!contains(github.event.pull_request.labels.*.name, '0 diff trivial')"
     runs-on: ubuntu-latest
     container:
-      image: gmao/ubuntu20-geos-env-mkl:v6.2.4-openmpi_4.0.5-gcc_10.3.0
+      image: gmao/ubuntu20-geos-env-mkl:v6.2.8-openmpi_4.0.6-gcc_11.2.0
       credentials:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
         password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -43,7 +44,6 @@ jobs:
         run: |
           mepo clone
           mepo status
-          mepo status
       - name: Update other branches
         if:
           "!contains('refs/heads/main,refs/heads/develop', github.ref)"

CMakeLists.txt

@@ -34,6 +34,7 @@ set (FV_PRECISION "R8" CACHE STRING "Precision of FV3 core (R4, R4R8, R8)")
 foreach (dir cmake @cmake cmake@)
   if (EXISTS ${CMAKE_CURRENT_LIST_DIR}/${dir})
     list (APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/${dir}")
+    set (ESMA_CMAKE_PATH "${CMAKE_CURRENT_LIST_DIR}/${dir}" CACHE PATH "Path to ESMA_cmake code")
   endif ()
 endforeach ()
 include (esma)
@@ -63,5 +64,14 @@ install(
    DESTINATION ${CMAKE_INSTALL_PREFIX}
    )
 
-# Adds abiilty to tar source
+# Adds ability to tar source
 include (esma_cpack)
+
+# This installs a tarball of the source code
+# in the installation directory.
+# MUST BE THE LAST CODE IN THIS FILE
+option(INSTALL_SOURCE_TARFILE "Create and install source tarfile" OFF)
+if(INSTALL_SOURCE_TARFILE)
+  install(CODE "set(CMAKE_PROJECT_NAME \"${CMAKE_PROJECT_NAME}\")")
+  install(SCRIPT "${ESMA_CMAKE_PATH}/esma_postinstall.cmake")
+endif()

README.md

@@ -101,6 +101,20 @@ you choose.
 
 If all you wish is to build the model, you can run `parallel_build.csh` from a head node. Doing so will checkout all the external repositories of the model and build it. When done, the resulting model build will be found in `build/` and the installation will be found in `install/` with setup scripts like `ctm_setup` in `install/bin`.
 
+#### Develop Version of GEOS CTM
+
+`parallel_build.csh` provides a special flag for checking out the
+development branch of GMAO_Shared. If you run:
+
+```
+parallel_build.csh -develop
+```
+then `mepo` will run:
+
+```
+mepo develop GMAO_Shared
+```
+
 #### Debug Version of GEOS
 
 To obtain a debug version, you can run `parallel_build.csh -debug` which will build with debugging flags. This will build in `build-Debug/` and install into `install-Debug/`.
@@ -126,6 +140,20 @@ The first command initializes the multi-repository and the second one
 clones and assembles all the sub-repositories according to
 `components.yaml`
 
+#### Checking out develop branches of GEOSgcm_GridComp, GEOSgcm_App, and GMAO_Shared
+
+To get the development branch of GMAO_Shared (a la
+the `-develop` flag for `parallel_build.csh`, one needs to run the
+equivalent `mepo` command. As mepo itself knows (via `components.yaml`) what the development branch of each
+subrepository is, the equivalent of `-develop` for `mepo` is to
+checkout the development branch of GMAO_Shared:
+```
+mepo develop GMAO_Shared
+```
+
+This must be done *after* `mepo clone` as it is running a git command in
+each sub-repository.
+
 #### Build the Model
 
 ##### Load Compiler, MPI Stack, and Baselibs
@@ -157,6 +185,14 @@ This will install to a directory parallel to your `build` directory. If you pref
 ```
 and CMake will install there.
 
+###### Create and install source tarfile
+
+Note that running with `parallel_build.csh` will create and install a tarfile of the source code at build time. But if CMake is run by hand, this is not the default action (as many who build with CMake by hand are developers and not often running experiments). In order to enable this at install time, add:
+```
+-DINSTALL_SOURCE_TARFILE=ON
+```
+to your CMake command.
+
 ##### Build and Install with Make
 ```
 make -jN install

components.yaml

@@ -5,13 +5,13 @@ GEOSctm:
 env:
   local: ./@env
   remote: ../ESMA_env.git
-  tag: v3.4.0
+  tag: v3.6.0
   develop: main
 
 cmake:
   local: ./@cmake
   remote: ../ESMA_cmake.git
-  tag: v3.6.2
+  tag: v3.7.2
   develop: develop
 
 ecbuild:
@@ -22,14 +22,14 @@ ecbuild:
 GMAO_Shared:
   local: ./src/Shared/@GMAO_Shared
   remote: ../GMAO_Shared.git
-  tag: v1.4.10
+  tag: v1.4.11
   sparse: ./config/GMAO_Shared.sparse
   develop: main
 
 MAPL:
   local: ./src/Shared/@MAPL
   remote: ../MAPL.git
-  tag: v2.8.6
+  tag: v2.12.1
   develop: develop
 
 FMS:
@@ -41,13 +41,13 @@ FMS:
 FVdycoreCubed_GridComp:
   local: ./src/Components/GEOSctm_GridComp/@FVdycoreCubed_GridComp
   remote: ../FVdycoreCubed_GridComp.git
-  tag: v1.2.17
+  tag: v1.3.0
   develop: develop
 
 fvdycore:
   local: ./src/Components/GEOSctm_GridComp/@FVdycoreCubed_GridComp/@fvdycore
   remote: ../GFDL_atmos_cubed_sphere.git
-  tag: geos/v1.1.7
+  tag: geos/v1.2.0
   develop: geos/develop
 
 GEOSchem_GridComp:

parallel_build.csh

@@ -32,7 +32,7 @@ end
 
 if (-d ${ESMADIR}/@env || -d ${ESMADIR}/env@ || -d ${ESMADIR}/env) then
    if ( "$DEVELOP" == "TRUE" ) then
-      echo "Checking out development branches of GMAO_Shared"
+      echo "Checking out development branch of GMAO_Shared"
       mepo develop GMAO_Shared
    endif
 else
@@ -46,7 +46,7 @@ else
          mepo init
          mepo clone
       if ( "$DEVELOP" == "TRUE" ) then
-         echo "Checking out development branches of GEOSgcm_GridComp, GEOSgcm_App, and GMAO_Shared"
+         echo "Checking out development branch of GMAO_Shared"
          mepo develop GMAO_Shared
       endif
       endif

src/Applications/GEOSctm_App/CMakeLists.txt

@@ -50,6 +50,12 @@ else ()
   set(CFG_BUILT_ON_ROME FALSE)
 endif ()
 
+if(INSTALL_SOURCE_TARFILE)
+  set(CFG_INSTALL_SOURCE_TARFILE TRUE)
+else()
+  set(CFG_INSTALL_SOURCE_TARFILE FALSE)
+endif()
+
 set (setup_scripts
    ctm_setup
    )
@@ -59,6 +65,5 @@ foreach (file ${setup_scripts})
    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${file} DESTINATION bin)
 endforeach ()
 
-
 configure_file(.GEOSCTM_VERSION .GEOSCTM_VERSION @ONLY)
 install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/.GEOSCTM_VERSION DESTINATION etc)

src/Applications/GEOSctm_App/ctm_convert.j

@@ -85,9 +85,9 @@ set  GEOSCTM_LM = `grep  GEOSctm_LM: $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
 set     OGCM_IM = `grep      "OGCM\.IM_WORLD:" $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
 set     OGCM_JM = `grep      "OGCM\.JM_WORLD:" $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
 
->>>COUPLED<<<set  OGCM_LM  = `grep "OGCM\.LM:" $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
->>>COUPLED<<<set       NX = `grep  "OGCM\.NX:" $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
->>>COUPLED<<<set       NY = `grep  "OGCM\.NY:" $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
+@COUPLED set  OGCM_LM  = `grep "OGCM\.LM:" $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
+@COUPLED set       NX = `grep  "OGCM\.NX:" $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
+@COUPLED set       NY = `grep  "OGCM\.NY:" $HOMDIR/GEOSCTM.rc | cut -d':' -f2`
 
 # Set ATMOS and OCEAN Horizontal Resolution Tags
 # ----------------------------------------------
@@ -97,8 +97,8 @@ set OGCM_IM_Tag = `echo $OGCM_IM | awk '{printf "%4.4i", $1}'`
 set OGCM_JM_Tag = `echo $OGCM_JM | awk '{printf "%4.4i", $1}'`
 
 >>>FVCUBED<<<set ATMOStag = CF${GEOSCTM_IM_Tag}x6C
->>>DATAOCEAN<<<set OCEANtag = DE${OGCM_IM_Tag}xPE${OGCM_JM_Tag}
->>>COUPLED<<<set OCEANtag = TM${OGCM_IM_Tag}xTM${OGCM_JM_Tag}
+@DATAOCEAN set OCEANtag = DE${OGCM_IM_Tag}xPE${OGCM_JM_Tag}
+@COUPLED set OCEANtag = TM${OGCM_IM_Tag}xTM${OGCM_JM_Tag}
 
 #######################################################################
 #   Move to Scratch Directory and Copy RC Files from Home Directory
@@ -191,13 +191,13 @@ endif
 setenv BCSDIR   @BCSDIR
 setenv SSTDIR   @SSTDIR
 setenv CHMDIR   @CHMDIR
->>>DATAOCEAN<<<setenv BCRSLV    @ATMOStag_@OCEANtag
->>>COUPLED<<<setenv BCRSLV    @ATMOStag_DE0360xPE0180
+@DATAOCEAN setenv BCRSLV    @ATMOStag_@OCEANtag
+@COUPLED setenv BCRSLV    @ATMOStag_DE0360xPE0180
 setenv DATELINE DC
 
->>>COUPLED<<<setenv GRIDDIR  @COUPLEDIR/a${GEOSCTM_IM}x${GEOSCTM_JM}_o${OGCM_IM}x${OGCM_JM}
->>>COUPLED<<<setenv BCTAG `basename $GRIDDIR`
->>>DATAOCEAN<<<setenv BCTAG `basename $BCSDIR`
+@COUPLED setenv GRIDDIR  @COUPLEDIR/a${GEOSCTM_IM}x${GEOSCTM_JM}_o${OGCM_IM}x${OGCM_JM}
+@COUPLED setenv BCTAG `basename $GRIDDIR`
+@DATAOCEAN setenv BCTAG `basename $BCSDIR`
 
 >>>OSTIA<<<set YEAR = `cat cap_restart | cut -c1-4`
 
@@ -206,24 +206,24 @@ set             FILE = linkbcs
 cat << _EOF_ > $FILE
 #!/bin/csh -f
 
->>>COUPLED<<</bin/mkdir -p RESTART
+@COUPLED /bin/mkdir -p RESTART
 /bin/mkdir -p            ExtData
 /bin/ln    -sf $CHMDIR/* ExtData
 
->>>COUPLED<<</bin/ln -sf $GRIDDIR/SEAWIFS_KPAR_mon_clim.${OGCM_IM}x${OGCM_JM} SEAWIFS_KPAR_mon_clim.data
->>>COUPLED<<</bin/ln -sf $GRIDDIR/@[email protected]   tile.data
->>>COUPLED<<</bin/ln -sf $GRIDDIR/@[email protected]   runoff.bin
->>>COUPLED<<</bin/ln -sf $GRIDDIR/tripolar_${OGCM_IM}x${OGCM_JM}.ascii .
->>>COUPLED<<</bin/ln -sf $GRIDDIR/vgrid${OGCM_LM}.ascii ./vgrid.ascii
->>>COUPLED<<</bin/ln -s @COUPLEDIR/a@HIST_IMx@HIST_JM_o${OGCM_IM}x${OGCM_JM}/DC0@HIST_IMxPC0@[email protected] tile_hist.data
+@COUPLED /bin/ln -sf $GRIDDIR/SEAWIFS_KPAR_mon_clim.${OGCM_IM}x${OGCM_JM} SEAWIFS_KPAR_mon_clim.data
+@COUPLED /bin/ln -sf $GRIDDIR/@[email protected]   tile.data
+@COUPLED /bin/ln -sf $GRIDDIR/@[email protected]   runoff.bin
+@COUPLED /bin/ln -sf $GRIDDIR/tripolar_${OGCM_IM}x${OGCM_JM}.ascii .
+@COUPLED /bin/ln -sf $GRIDDIR/vgrid${OGCM_LM}.ascii ./vgrid.ascii
+@COUPLED /bin/ln -s @COUPLEDIR/a@HIST_IMx@HIST_JM_o${OGCM_IM}x${OGCM_JM}/DC0@HIST_IMxPC0@[email protected] tile_hist.data
 
 # Precip correction
 #/bin/ln -s /discover/nobackup/projects/gmao/share/gmao_ops/fvInput/merra_land/precip_CPCUexcludeAfrica-CMAP_corrected_MERRA/GEOSdas-2_1_4 ExtData/PCP
 
->>>DATAOCEAN<<</bin/ln -sf $BCSDIR/$BCRSLV/${BCRSLV}-Pfafstetter.til  tile.data
->>>DATAOCEAN<<<if(     -e  $BCSDIR/$BCRSLV/${BCRSLV}-Pfafstetter.TIL) then
->>>DATAOCEAN<<</bin/ln -sf $BCSDIR/$BCRSLV/${BCRSLV}-Pfafstetter.TIL  tile.bin
->>>DATAOCEAN<<<endif
+@DATAOCEAN /bin/ln -sf $BCSDIR/$BCRSLV/${BCRSLV}-Pfafstetter.til  tile.data
+@DATAOCEAN if(     -e  $BCSDIR/$BCRSLV/${BCRSLV}-Pfafstetter.TIL) then
+@DATAOCEAN /bin/ln -sf $BCSDIR/$BCRSLV/${BCRSLV}-Pfafstetter.TIL  tile.bin
+@DATAOCEAN endif
 
 # DAS or REPLAY Mode (GEOSCTM.rc:  pchem_clim_years = 1-Year Climatology)
 # --------------------------------------------------------------------
@@ -240,22 +240,22 @@ cat << _EOF_ > $FILE
 /bin/ln -sf $BCSDIR/Shared/*bin .
 /bin/ln -sf $BCSDIR/Shared/*c2l*.nc4 .
 
->>>DATAOCEAN<<</bin/ln -sf $BCSDIR/$BCRSLV/visdf_@RES_DATELINE.dat visdf.dat
->>>DATAOCEAN<<</bin/ln -sf $BCSDIR/$BCRSLV/nirdf_@RES_DATELINE.dat nirdf.dat
->>>DATAOCEAN<<</bin/ln -sf $BCSDIR/$BCRSLV/vegdyn_@RES_DATELINE.dat vegdyn.data
->>>DATAOCEAN<<</bin/ln -sf $BCSDIR/$BCRSLV/lai_clim_@RES_DATELINE.data lai.data
->>>DATAOCEAN<<</bin/ln -sf $BCSDIR/$BCRSLV/green_clim_@RES_DATELINE.data green.data
+@DATAOCEAN /bin/ln -sf $BCSDIR/$BCRSLV/visdf_@RES_DATELINE.dat visdf.dat
+@DATAOCEAN /bin/ln -sf $BCSDIR/$BCRSLV/nirdf_@RES_DATELINE.dat nirdf.dat
+@DATAOCEAN /bin/ln -sf $BCSDIR/$BCRSLV/vegdyn_@RES_DATELINE.dat vegdyn.data
+@DATAOCEAN /bin/ln -sf $BCSDIR/$BCRSLV/lai_clim_@RES_DATELINE.data lai.data
+@DATAOCEAN /bin/ln -sf $BCSDIR/$BCRSLV/green_clim_@RES_DATELINE.data green.data
 /bin/ln -sf $BCSDIR/$BCRSLV/ndvi_clim_@RES_DATELINE.data ndvi.data
 
->>>COUPLED<<<if( $OGCM_IM == 1440 ) then
->>>COUPLED<<</bin/ln -sf $GRIDDIR/ndvi.data ndvi.data
->>>COUPLED<<<endif 
+@COUPLED if( $OGCM_IM == 1440 ) then
+@COUPLED /bin/ln -sf $GRIDDIR/ndvi.data ndvi.data
+@COUPLED endif 
 
->>>COUPLED<<</bin/ln -sf $GRIDDIR/visdf.dat visdf.dat
->>>COUPLED<<</bin/ln -sf $GRIDDIR/nirdf.dat nirdf.dat
->>>COUPLED<<</bin/ln -sf $GRIDDIR/vegdyn.data vegdyn.data
->>>COUPLED<<</bin/ln -sf $GRIDDIR/lai.dat lai.data
->>>COUPLED<<</bin/ln -sf $GRIDDIR/green.dat green.data
+@COUPLED /bin/ln -sf $GRIDDIR/visdf.dat visdf.dat
+@COUPLED /bin/ln -sf $GRIDDIR/nirdf.dat nirdf.dat
+@COUPLED /bin/ln -sf $GRIDDIR/vegdyn.data vegdyn.data
+@COUPLED /bin/ln -sf $GRIDDIR/lai.dat lai.data
+@COUPLED /bin/ln -sf $GRIDDIR/green.dat green.data
 /bin/ln -sf $BCSDIR/$BCRSLV/topo_DYN_ave_@RES_DATELINE.data topo_dynave.data
 /bin/ln -sf $BCSDIR/$BCRSLV/topo_GWD_var_@RES_DATELINE.data topo_gwdvar.data
 /bin/ln -sf $BCSDIR/$BCRSLV/topo_TRB_var_@RES_DATELINE.data topo_trbvar.data
@@ -264,10 +264,10 @@ cat << _EOF_ > $FILE
 >>>FVCUBED<<</bin/ln -sf $BCSDIR/$BCRSLV/Gnomonic_$BCRSLV.dat .
 >>>FVCUBED<<<endif
 
->>>COUPLED<<<@CPEXEC $HOMDIR/*_table .
->>>COUPLED<<<@CPEXEC $GRIDDIR/INPUT/* INPUT
->>>COUPLED<<</bin/ln -sf $GRIDDIR/cice/kmt_cice.bin .
->>>COUPLED<<</bin/ln -sf $GRIDDIR/cice/grid_cice.bin .
+@COUPLED @CPEXEC $HOMDIR/*_table .
+@COUPLED @CPEXEC $GRIDDIR/INPUT/* INPUT
+@COUPLED /bin/ln -sf $GRIDDIR/cice/kmt_cice.bin .
+@COUPLED /bin/ln -sf $GRIDDIR/cice/grid_cice.bin .
 
 _EOF_
 
@@ -441,7 +441,7 @@ end
 
 @CPEXEC $FNDDIR/cap_restart $ORGDIR
 
->>>COUPLED<<<@CPEXEC $CNVDIR/RESTART/* INPUT
+@COUPLED @CPEXEC $CNVDIR/RESTART/* INPUT
 
 #######################################################################
 #             Set Experiment Run Parameters that were altered