Update develop from gsd/develop 2020/11/20: Unified gravity wave drag…

…, updates to other GSL physics (ufs-community#297)

- add unified gravity wave drag (called unified ugwp) that combines the UGWP v1 with the GSL drag suite
- replace high-resolution SAR (standalone regional) regression test with 25km SAR regression test
- update submodule pointer for fv3atm for the changes described in the associated PRs listed below
- add `rt_ccpp_dev.conf` that contains the developmental CCPP tests used by GSL and DTC (so that folks are aware of what is tested and how by DTC and GSL, in addition to what is in `rt.conf` and `rt_gnu.conf`)
- turn on calls to `gcycle`/`sfcsub` for RUC LSM
- regression test configuration scripts for MYNN surface layer
- add `fv3_debug` modules for cheyenne.intel and cheyenne.gnu (per request from @DeniseWorthen)
- bugfix in `rt.sh` to copy two missing input directories `fv3_regional_quilt_netcdf_parallel` and `fv3_stretched_nest_debug` when creating new baselines using `rt.sh -c`
- enable regression testing on Gaea with Intel using the current hpc-stack-nco installation, can now use ecflow
- update of CI tests and small bugfix when comparing results using `tests/compare_ncfile.py` from @MinsukJi-NOAA (see ufs-community#299 for details) - note, the update to `tests/compare_ncfile.py` had to be reverted

Co-authored-by: DomHeinzeller <[email protected]>
Co-authored-by: samuel.trahan <[email protected]>
Co-authored-by: hannah barnes <[email protected]>
Co-authored-by: Michael Toy <[email protected]>
Co-authored-by: Samuel Trahan (NOAA contractor) <[email protected]>
Co-authored-by: MinsukJi-NOAA <[email protected]>

.github/workflows/main.yml

@@ -68,7 +68,7 @@ jobs:
     - name: Free up disk space
       run: |
         sudo docker rmi $(sudo docker image ls | grep -E -m1 '<none>' | awk '{ print $3 }')
-        sudo docker rmi $(sudo docker image ls | awk '/ci-test-base/ { print $3 }')
+        sudo docker rmi $(sudo docker image ls | awk '/ubuntu-hpc/ { print $3 }')
 
     - name: Prepare artifacts
       run: |

.github/workflows/manage.yml

@@ -22,15 +22,15 @@ jobs:
           tr_id=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py get_trigger_id)
           tr_br=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py get_trigger_br)
           check=$(cat ${GITHUB_EVENT_PATH} | ./json_helper.py check_skip)
-          echo "::set-env name=TRIGGER_ID::${tr_id}"
-          echo "::set-env name=TRIGGER_BR::${tr_br}"
+          echo "TRIGGER_ID=${tr_id}" >> $GITHUB_ENV
+          echo "TRIGGER_BR=${tr_br}" >> $GITHUB_ENV
           echo "skip-ci: ${check}"
           if [[ $check == yes ]]; then
             echo "skip-ci is requested"
-            echo '::set-env name=CURR_JOB::cancelled'
+            echo "CURR_JOB=cancelled" >> $GITHUB_ENV
             curl -X POST -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" -H "Accept: application/vnd.github.v3+json" ${repo}/$tr_id/cancel
           else
-            echo '::set-env name=CURR_JOB::running'
+            echo "CURR_JOB=running" >> $GITHUB_ENV
           fi
 
       - name: Cancel redundant jobs

cmake/configure_cheyenne.intel.cmake

@@ -1,2 +1,3 @@
-set(INLINE_POST     ON CACHE BOOL "Enable inline post" FORCE)
+set(INLINE_POST     ON  CACHE BOOL "Enable inline post" FORCE)
+set(PARALLEL_NETCDF ON  CACHE BOOL "Enable parallel NetCDF" FORCE)
 set(DEBUG_LINKMPI   OFF CACHE BOOL "Enable linkmpi option when DEBUG mode is on" FORCE)

cmake/configure_gaea.intel.cmake

@@ -1,2 +1,3 @@
-set(INLINE_POST     ON CACHE BOOL "Enable inline post" FORCE)
+set(INLINE_POST     ON  CACHE BOOL "Enable inline post" FORCE)
+set(PARALLEL_NETCDF ON  CACHE BOOL "Enable parallel NetCDF" FORCE)
 set(DEBUG_LINKMPI   OFF CACHE BOOL "Enable linkmpi option when DEBUG mode is on" FORCE)

modulefiles/cheyenne.gnu/fv3_debug

@@ -0,0 +1,45 @@
+#%Module
+
+proc ModulesHelp {} {
+  puts stderr "\tcit - loads modules required for building and running UFS Model on Cheyenne/GNU"
+}
+
+module-whatis "loads UFS Model prerequisites for Cheyenne/GNU"
+
+module load cmake/3.16.4
+setenv CMAKE_C_COMPILER mpicc
+setenv CMAKE_CXX_COMPILER mpicxx
+setenv CMAKE_Fortran_COMPILER mpif90
+setenv CMAKE_Platform cheyenne.gnu
+
+# load programming environment
+module load ncarenv/1.3
+module load gnu/9.1.0
+module load mpt/2.22
+module load ncarcompilers/0.5.0
+module unload netcdf
+
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-nco-20201113/modulefiles/stack
+module load hpc/1.0.0-beta1
+module load hpc-gnu/9.1.0
+module load hpc-mpt/2.22
+
+module load jasper/2.0.22
+module load zlib/1.2.11
+module load png/1.6.35
+
+module load hdf5/1.10.6
+module load netcdf/4.7.4
+module load pio/2.5.1
+module load esmf/8_1_0_beta_snapshot_27-debug
+
+module load bacio/2.4.1
+module load crtm/2.3.0
+module load g2/3.4.1
+module load g2tmpl/1.9.1
+module load ip/3.3.3
+module load nemsio/2.5.2
+module load sp/2.3.3
+module load w3emc/2.7.3
+module load w3nco/2.4.1
+module load upp/10.0.0

modulefiles/cheyenne.intel/fv3_debug

@@ -0,0 +1,45 @@
+#%Module
+
+proc ModulesHelp {} {
+  puts stderr "\tcit - loads modules required for building and running UFS Model on Cheyenne/Intel"
+}
+
+module-whatis "loads UFS Model prerequisites for Cheyenne/Intel"
+
+module load cmake/3.16.4
+setenv CMAKE_C_COMPILER mpicc
+setenv CMAKE_CXX_COMPILER mpicxx
+setenv CMAKE_Fortran_COMPILER mpif90
+setenv CMAKE_Platform cheyenne.intel
+
+# load programming environment
+module load ncarenv/1.3
+module load intel/19.1.1
+module load mpt/2.22
+module load ncarcompilers/0.5.0
+module unload netcdf
+
+module use /glade/p/ral/jntp/GMTB/tools/hpc-stack-nco-20201113/modulefiles/stack
+module load hpc/1.0.0-beta1
+module load hpc-intel/19.1.1
+module load hpc-mpt/2.22
+
+module load jasper/2.0.22
+module load zlib/1.2.11
+module load png/1.6.35
+
+module load hdf5/1.10.6
+module load netcdf/4.7.4
+module load pio/2.5.1
+module load esmf/8_1_0_beta_snapshot_27-debug
+
+module load bacio/2.4.1
+module load crtm/2.3.0
+module load g2/3.4.1
+module load g2tmpl/1.9.1
+module load ip/3.3.3
+module load nemsio/2.5.2
+module load sp/2.3.3
+module load w3emc/2.7.3
+module load w3nco/2.4.1
+module load upp/10.0.0

modulefiles/gaea.intel/fv3

@@ -1,59 +1,50 @@
-#%Module######################################################################
-##
-##    NEMS FV3 Prerequisites: Gaea/Intel
+#%Module
 
 proc ModulesHelp {} {
-  puts stderr "\tcit - loads modules required for building and running FV3 under NEMS on Gaea/Intel"
+  puts stderr "\tcit - loads modules required for building and running UFS Model on Gaea/Intel"
 }
 
-module-whatis "loads NEMS FV3 prerequisites for Gaea/Intel"
+module-whatis "loads UFS Model prerequisites for Gaea/Intel"
 
-# NOTE: the "module purge" and loading of the module command are
-# handled by the module-setup.sh (or .csh) script.
-
-##
-## load programming environment
-## this typically includes compiler, MPI and job scheduler
-##
 module load PrgEnv-intel/6.0.5
 module rm intel
 module rm cray-mpich
 module rm netcdf
 module load intel/18.0.6.288
 module load cray-mpich/7.7.11
+module load cray-python/3.7.3.2
+
+module load cmake/3.17.0
+setenv CMAKE_C_COMPILER cc
+setenv CMAKE_CXX_COMPILER CC
+setenv CMAKE_Fortran_COMPILER ftn
+setenv CMAKE_Platform gaea.intel
+
+module use /lustre/f2/pdata/esrl/gsd/ufs/hpc-stack-nco-20201116/modulefiles/stack
 
-##
-## use pre-compiled PNG, NetCDF, ESMF and NCEP libraries for above compiler / MPI combination
-##
-module use -a /lustre/f2/pdata/esrl/gsd/ufs/ufs-stack-20200909/intel-18.0.6.288/cray-mpich-7.7.11/modules
+module load hpc/1.0.0-beta1
+module load hpc-intel/18.0.6.288
+module load hpc-cray-mpich/7.7.11
 
-module load libpng/1.6.35
+module load jasper/2.0.15
+module load zlib/1.2.11
+module load png/1.6.35
+
+module load hdf5/1.10.6
 module load netcdf/4.7.4
-module load esmf/8.1.0bs27
+module load pio/2.5.1
+module load esmf/8_1_0_beta_snapshot_27
 
-module load bacio/2.4.0
+module load bacio/2.4.1
 module load crtm/2.3.0
-module load g2/3.4.0
-module load g2tmpl/1.9.0
-module load ip/3.3.0
-module load nceppost/dceca26
-module load nemsio/2.5.1
-module load sp/2.3.0
-module load w3emc/2.7.0
-module load w3nco/2.4.0
-
-module load gfsio/1.4.0
-module load sfcio/1.4.0
-module load sigio/2.3.0
+module load g2/3.4.1
+module load g2tmpl/1.9.1
+module load ip/3.3.3
+module load nemsio/2.5.2
+module load sp/2.3.3
+module load w3emc/2.7.3
+module load w3nco/2.4.1
+module load upp/10.0.0
 
 # Needed at runtime:
 module load alps
-
-##
-## load cmake
-##
-module load cmake/3.17.0
-setenv CMAKE_C_COMPILER cc
-setenv CMAKE_CXX_COMPILER CC
-setenv CMAKE_Fortran_COMPILER ftn
-setenv CMAKE_Platform gaea.intel

modulefiles/linux.gnu/fv3

@@ -26,7 +26,7 @@ export CMAKE_Fortran_COMPILER=${FC}
 ##
 ## use own NetCDF library
 ##
-export NETCDF=${NETCDF:-/usr/local}
+export NETCDF=${NETCDF:-/home/builder/opt}
 
 ##
 ## use SIONlib library if installed and environment variable is set
@@ -41,10 +41,10 @@ fi
 ##
 ## use pre-compiled EMSF library for above compiler / MPI combination
 ##
-export ESMFMKFILE=${ESMFMKFILE:-/usr/local/lib/esmf.mk}
+export ESMFMKFILE=${ESMFMKFILE:-/home/builder/opt/lib/esmf.mk}
 
 ##
 ## NCEP libraries (need to download and build manually, see doc/README_{UBUNTU,CENTOS,...}.txt and https://github.com/NCAR/NCEPlibs)
 ##
-export NCEPLIBS_DIR=${NCEPLIBS_DIR:-/usr/local/NCEPlibs}
+export NCEPLIBS_DIR=${NCEPLIBS_DIR:-/home/builder/opt}
 export CMAKE_PREFIX_PATH=${NCEPLIBS_DIR}