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Bugfixes and gfs physics update (ufs-community#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
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‎FV3‎

Submodule FV3 updated from 45dbc34 to 5bfd3c6

‎README.md‎

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

‎WW3‎

Submodule WW3 updated 284 files

‎compsets/all.input‎

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

‎compsets/fv3.input‎

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

‎compsets/hera.input‎

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

‎compsets/wcoss.input‎

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LONG_TEST_QUEUE='&LONGQ;'
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BUILD_QUEUE='&BUILDQ;'
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MACHINE_ID='wcoss.phase2'
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BASELINE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
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BASELINE_TEMPLATE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
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BASELINE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
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BASELINE_TEMPLATE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
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default_resources={
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cores_per_node=16
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cpus_per_core=2
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MACHINE_ID='wcoss.phase1'
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BASELINE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
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BASELINE_TEMPLATE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
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BASELINE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
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BASELINE_TEMPLATE="/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
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DEFAULT_TEST_WALLTIME=2700
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BASELINE="/gpfs/dell2/emc/modeling/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
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BASELINE_TEMPLATE="/gpfs/dell2/emc/modeling/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
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BASELINE="/gpfs/dell2/emc/modeling/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
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BASELINE_TEMPLATE="/gpfs/dell2/emc/modeling/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
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BUILD_WALLTIME="3600"
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DEFAULT_TEST_WALLTIME=1800
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BASELINE="/gpfs/hps3/emc/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
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BASELINE_TEMPLATE="/gpfs/hps3/emc/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191021"
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BASELINE="/gpfs/hps3/emc/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
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BASELINE_TEMPLATE="/gpfs/hps3/emc/nems/noscrub/emc.nemspara/RT/NEMSfv3gfs/trunk-20191109"
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execution_time_modules=[[[
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module load alps

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