Update develop from gsd/develop 2020/11/20: Unified gravity wave drag, updates to other GSL physics

.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}