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gsd/develop: update from NOAA-EMC develop #22

Merged
merged 22 commits into from
May 20, 2020
Merged

gsd/develop: update from NOAA-EMC develop #22

merged 22 commits into from
May 20, 2020

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climbfuji
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@climbfuji climbfuji commented May 15, 2020 •
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This PR updates the NOAA-GSD gsd/develop branch of ufs-weather-model with the latest version from NOAA-EMC (ufs-community) develop.

Associated PRs:

NOAA-GSL/GFDL_atmos_cubed_sphere#2
NOAA-GSL/ccpp-framework#3
NOAA-GSL/ccpp-physics#28
NOAA-GSL/fv3atm#28
#22

See below for regression testing information.

junwang-noaa and others added 19 commits February 4, 2020 14:42
@junwang-noaa @DusanJovic-NOAA
parallel netcdf writes, inpost with no thread (ufs-community#43)
31821b0 
* update parallel netcdf module files on dell

* update fv3 to netcdf_parallel branch

* update module files for hera, dell and conf file for cray

* update post lib in cray module file

* fix netlib on hera

* Update FV3 submodule

* Update baselines to develop-20200202

* Regtest logs on wcoss_dell_p3

* Regtest logs on wcoss_cray

* Regtest logs on hera

* update FV3 to point to NOAA-EMC develop branch

Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
@junwang-noaa
Iaudrymass coupledfield ww3 (ufs-community#56)
47c7f9b 
* update with new iau_drymassfixer option
* fix syntax error in fv3
* update fv3_iau test case
* revert iau-drymassfixer change in fv3_gfdlmprad_32bit_post
* update ww3 with bug fix for OpenMp b4b
* update fv3 with coupled model dump field changes
* update nemscompset run c768 fv3-ww3 to use threads
* update NEMS to the latest version
* update post lib to 8.0.5
@junwang-noaa @DusanJovic-NOAA
Sm feb242020 (ufs-community#72)
efd63fb 
* add 2 way atm-wav test

* update FV3 with gcycle change reverted

* update RTPWD and change the coupling frequency

* update RT baseline directory

* Regression test log files on WCOSS Dell

* Regression test log files on WCOSS Cray

* Regression test log files on Hera

* Update FV3 submodule

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
@DusanJovic-NOAA
fix omp error in dycore and atmos_model.F90 (ufs-community#80)
0a88706 
* Update FV3 submodule

* Regression test log files on Hera

* Regression test log files on WCOSS Cray

* Regression test log files on WCOSS Dell

* Update FV3 submodule
@climbfuji
Update EMC develop from NCAR dtc/develop 2020/03/17 (ufs-community#84)
44604a0 
* hera.gnu build target with regression test config rt_gnu.conf (same as used on Cheyenne); this initial version uses the UFS public release v1.0.0 NCEPLIBS
* re-enable IPD REPRO, CCPP REPRO, CCPP PROD regression tests; IPD REPRO and CCPP REPRO are bit-for-bit identical
* bugfixes for some CCPP regression tests (IAU dry mass fixer)
* addition of two-way coupled CCPP regression tests, removal of old IPD Thompson test, addition of several debug tests (Thompson non-aero and GSD suite) to cover more physics options in DEBUG mode
* change logic in rt.sh that COMPILE or APPBUILD lines without a machine name are executed on all machines (similar to what is done for the RUN lines)
@climbfuji
Coupled model: IPD-CCPP b4b for coupled model, bugfix for stochastic …
db103ca 
…physics (ufs-community#91)

* Update .gitmodules and submodule pointer for fv3atm for code review and testing

* Regression test logs for hera.intel using rt.sh

* Regression test logs for wcoss_dell_p3 using NEMSCompsetRun

* Update submodule pointer for FV3 after renaming S2S suite suite_FV3_GFS_2017_coupled_satmedmf.xml to suite_FV3_GFS_2017_satmedmf_coupled.xml

* Regression test logs for wcoss_dell_p3 using rt.sh; regression test logs for wcoss_cray using rt.sh and NEMSCompsetRun

* Regression test logs for hera.intel using NEMSCompsetRun

* Revert change to .gitmodules and update submodule pointer for fv3atm
@TomBlack-NOAA
Regional BC blending and BCs into GSI (ufs-community#83)
7097078
@AnningCheng-NOAA
Options for IN/CNN and MERRA2 climo of microphysics (ufs-community#90)
7c3cdca 
Add two options for IN/CCN activation and have total three options now:
* iccn=0 for temperature dependence, iccn=1 for climatological IN/CCN, and iccn=2 for MERRA2aersol
* add the option to enable RRTMg aerosol attenuation to be determined from prescribed MERRA2 climatology
* add aerosol optical depth outputs for total, dust, black carbon, organic carbon, sulfate, and sea salt

Add 4 regression tests:
 1) SAS+GFDL with enabled RRTMg aerosol attenuation from prescribed MERRA2 climatology (fv3_gocart_clm in rt.conf_csaw),
 2) CSAW+MG3 with with enabledRRTMg aerosol attenuation from prescribed MERRA2 climatology (fv3_gfsv16_csawmg  in rt.conf_csaw),
 3) CSAW+MG3 with enabled RRTMg aerosol attenuation from OPAC (fv3_gfsv16_csawmgt in rt.conf_csaw), and
 4) CSAW+MG3 with climatological IN/CCN with enabled RRTMg aerosol attenuation from prescribed MERRA2climatology (fv3_csawmg)
@climbfuji @aerorahul
Merge NCAR:dtc/develop into develop 2020/04/14 (ufs-community#102)
3b16cad 
* add s4 rules

* update submodule pointers

* update the branch in gitmodules to point to NEMS::feature/s4

* Update .gitmodules and submodule pointer for ccpp-physics for code review and testing

* Merge NCAR:dtc/develop into ufs-community:develop

- for macOS with LLVM clang, turn off OpenMP (from UFS public release)
- switch to Intel 18 on wcoss_cray
- new regression tests with RRTMGP using current control as basis

Co-authored-by: Rahul Mahajan <rmahajan@s4-submit.ssec.wisc.edu>
Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com>
@DusanJovic-NOAA
Port to Orion (ufs-community#105)
8baa79d
@climbfuji
Remove dynamic CCPP build (ufs-community#107)
ce9fefb 
* Remove CCPP dynamic build from ufs-weather-model
* Remove LD_LIBRARY_PATH entries in regression test setup scripts
@junwang-noaa @JongilHan66
@jswhit2 @DomHeinzeller @climbfuji @DeniseWorthen
Chsp latlon post (ufs-community#108)
d202a02 
* update post lib to 8.0.6
* Add chsp to gfsphysics and ccpp-physics
add global_latlon grid on write grid comp for netcdf output
add landsfcmdl attribute to fv3 sfc history file
update post to post/8.0.6
* Bugfix for Intel 18 on wcoss_cray, remove Intel 16 options for gaea
* add global latlon grid test
* Add regression tests for lheatstrg to IPD REPRO, CCPP REPRO, CCPP PROD; add regression tests for satmedmfvidfq for IPD PROD, IPD REPRO, CCPP REPRO, CCPP PROD; add ecflow config for cheyenne
* add cmeps integration changes

Co-authored-by: Jun Wang <junwang-noaa@users.noreply.github.com>
Co-authored-by: Jongil Han <Jongil.Han@noaa.gov>
Co-authored-by: Jeffrey Whitaker <Jeffrey.S.Whitaker@noaa.gov>
Co-authored-by: Dom Heinzeller <dom.heinzeller@noaa.gov>
Co-authored-by: Dom Heinzeller <climbfuji@ymail.com>
Co-authored-by: Denise Worthen <Denise.Worthen@noaa.gov>
Co-authored-by: Jun Wang <junwang@Orion-login-3.HPC.MsState.Edu>
@lisa-bengtsson
Ca develop (ufs-community#96)
6585dd5 
Updates to cellular automata stochastic physics. Added new regression test. Added possibility to run global and sub-grid CA, updates to coupling to convection.
@DusanJovic-NOAA
Remove all IPD and all REPRO tests from rt.conf (ufs-community#117)
8b0d9b7
@DusanJovic-NOAA
Bugfixes from public release (ufs-community#119)
95fcb7c 
* Remove unused and unsupported code (See ufs-community#21)
* Remove APPBUILD step from rt.conf
@climbfuji
Bring hotfixes for ccpp-framework and ccpp-physics from release/publi…
237388e 
…c-v4 back to master (ufs-community#120)

* Bugfixes for CCPP: check for and correct syntax of \htmlinclude lines
* Fix formatting (tabs, whitespaces) in tests/rt.conf
@climbfuji @DusanJovic-NOAA
Call ccpp_prebuild.py from cmake, CCPP suites argument optional, upda…
e661c03 
…te regional tests, ... (ufs-community#126)

* Move ccpp_prebuild from build scripts to CMakeLists.txt
* Add find_package(Python) to CMakeLists.txt
* Update to compile scripts and top-level CMakeLists.txt for not specifying suites for CCPP
* Update of regional tests to reflect changes in suite definition files
* Use cmake 3.16.1 on hera
* Require cmake 3.15 or later in top-level CMakeLists.txt
* Bugfix in tests/fv3_conf/ccpp_regional_run.IN
* Python 3 compatibility for tests/abort_dep_tasks.py

Co-authored-by: Dusan Jovic <dusan.jovic@noaa.gov>
@climbfuji
Update .gitmodules and submodule pointer for fv3atm for code review a…
656c597 
…nd testing
@climbfuji
Merge branch 'develop' of https://github.com/ufs-community/ufs-weathe…
cad5238 
…r-model into update_gsd_develop_from_develop
@climbfuji
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Regression testing on hera.intel against official EMC baseline using rt.conf.
All tests pass except those expected to fail (because of our updates to Thompson MP and other physics used in the GSD suite).

rt_full_hera_intel.log

bash-4.2$ grep -e FAIL log_hera.intel/*
log_hera.intel/rt_036_fv3_ccpp_gsd_prod.log:Test 036 fv3_ccpp_gsd FAIL
log_hera.intel/rt_037_fv3_ccpp_thompson_prod.log:Test 037 fv3_ccpp_thompson FAIL
log_hera.intel/rt_038_fv3_ccpp_thompson_no_aero_prod.log:Test 038 fv3_ccpp_thompson_no_aero FAIL
log_hera.intel/rt_045_fv3_ccpp_gsd_debug_prod.log:Test 045 fv3_ccpp_gsd_debug FAIL
log_hera.intel/rt_046_fv3_ccpp_thompson_debug_prod.log:Test 046 fv3_ccpp_thompson_debug FAIL
log_hera.intel/rt_047_fv3_ccpp_thompson_no_aero_debug_prod.log:Test 047 fv3_ccpp_thompson_no_aero_debug FAIL
bash-4.2$ grep -e PASS log_hera.intel/*
log_hera.intel/rt_001_fv3_ccpp_control_prod.log:Test 001 fv3_ccpp_control PASS
log_hera.intel/rt_002_fv3_ccpp_decomp_prod.log:Test 002 fv3_ccpp_decomp PASS
log_hera.intel/rt_003_fv3_ccpp_2threads_prod.log:Test 003 fv3_ccpp_2threads PASS
log_hera.intel/rt_004_fv3_ccpp_restart_prod.log:Test 004 fv3_ccpp_restart PASS
log_hera.intel/rt_005_fv3_ccpp_read_inc_prod.log:Test 005 fv3_ccpp_read_inc PASS
log_hera.intel/rt_006_fv3_ccpp_wrtGauss_netcdf_esmf_prod.log:Test 006 fv3_ccpp_wrtGauss_netcdf_esmf PASS
log_hera.intel/rt_007_fv3_ccpp_wrtGauss_netcdf_prod.log:Test 007 fv3_ccpp_wrtGauss_netcdf PASS
log_hera.intel/rt_008_fv3_ccpp_wrtGlatlon_netcdf_prod.log:Test 008 fv3_ccpp_wrtGlatlon_netcdf PASS
log_hera.intel/rt_009_fv3_ccpp_wrtGauss_nemsio_prod.log:Test 009 fv3_ccpp_wrtGauss_nemsio PASS
log_hera.intel/rt_010_fv3_ccpp_wrtGauss_nemsio_c192_prod.log:Test 010 fv3_ccpp_wrtGauss_nemsio_c192 PASS
log_hera.intel/rt_011_fv3_ccpp_stochy_prod.log:Test 011 fv3_ccpp_stochy PASS
log_hera.intel/rt_012_fv3_ccpp_iau_prod.log:Test 012 fv3_ccpp_iau PASS
log_hera.intel/rt_013_fv3_ccpp_ca_prod.log:Test 013 fv3_ccpp_ca PASS
log_hera.intel/rt_014_fv3_ccpp_lheatstrg_prod.log:Test 014 fv3_ccpp_lheatstrg PASS
log_hera.intel/rt_015_fv3_ccpp_gfdlmprad_prod.log:Test 015 fv3_ccpp_gfdlmprad PASS
log_hera.intel/rt_016_fv3_ccpp_gfdlmprad_atmwav_prod.log:Test 016 fv3_ccpp_gfdlmprad_atmwav PASS
log_hera.intel/rt_017_fv3_ccpp_wrtGauss_nemsio_c768_prod.log:Test 017 fv3_ccpp_wrtGauss_nemsio_c768 PASS
log_hera.intel/rt_018_fv3_ccpp_control_32bit_prod.log:Test 018 fv3_ccpp_control_32bit PASS
log_hera.intel/rt_019_fv3_ccpp_stretched_prod.log:Test 019 fv3_ccpp_stretched PASS
log_hera.intel/rt_020_fv3_ccpp_stretched_nest_prod.log:Test 020 fv3_ccpp_stretched_nest PASS
log_hera.intel/rt_021_fv3_ccpp_regional_control_prod.log:Test 021 fv3_ccpp_regional_control PASS
log_hera.intel/rt_022_fv3_ccpp_regional_restart_prod.log:Test 022 fv3_ccpp_regional_restart PASS
log_hera.intel/rt_023_fv3_ccpp_regional_quilt_prod.log:Test 023 fv3_ccpp_regional_quilt PASS
log_hera.intel/rt_024_fv3_ccpp_regional_c768_prod.log:Test 024 fv3_ccpp_regional_c768 PASS
log_hera.intel/rt_025_fv3_ccpp_control_debug_prod.log:Test 025 fv3_ccpp_control_debug PASS
log_hera.intel/rt_026_fv3_ccpp_stretched_nest_debug_prod.log:Test 026 fv3_ccpp_stretched_nest_debug PASS
log_hera.intel/rt_027_fv3_ccpp_gfdlmp_prod.log:Test 027 fv3_ccpp_gfdlmp PASS
log_hera.intel/rt_028_fv3_ccpp_gfdlmprad_gwd_prod.log:Test 028 fv3_ccpp_gfdlmprad_gwd PASS
log_hera.intel/rt_029_fv3_ccpp_gfdlmprad_noahmp_prod.log:Test 029 fv3_ccpp_gfdlmprad_noahmp PASS
log_hera.intel/rt_030_fv3_ccpp_csawmg_prod.log:Test 030 fv3_ccpp_csawmg PASS
log_hera.intel/rt_031_fv3_ccpp_satmedmf_prod.log:Test 031 fv3_ccpp_satmedmf PASS
log_hera.intel/rt_032_fv3_ccpp_satmedmfq_prod.log:Test 032 fv3_ccpp_satmedmfq PASS
log_hera.intel/rt_033_fv3_ccpp_gfdlmp_32bit_prod.log:Test 033 fv3_ccpp_gfdlmp_32bit PASS
log_hera.intel/rt_034_fv3_ccpp_gfdlmprad_32bit_post_prod.log:Test 034 fv3_ccpp_gfdlmprad_32bit_post PASS
log_hera.intel/rt_035_fv3_ccpp_cpt_prod.log:Test 035 fv3_ccpp_cpt PASS
log_hera.intel/rt_039_fv3_ccpp_gfs_v15p2_prod.log:Test 039 fv3_ccpp_gfs_v15p2 PASS
log_hera.intel/rt_040_fv3_ccpp_gfs_v16beta_prod.log:Test 040 fv3_ccpp_gfs_v16beta PASS
log_hera.intel/rt_041_fv3_ccpp_rrtmgp_prod.log:Test 041 fv3_ccpp_rrtmgp PASS
log_hera.intel/rt_042_fv3_ccpp_gfs_v15p2_debug_prod.log:Test 042 fv3_ccpp_gfs_v15p2_debug PASS
log_hera.intel/rt_043_fv3_ccpp_gfs_v16beta_debug_prod.log:Test 043 fv3_ccpp_gfs_v16beta_debug PASS
log_hera.intel/rt_044_fv3_ccpp_rrtmgp_debug_prod.log:Test 044 fv3_ccpp_rrtmgp_debug PASS
log_hera.intel/rt_048_fv3_ccpp_gfsv16_csawmg_prod.log:Test 048 fv3_ccpp_gfsv16_csawmg PASS
log_hera.intel/rt_049_fv3_ccpp_gfsv16_csawmgt_prod.log:Test 049 fv3_ccpp_gfsv16_csawmgt PASS
log_hera.intel/rt_050_fv3_ccpp_gocart_clm_prod.log:Test 050 fv3_ccpp_gocart_clm PASS

This was referenced May 15, 2020
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@climbfuji climbfuji marked this pull request as ready for review May 15, 2020 20:24
@climbfuji climbfuji requested a review from DomHeinzeller as a code owner May 15, 2020 20:24
@climbfuji climbfuji force-pushed the update_gsd_develop_from_develop branch from bd18eea to 935d124 Compare May 15, 2020 20:27
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Regression testing on hera.intel using rt_ccpp_gsd.conf against previous GSD baseline (created from the head of gsd/develop): all tests fail. This is expected because of the changes merged from the authoritative repository.

rt_ccpp_gsd_against_existing_baseline.log

bash-4.2$ grep -e FAIL log_hera.intel/*
log_hera.intel/rt_001_fv3_ccpp_thompson_mynn_repro.log:Test 001 fv3_ccpp_thompson_mynn FAIL
log_hera.intel/rt_002_fv3_ccpp_gf_thompson_repro.log:Test 002 fv3_ccpp_gf_thompson FAIL
log_hera.intel/rt_003_fv3_ccpp_gsd_repro.log:Test 003 fv3_ccpp_gsd FAIL
log_hera.intel/rt_004_fv3_ccpp_gsd_coldstart_repro.log:Test 004 fv3_ccpp_gsd_coldstart FAIL
log_hera.intel/rt_005_fv3_ccpp_gsd_warmstart_repro.log:Test 005 fv3_ccpp_gsd_warmstart FAIL
log_hera.intel/rt_006_fv3_ccpp_gsd_noah_repro.log:Test 006 fv3_ccpp_gsd_noah FAIL
log_hera.intel/rt_007_fv3_ccpp_gsd_mynnsfc_repro.log:Test 007 fv3_ccpp_gsd_mynnsfc FAIL
log_hera.intel/rt_008_fv3_ccpp_gsd_noah_mynnsfc_repro.log:Test 008 fv3_ccpp_gsd_noah_mynnsfc FAIL
log_hera.intel/rt_009_fv3_ccpp_thompson_repro.log:Test 009 fv3_ccpp_thompson FAIL
log_hera.intel/rt_010_fv3_ccpp_thompson_no_aero_repro.log:Test 010 fv3_ccpp_thompson_no_aero FAIL
log_hera.intel/rt_011_fv3_ccpp_gf_repro.log:Test 011 fv3_ccpp_gf FAIL
log_hera.intel/rt_012_fv3_ccpp_mynn_repro.log:Test 012 fv3_ccpp_mynn FAIL
log_hera.intel/rt_013_fv3_ccpp_gsd_drag_suite_repro.log:Test 013 fv3_ccpp_gsd_drag_suite FAIL
log_hera.intel/rt_014_fv3_ccpp_gsd_sar_repro.log:Test 014 fv3_ccpp_gsd_sar FAIL
log_hera.intel/rt_015_fv3_ccpp_gsd_debug_prod.log:Test 015 fv3_ccpp_gsd_debug FAIL
log_hera.intel/rt_016_fv3_ccpp_gsd_diag3d_debug_prod.log:Test 016 fv3_ccpp_gsd_diag3d_debug FAIL
log_hera.intel/rt_017_fv3_ccpp_gsd_mynnsfc_debug_prod.log:Test 017 fv3_ccpp_gsd_mynnsfc_debug FAIL
log_hera.intel/rt_018_fv3_ccpp_gsd_noah_mynnsfc_debug_prod.log:Test 018 fv3_ccpp_gsd_noah_mynnsfc_debug FAIL
log_hera.intel/rt_019_fv3_ccpp_thompson_no_aero_debug_prod.log:Test 019 fv3_ccpp_thompson_no_aero_debug FAIL
log_hera.intel/rt_020_fv3_ccpp_gsd_sar_25km_debug_prod.log:Test 020 fv3_ccpp_gsd_sar_25km_debug FAIL
bash-4.2$ grep -e PASS log_hera.intel/*
bash-4.2$

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Regression testing on hera.intel using rt_ccpp_gsd.conf: first create new baseline, then verify against it: all tests pass.

rt_ccpp_gsd_create.log
rt_ccpp_gsd_verify.log

@climbfuji
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These PRs are ready to merge pending code review and testing by the GSL physics developers.

@haiqinli @hannahcbarnes @joeolson42 @tanyasmirnova @shansun6

@climbfuji
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@haiqinli @hannahcbarnes @joeolson42 @tanyasmirnova see commit bd1c7c9 for the new regression test fv3_ccpp_raphrrr. Note the "inconsistency" of running the RAP-HRRR suite with a C96 global configuration in the regression tests, but running the full 3km SAR domain takes way too long for regression tests. And the main point here is to make sure the suite runs to completion and to catch unintended changes in following commits. In future commits, I will add restart an debug tests.

@climbfuji
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Regression testing of updated version of the code (after commits NOAA-GSL/ccpp-physics@6e4c787, NOAA-GSL/fv3atm@dabf9e6, bd1c7c9) on hera.intel against official EMC baseline: all tests pass except those expected to fail:

log_hera.intel/rt_036_fv3_ccpp_gsd_prod.log:Test 036 fv3_ccpp_gsd FAIL
log_hera.intel/rt_037_fv3_ccpp_thompson_prod.log:Test 037 fv3_ccpp_thompson FAIL
log_hera.intel/rt_038_fv3_ccpp_thompson_no_aero_prod.log:Test 038 fv3_ccpp_thompson_no_aero FAIL
log_hera.intel/rt_045_fv3_ccpp_gsd_debug_prod.log:Test 045 fv3_ccpp_gsd_debug FAIL
log_hera.intel/rt_046_fv3_ccpp_thompson_debug_prod.log:Test 046 fv3_ccpp_thompson_debug FAIL
log_hera.intel/rt_047_fv3_ccpp_thompson_no_aero_debug_prod.log:Test 047 fv3_ccpp_thompson_no_aero_debug FAIL

rt_full_hera_intel.log
rt_full_hera_intel_fail_test.log

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Regression testing of updated version of the code (after commits NOAA-GSL/ccpp-physics@6e4c787, NOAA-GSL/fv3atm@dabf9e6, bd1c7c9) on hera.intel using rt_ccpp_gsd.conf: first create new baseline, then verify against it: all tests pass.

rt_ccpp_gsd_create.log
rt_ccpp_gsd_verify.log

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@haiqinli @hannahcbarnes @joeolson42 @tanyasmirnova all tests pass as expected. Please let me know if you are happy with the PRs and I will start the merge process. Thanks!

@DomHeinzeller DomHeinzeller merged commit 6671b15 into NOAA-GSL:gsd/develop May 20, 2020
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@climbfuji @DomHeinzeller @junwang-noaa @DusanJovic-NOAA @TomBlack-NOAA @AnningCheng-NOAA @lisa-bengtsson