Bugfixes and gfs physics update (NOAA-EMC#9)

* Squashed commit from JessicaMeixner-NOAA/ww3update branch
* remove fv3_regional_c768 test on cray
* remove jobs with exclusive nodes on hera and jet
* add ww3 files in rt.sh
* add README.md and reset tasks for rt.sh test fv3_gfdlmprad
* comment out rt.sh fv3_wrtGauss_nemsio_c768 as it takes too long to run
* remove weightfiles for comparison in fv3-ww3 tests
* update regression test log files from dell and cray
* update regression log files on hera
* update fv3atm repo to NOAA-EMC

README.md

@@ -0,0 +1,46 @@
+[![Read The Docs Status](https://readthedocs.org/projects/ufs-weather-model/badge/?badge=latest)](http://ufs-weather-model.readthedocs.io/)
+
+# ufs-weather-model
+
+This is the UFS weather model code.
+
+# Where to find information
+
+Start at the [ufs-weather-model wiki](https://github.com/ufs-community/ufs-weather-model/wiki) which has quick start instructions.
+
+[User's reference guide](http://ufs-weather-model.readthedocs.io/) is hosted on read the docs.
+
+# What files are what
+
+The top level directory structure groups source code and input files as follow:
+
+| File/directory    | Purpose |
+| --------------    | ------- |
+| ```LICENSE.md```  | A copy of the Gnu lesser general public license, version 3. |
+| ```README.md```   | This file with basic pointers to more information. |
+| ```FMS/```        | Contains Flexible Modeling System source code. |
+| ```NEMS/```       | Contains NOAA Environmental Modeling System source code and nems compset runi scripts. |
+| ```FV3/```        | Contains FV3 atmosphere model component including fv3 dynamics core, dynsmics to physics driver, physics and io. |
+| ```WW3/```        | Contains community wave modeling framework WW3. |
+| ```stochastic physics/``` | Contains the stochastic physics source code. |
+| ```conf/```       | Contains compile option files on various platforms. |
+| ```compsets/```   | Contains NEMSCompsetRun regression test compset information. |
+| ```log/```        | Contains log files from NEMSCompsetRun regression test.|
+| ```modulefiles/``` | Contains module files on various platforms.|
+| ```parm/```       | Contains model configuration and namelist templates.|
+| ```doc/```        | Workspace for documentation. |
+
+# Disclaimer
+
+The United States Department of Commerce (DOC) GitHub project code is provided
+on an "as is" basis and the user assumes responsibility for its use. DOC has
+relinquished control of the information and no longer has responsibility to
+protect the integrity, confidentiality, or availability of the information. Any
+claims against the Department of Commerce stemming from the use of its GitHub
+project will be governed by all applicable Federal law. Any reference to
+specific commercial products, processes, or services by service mark,
+trademark, manufacturer, or otherwise, does not constitute or imply their
+endorsement, recommendation or favoring by the Department of Commerce. The
+Department of Commerce seal and logo, or the seal and logo of a DOC bureau,
+shall not be used in any manner to imply endorsement of any commercial product
+or activity by DOC or the United States Government.

compsets/all.input

@@ -7,7 +7,7 @@ run fv3_ccpp_control            @ fv3, standard, ccpptrans, plat==hera.intel
 run fv3_restart                 @ fv3, standard, baseline
 run fv3_read_inc                @ fv3, standard, baseline
 run fv3_gfdlmp                  @ fv3, standard, baseline
-run fv3_gfdlmprad               @ fv3, standard, baseline, ww3, plat==wcoss_dell_p3,plat==wcoss.cray
+run fv3_gfdlmprad               @ fv3, standard, baseline, ww3, plat==hera.intel,plat==wcoss_dell_p3,plat==wcoss.cray
 run fv3_gfdlmprad_gwd           @ fv3, standard, baseline
 run fv3_gfdlmprad_noahmp        @ fv3, standard, baseline
 run fv3_thompson                @ fv3, standard, baseline
@@ -22,7 +22,7 @@ run fv3_wrtGauss_netcdf_esmf    @ fv3, standard, baseline
 run fv3_wrtGauss_netcdf         @ fv3, standard, baseline
 run fv3_wrtGauss_nemsio         @ fv3, standard, baseline
 
-run fv3_wrtGauss_nemsio_c768    @ fv3,           baseline, ww3, plat==wcoss.cray
+run fv3_wrtGauss_nemsio_c768    @ fv3,           baseline, ww3, plat==hera.intel, plat==wcoss.cray, plat==wcoss_dell_p3
 run fv3_wrtGauss_nemsio_c192    @ fv3, standard, baseline
 run fv3_stochy                  @ fv3, standard, baseline
 run fv3_iau                     @ fv3, standard, baseline
@@ -38,7 +38,7 @@ run fv3_stretched_nest_quilt    @ fv3, standard, baseline, plat==wcoss.cray, pla
 run fv3_regional_control        @ fv3, standard, baseline
 run fv3_regional_restart        @ fv3, standard, baseline
 run fv3_regional_quilt          @ fv3, standard, baseline
-run fv3_regional_c768           @ fv3, standard, baseline
+run fv3_regional_c768           @ fv3, standard, baseline, plat==wcoss_dell_p3, plat==wcoss.phase1, plat==wcoss.phase2,plat==hera.intel
 
 run fv3_control_debug           @ fv3, standard,           plat==hera.intel
 run fv3_stretched_nest_debug    @ fv3, standard,           plat==hera.intel

compsets/fv3.input

@@ -1210,10 +1210,10 @@ test fv3_gfdlmprad: fv3_ww3.exe {
         'RESTART/sfc_data.tile4.nc'             .bitcmp. "@[CNTL]/RESTART/"
         'RESTART/sfc_data.tile5.nc'             .bitcmp. "@[CNTL]/RESTART/"
         'RESTART/sfc_data.tile6.nc'             .bitcmp. "@[CNTL]/RESTART/"
+        'out_grd.glo_30m'                       .bitcmp. "@[CNTL]"
         "@[build%target]" .md5cmp. "@[fv3_ww3.exe%md5sum]"
     }
 
-
     spawn execute {
         {"@[build%target]", ranks="@[TASKS]" }
     }
@@ -1634,7 +1634,6 @@ test fv3_wrtGauss_netcdf_esmf: fv3.exe {
     }
 }
 
-
 ########################################################################
 
 test fv3_wrtGauss_nemsio_c192: fv3.exe {
@@ -1763,7 +1762,6 @@ test fv3_wrtGauss_nemsio_c768: fv3_ww3.exe {
     CNTL_NAME="fv3_wrtGauss_nemsio_c768"
 
     TASKS='1752'
-    TPN='12'
     PPN="@[plat%C768_PPN]"
     INPES='16'
     JNPES='16'
@@ -1878,7 +1876,7 @@ test fv3_wrtGauss_nemsio_c768: fv3_ww3.exe {
         'RESTART/sfc_data.tile4.nc'             .bitcmp. "@[CNTL]/RESTART/"
         'RESTART/sfc_data.tile5.nc'             .bitcmp. "@[CNTL]/RESTART/"
         'RESTART/sfc_data.tile6.nc'             .bitcmp. "@[CNTL]/RESTART/"
-
+        'out_grd.glo_30m'                       .bitcmp. "@[CNTL]"
       # Executable validation.  This makes an MD5 sum of the fv3.exe
       # for comparison against the MD5 sum made in the build job.
       # This is to ensure the executable did not change during the

compsets/hera.input

@@ -16,8 +16,12 @@ platform hera.intel {
 
     cores_per_node=40 # Number of cores per node on compute nodes
     cpus_per_core=2
+    C768_PPN=30
 
-    # The *nems locations are in NEMS checkout areas.
+ # hera testing: using longer run time
+    DEFAULT_TEST_WALLTIME=3000
+
+ #  The *nems locations are in NEMS checkout areas.
     HOMEnems=PWD_UP5
 
     # The *rt locations are auto-generated areas.
@@ -26,8 +30,8 @@ platform hera.intel {
     # INPUTS is the input directory, which should contain fix and parm
     # files, plus any restarts or other inputs.
 
-    BASELINE="/scratch1/NCEPDEV/nems/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
-    BASELINE_TEMPLATE="/scratch1/NCEPDEV/nems/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
+    BASELINE="/scratch1/NCEPDEV/nems/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
+    BASELINE_TEMPLATE="/scratch1/NCEPDEV/nems/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
     INPUTS="@[BASELINE]"
 
     default_resources={

compsets/wcoss.input

@@ -26,8 +26,8 @@ platform wcoss.phase2 {
     LONG_TEST_QUEUE='&LONGQ;'
     BUILD_QUEUE='&BUILDQ;'
     MACHINE_ID='wcoss.phase2'
-    BASELINE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
-    BASELINE_TEMPLATE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
+    BASELINE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
+    BASELINE_TEMPLATE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
 
     default_resources={
         TASKS=156
@@ -121,8 +121,8 @@ platform wcoss.phase1 {
     cores_per_node=16
     cpus_per_core=2
     MACHINE_ID='wcoss.phase1'
-    BASELINE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
-    BASELINE_TEMPLATE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
+    BASELINE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
+    BASELINE_TEMPLATE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
 
     # WCOSS Phase 2 has been slow of late.
     DEFAULT_TEST_WALLTIME=2700
@@ -206,8 +206,8 @@ platform wcoss_dell_p3 {
     LONG_TEST_QUEUE='&LONGQ;'
     BUILD_QUEUE='&BUILDQ;'
 
-    BASELINE="/gpfs/dell2/emc/modeling/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
-    BASELINE_TEMPLATE="/gpfs/dell2/emc/modeling/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
+    BASELINE="/gpfs/dell2/emc/modeling/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
+    BASELINE_TEMPLATE="/gpfs/dell2/emc/modeling/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
 
     default_resources={
         TASKS=156
@@ -304,8 +304,8 @@ platform wcoss.cray {
     BUILD_WALLTIME="3600"
     DEFAULT_TEST_WALLTIME=1800
 
-    BASELINE="/gpfs/hps3/emc/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
-    BASELINE_TEMPLATE="/gpfs/hps3/emc/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
+    BASELINE="/gpfs/hps3/emc/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
+    BASELINE_TEMPLATE="/gpfs/hps3/emc/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
 
     execution_time_modules=[[[
       module load alps