Change output file name of run_post to meet NCO standards #758

chan-hoo · 2022-05-05T18:08:48Z

DESCRIPTION OF CHANGES:

The output file name of the 'run_post' task is changed to meet the latest version of the NCO standards (Ver 11.0.0; January 19, 2022; page 6).
The file name should be "{NET}.t{cyc}z.[var_info].fHHH.{domain}.grib2".
The python scripts for workflow generation are updated with the recent changes in bash scripts.

TESTS CONDUCTED:

WE2E tests:
community_ensemble_2mems
grid_RRFS_CONUS_13km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16
grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_2017_gfdlmp_regional
grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v15p2
grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16
grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_RAP_suite_HRRR
grid_RRFS_CONUS_3km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v15_thompson_mynn_lam3km
grid_RRFS_CONUScompact_13km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16
grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_HRRR_suite_RRFS_v1beta
grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_RRFS_v1alpha
grid_RRFS_NA_3km_ics_FV3GFS_lbcs_FV3GFS_suite_RRFS_v1alpha
MET_ensemble_verification
MET_verification
nco_grid_RRFS_CONUS_13km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16
nco_grid_RRFS_CONUS_3km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v15_thompson_mynn_lam3km
nco_grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_HRRR

ush/config_defaults.sh

JeffBeck-NOAA · 2022-05-05T22:08:26Z

scripts/exregional_run_fcst.sh

@@ -539,15 +538,15 @@ if [ ${WRITE_DOPOST} = "TRUE" ]; then
    post_mn=${post_time:10:2}
    post_mn_or_null=""
    post_fn_suffix="GrbF${fhr_d}"
-    post_renamed_fn_suffix="f${fhr}${post_mn_or_null}.${tmmark}.grib2"
+    post_renamed_fn_suffix="f${fhr}${post_mn_or_null}.${FN_OUT_DOMAIN}.grib2"



@chan-hoo, is there a reason to have "post_fn_suffix" and "post_renamed_fn_suffix"?

@JeffBeck-NOAA, when I added this part for the inline post option, I copied the corresponding part in 'exregional_run_post.sh' as you pointed below. I am not the original developer of the script, but I can interpret them as follows: (1) The output file name of UPP and inline post is 'post_orig_fn' including 'post_fn_suffix'. (2) The output file name required by NCO is 'post_renamed_fn' including 'post_renamed_fn_suffix'. (3) File (1) is renamed to File (2), and the original file name (1) is soft-linked to file (2).

JeffBeck-NOAA · 2022-05-05T22:09:03Z

scripts/exregional_run_post.sh

@@ -314,7 +303,7 @@ fids=( "prslev" "natlev" )
 for fid in "${fids[@]}"; do
  FID=$(echo_uppercase $fid)
  post_orig_fn="${FID}.${post_fn_suffix}"
-  post_renamed_fn="${NET}.t${cyc}z.${fid}${post_renamed_fn_suffix}"
+  post_renamed_fn="${NET}.t${cyc}z.${fid}.${post_renamed_fn_suffix}"
  mv_vrfy ${tmp_dir}/${post_orig_fn} ${post_renamed_fn}


Same question as above, but this time post_orig_fn vs post_renamed_fn.

Explained above.

JeffBeck-NOAA · 2022-05-05T22:10:33Z

scripts/exregional_run_fcst.sh

@@ -539,15 +538,15 @@ if [ ${WRITE_DOPOST} = "TRUE" ]; then
    post_mn=${post_time:10:2}
    post_mn_or_null=""
    post_fn_suffix="GrbF${fhr_d}"
-    post_renamed_fn_suffix="f${fhr}${post_mn_or_null}.${tmmark}.grib2"
+    post_renamed_fn_suffix="f${fhr}${post_mn_or_null}.${FN_OUT_DOMAIN}.grib2"



Do you have an example of what a full post file name looks like after this change? Does it still have the "prslev" and "natlev" names in the files?

It should be ${NET}.t{cyc}z.[var_info].fHHH.${POST_OUTPUT_DOMAIN_NAME}.grib2 (described in 'config_default.sh'). Yes, "prslev" or "natlev" is placed in [var_info]. For example, "rrfs.t00z.prslev.f003.conus_3km.grib2"

gsketefian · 2022-05-06T17:05:29Z

ush/setup.sh

@@ -1174,6 +1177,9 @@ else
  COMROOT=""
  COMOUT_BASEDIR=""
 fi
+
+POST_OUTPUT_DOMAIN_NAME="${POST_OUTPUT_DOMAIN_NAME:-${PREDEF_GRID_NAME}}"
+POST_OUTPUT_DOMAIN_NAME=$(echo_lowercase ${POST_OUTPUT_DOMAIN_NAME})


@chan-hoo If someone is using a custom grid (in which case PREDEF_GRID_NAME will be set to an empty string) and forgets to explicitly set POST_OUTPUT_DOMAIN_NAME in config.sh, then this code will leave POST_OUTPUT_DOMAIN_NAME empty. It would be good to put in a check for that after this and if it is empty, tell the user to set POST_OUTPUT_DOMAIN_NAME in their config.sh file (unless they are neither running inline post nor the run_post metatask). [I guess all comments for the bash scripts also apply to the python ones, but I'm not sure if you're going to change the python or @danielabdi-noaa.]

@gsketefian, I got it. I'll add a check for the case.

@gsketefian I am working on a branch that will remove the shell workflow generation. In the mean time, it would be very helpful if developers run both the shell and python workflow generator when running test cases -- although I will run the regression tests on platforms I have access too. Thanks @chan-hoo for making changes to both workflows!

@chan-hoo Instead of

if [ -z "${POST_OUTPUT_DOMAIN_NAME}" ] && [ -z "${PREDEF_GRID_NAME}" ]; then

you can just use

if [ -z "${POST_OUTPUT_DOMAIN_NAME}" ]; then

since at this point, POST_OUTPUT_DOMAIN_NAME will be null only if PREDEF_GRID_NAME is also null.

Also, for the message, it would be good to give a bit more info to the user, something like:

The domain name used in naming the UPP output files (POST_OUTPUT_DOMAIN_NAME) has not been set: POST_OUTPUT_DOMAIN_NAME = \"${POST_OUTPUT_DOMAIN_NAME}\"" If this experiment is not using a predefined grid (i.e. if PREDEF_GRID_NAME is set to a null string), POST_OUTPUT_DOMAIN_NAME must be set in the SRW App's configuration file (\"${EXPT_CONFIG_FN}\")."

@danielabdi-noaa Sounds good, thanks for letting us know!

ush/setup.sh

gsketefian · 2022-05-06T18:46:47Z

scripts/exregional_run_fcst.sh

@@ -539,15 +538,15 @@ if [ ${WRITE_DOPOST} = "TRUE" ]; then
    post_mn=${post_time:10:2}
    post_mn_or_null=""
    post_fn_suffix="GrbF${fhr_d}"
-    post_renamed_fn_suffix="f${fhr}${post_mn_or_null}.${tmmark}.grib2"
+    post_renamed_fn_suffix="f${fhr}${post_mn_or_null}.${POST_OUTPUT_DOMAIN_NAME}.grib2"


@chan-hoo From this code, it looks like POST_OUTPUT_DOMAIN_NAME is used regardless of whether running in NCO more or community mode. Is that correct? If so, can you move where it's defined in config_defaults.sh so that it's not in the NCO-only section? Thanks.

@gsketefian, yes. I'll move it to common area.

…orkflow into feature/filename_nco

chan-hoo · 2022-05-09T20:18:41Z

@danielabdi-noaa, idx = EXTRN_MDL_SOURCE_BASEDIR_ICS.find("$") doesn't work correctly. @gsketefian, how can we interpret "${EXTRN_MDL_SOURCE_BASEDIR_ICS%%$*}"? print(os.path.exists(EXTRN_MDL_SOURCE_BASEDIR_ICS)) => true, however, print(os.path.exists(EXTRN_MDL_SOURCE_BASEDIR_ICS[:idx])) => false

danielabdi-noaa · 2022-05-09T21:59:45Z

@danielabdi-noaa, idx = EXTRN_MDL_SOURCE_BASEDIR_ICS.find("$") doesn't work correctly. @gsketefian, how can we interpret "${EXTRN_MDL_SOURCE_BASEDIR_ICS%%$*}"? print(os.path.exists(EXTRN_MDL_SOURCE_BASEDIR_ICS)) => true, however, print(os.path.exists(EXTRN_MDL_SOURCE_BASEDIR_ICS[:idx])) => false

What is the example path you are using for EXTRN_MDL_SOURCE_BASEDIR_ICS ? My understanding from the comment is that the path is a "template" so it could have "$" sign in it.

# Check for the base directory up to the first templated field.

For example

>>> XX="/path/to/$some/where"
>>> idx=XX.find("$")
>>> print(XX[:idx])
/path/to/

And equivalent bash

$ XX="/path/to/\$some/where"
$ echo ${XX%%\$*}
/path/to/

danielabdi-noaa · 2022-05-09T22:12:01Z

@chan-hoo I think the problem is because the path you are testing is not templated and doesn't have the "$" sign.
So we need to do a check on the value of idx==-1, in which case idx=len(EXTRN_MDL_SOURCE_BASEDIR_ICS) instead.

chan-hoo · 2022-05-10T07:33:30Z

@danielabdi-noaa, it worked. Thanks!

@willmayfield

* Add Gaea as a supported platform for the regional_workflow (#734) * Updates to port regional workflow to gaea * Temp change with -v as batch option * new fixes for gaea/slurm * Updated time for make lbcs * added TEST data directory path * Update gaea.sh * fixes for PR * Add more parameters to CSV file containing WE2E test info (#740) ## DESCRIPTION OF CHANGES: The script/function `get_WE2Etest_names_subdirs_descs.sh` (which is called from `run_WE2E_tests.sh` if needed) creates a CSV (Comma-Separated Value) file named `WE2E_test_info.csv` that contains information about the WE2E tests. Currently, this CSV file contains only 3 columns: the test name, the names of any alternate names for the test, and the test description. In order to have a more complete summary of the WE2E tests, this PR modifies `get_WE2Etest_names_subdirs_descs.sh` so that additional information is included in the CSV file. This additional information consists of the values of the following experiment variables for each test: ``` PREDEF_GRID_NAME CCPP_PHYS_SUITE EXTRN_MDL_NAME_ICS EXTRN_MDL_NAME_LBCS DATE_FIRST_CYCL DATE_LAST_CYCL CYCL_HRS INCR_CYCL_FREQ FCST_LEN_HRS LBC_SPEC_INTVL_HRS NUM_ENS_MEMBERS ``` In addition, the script uses this information to calculate the number of times each test calls the forecast model (e.g. if the test uses 3 different cycle dates, then the forecast model will be called 3 times; if it is an ensemble test for a single cycle, the test will call the forecast model as many times as the number of ensemble members). ## TESTS CONDUCTED: The script `run_WE2E_tests.sh` was called that in turn calls `get_WE2Etest_names_subdirs_descs.sh`. This created a new CSV file that contained the new fields (columns). The CSV file was imported into Google Sheets (using "|" as the field/column separator) and looked correct. ## DOCUMENTATION: The documentation is for the most part already within the `get_WE2Etest_names_subdirs_descs.sh`. This PR slightly modifies that documentation to update it. * Update directory structure of NCO mode (#743) * update vertical structure of NCO mode * update sample script for nco * Fix typo on write component of new RRFS CONUS * Default CCPP physics option is FV3_GFS_v16 (#746) * Updated the default CCPP physics option to FV3_GFS_v16 * Updated the default CCPP physics option to FV3_GFS_v16 in config_defaults.sh Co-authored-by: Natalie Perlin <Natalie@Natalies-MacBook-Air.local> * Adds an alternative python workflow generation path (#698) * Workflow in python starting to work. * Use new python_utils package structure. * Some bug fixes. * Use uppercase TRUE/FALSE in var_dfns * Use config.sh by default. * Minor bug fixes. * Remove config.yaml * Update to the latest develop * Remove quotes from numbers in predef grid. * Minor bug fix. * Move validity checker to the bottom of setup * Add more unit tests. * Update with python_utils changes. * Update to latest develop additions (Need to re-run regression test) * Use set_namelist and fill_jinja_template as python functions. * Replace sed regex searches with python re. * Use python realpath. * Construct settings as dictionary before passing to fill_jinja and set_namelist * Use yaml for setting predefined grid parameters. * Use xml parser for ccpp phys suite definition file. * Remove more run_command calls. * Simplify some func argument processing. * Move different config format parsers to same file. * Use os.path.join for the sake of macosx * Remove remaining func argument processing via os.environ. * Minor bug fix in set_extrn_mdl_params.sh * Add suite defn in test_data. * Minor fixes on unittest on jet. * Simplify boolean condition checks. * Include old in renaming of old directories * Fix conflicting yaml !join tag for paths and strings. * Bug fix with setting sfcperst dict. * Imitate "readlink -m" with os.path.realpath instead of os.readlink * Don't use /tmp as that is shared by multiple users. * Bug fix with cron line, maintain quotes around TRUE/FALSE. * Update to latest develop (untested) * Bug fix with existing cron line and quotes. * Bug fix with case-sensitive MACHINE name, and empty EXPT_DIR. * Update to latest develop * More updates. * Bug fix thanks to @willmayfield! Check both starting/ending characters are brackets for shell variable to be considered an array. * Make empty EXPT_BASEDIR workable. * Update to latest develop * Update in predef grid. * Check f90nml as well. Co-authored-by: Daniel Abdi <dabdi@Orion-login-2.HPC.MsState.Edu> * Fix typo and crontab issue on wcoss dell in workflow python scripts (#750) * Fix typo and failure on wcoss * fix new line issue on wcoss dell * remove capture_output * Get USER from environment Co-authored-by: Daniel Abdi <daniel.abdi@noaa.gov> * Add new WE2E configs (#748) ## DESCRIPTION OF CHANGES: Added two new WE2E config files for the Sub-CONUS Indianapolis domain to support the upcoming SRW release. In addition, modified the external data used in the `config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh` to match more common datasets used in the WE2E testing process. ## TESTS CONDUCTED: Successfully ran the new WE2E tests (`config.SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_HRRR.sh`, `config.SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta.sh`) and `config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh` on NOAA Parallel Works AWS instance. ## DEPENDENCIES: None. ## DOCUMENTATION: No documentation changes are required. * Added a fixed WoF grid and the python tool to determine the write component parameters (#733) * Added a fixed WoF grid and the python tool to determine the write component parameters * Update set_predef_grid_params.sh * Renamed file as recommended and removed unused lines * Modified comment Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com> Co-authored-by: WYH@MBP <yunheng.wang@4374-ywang.winstorm.nssl> * Replace env with modulefiles in scripts (#752) * change env to mod * update we2e script * WE2E script improvements for usability (#745) ## DESCRIPTION OF CHANGES: * Modifications to `run_WE2E_tests.sh`: * Add examples to help/usage statement * Modifications to `check_expts_status.sh`: * Add arguments list that can be processed by `process_args` * Add new optional arguments: `num_log_lines`, `verbose` * Include a help/usage message ## TESTS CONDUCTED: * Ran `run_WE2E_tests.sh --help` from the command line and got the expected help message. * Ran `check_expts_status.sh --help` from the command line and got the expected help message. * Used `run_WE2E_tests.sh` to run a set of 2 WE2E tests -- works as expected. * Used `check_expts_status` to check on the status of the 2 tests run above and got the expected status message. ## DEPENDENCIES: PR #[241](ufs-community/ufs-srweather-app#241) ## DOCUMENTATION: A lot of this PR is documentation in the scripts. There is an accompanying documentation PR #[241](ufs-community/ufs-srweather-app#241) into ufs-srweather-app. * Standardize static data across Tier-1 platforms; fix and improve IC and LBC data retrieval (#744) * Bug fixes (grid size + suppress screen output from module load) (#756) ## DESCRIPTION OF CHANGES: 1) Adjust y-direction size of write-component grid of `SUBCONUS_Ind_3km` predefined grid from 195 to 197 (this was just an oversight in PR #725 ). 2) Redirect output of module load in launch script (`launch_FV3LAM_wflow.sh`) to `/dev/null` to avoid unwanted screen output (which was introduced in PR #[238](ufs-community/ufs-srweather-app#238) in ufs-srweather-app and is about how to load the `regional_workflow` environment and is not relevant in this context). ## TESTS CONDUCTED: 1) Plotted the `SUBCONUS_Ind_3km` grid to ensure it has correct size (it does). 2) Manually ran `launch_FV3LAM_wflow.sh` from the command line to verify that screen output is suppressed (it is). * Update default SPP ISEED array in config_defaults.sh to use unique values (#759) * Modify RRFS North America 3- and 13-km domain configuration and WE2E test. * Modify default ISEED values for SPP * Fix grid in WE2E test * Update workflow python scripts (#760) * update python scripts * Change output file name of run_post to meet NCO standards (#758) * change output file name * change variable name * update python script * remove duplicates * add a check for empty variables * move variable to common area * clean up unnecessary comments * update scripts * remove duplicate * update python scripts * fix user-staged dir path issue in python script * Add POST_OUTPUT_DOMAIN_NAME to WE2E tests for new grids (#763) * Add new var to we2e tests for new grids * rename we2e tests for custom grid * remove unnecessary $ Co-authored-by: Mark Potts <33099090+mark-a-potts@users.noreply.github.com> Co-authored-by: gsketefian <31046882+gsketefian@users.noreply.github.com> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: Natalie Perlin <68030316+natalie-perlin@users.noreply.github.com> Co-authored-by: Natalie Perlin <Natalie@Natalies-MacBook-Air.local> Co-authored-by: danielabdi-noaa <52012304+danielabdi-noaa@users.noreply.github.com> Co-authored-by: Daniel Abdi <dabdi@Orion-login-2.HPC.MsState.Edu> Co-authored-by: Daniel Abdi <daniel.abdi@noaa.gov> Co-authored-by: EdwardSnyder-NOAA <96196752+EdwardSnyder-NOAA@users.noreply.github.com> Co-authored-by: Yunheng Wang <47898913+ywangwof@users.noreply.github.com> Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com> Co-authored-by: WYH@MBP <yunheng.wang@4374-ywang.winstorm.nssl> Co-authored-by: Michael Kavulich <kavulich@ucar.edu>

@mkavulich

* Add missing user-defined stochastic physics options; fix stochastic physics seed generation script (ufs-community#704) ## DESCRIPTION OF CHANGES: Add missing user-defined options for tendency-based stochastic physics and fix the ensemble-based seed generation script to work regardless of whether stochastic physics is turned on or not. ## TESTS CONDUCTED: Tested on Hera using the following WE2E configurations with and without stochastic physics: config.grid_RRFS_CONUS_3km_ics_HRRR_lbcs_RAP_suite_HRRR.sh config.community_ensemble_2mems.sh ## ISSUE (optional): [Issue ufs-community#702](ufs-community#702) ## CONTRIBUTORS (optional): Thanks to @mkavulich and @chan-hoo for finding this problem. * Add namelist option for netCDF4 when running with the 3-km NA domain; update NAM HPSS settings and WE2E tests (ufs-community#707) * Change to netcdf4 when using the NA 3-km domain * Update HPSS paths for NAM data * Update NAM HPSS locations and dates for WE2E tests. * Remove lines from merge. * Tweaks to allow compiler and build_env_fn to be specified in the run_WE2E_test.sh script (ufs-community#711) * Changed 20200304 to 20200303 in ush/mrms_pull_topofhour.py (ufs-community#712) * Remove unused rocoto directory in ush (ufs-community#720) * Fix bug for nco we2e tests on Orion; re-organize we2e input data and nco we2e tests (ufs-community#713) * Update machine script for orion * Update machine script for wcoss_dell_p3 * Update we2e run script for wcoss and orion * Reorganize nco we2e tests * remove machine based logic * Add symlink for nco inline post test * Added stand-alone verification scripts (feature/issue_683_standaloneVX) (ufs-community#726) * Grid-stat and point-stat run scripts. * Stand-alone scripts for verification. * Added comments to gridvx scripts. * Added qsub_job.sh and added comments to provide context on running Vx. * remove machine base logic (ufs-community#727) * Allow user-defined file names for input template files (ufs-community#717) * Allow multiple template names * parameterize file_TMPL_FN and add a we2e test * Increase maxtries_task for make_grid/orog/sfc_climo * Modify file name and description * Changes to RRFS 3- and 13-km domains, setup.sh script bug fixes, make_ics task modification, and tweaks to stochastic physics namelist settings (ufs-community#721) * Modify RRFS North America 3- and 13-km domain configuration and WE2E test. * Change sotyp_from_climo to "true" based on operational RAP grib2 files. * Update for changes to stochastic physics namelist options. * Check for DO_ENSEMBLE="TRUE" when running ensemble verification and turn of VX when running in NCO mode. * Revert to 3-km domain. * Remove commented-out GFDL grid for the RRFS_NA_13km domain * Add RRFS_NA_13km WE2E test * Changes to comments. * Adding 25 km tests to Jet/Hera suites. (ufs-community#718) * Add a small 3km predefined grid over Indianapolis for testing (ufs-community#725) * Add 3km grid over Indianapolis. This is about 600km x 600km in extent (200 x 200 grid points). It is intended for use in the WE2E tests. * Edit comments. * Use Python tool for get_extrnl_mdl_file tasks (ufs-community#681) These changes hook in the Python-based data ingest tool, replacing the previous scripts that handled this work as part of the get_extrn_mdl_file task. No attempt was made in this PR to replace the NOMADS fetching script with the Python utility, but the NOMADS data location has been added to the data_locations.yml file. The functionality to write the data summary file has also been added to the Python tool to match the capabilities of the existing workflow tools. * Increase size of RRFS CONUS grid (ufs-community#724) Co-authored-by: Benjamin.Blake EMC <Benjamin.Blake@v71a1.ncep.noaa.gov> Co-authored-by: Benjamin.Blake EMC <Benjamin.Blake@v72a1.ncep.noaa.gov> Co-authored-by: Benjamin.Blake EMC <Benjamin.Blake@v71a3.ncep.noaa.gov> Co-authored-by: chan-hoo <chan-hoo.jeon@noaa.gov> * add include-style quality mark options in metplus confs (ufs-community#738) * Add Gaea as a supported platform for the regional_workflow (ufs-community#734) * Updates to port regional workflow to gaea * Temp change with -v as batch option * new fixes for gaea/slurm * Updated time for make lbcs * added TEST data directory path * Update gaea.sh * fixes for PR * Add more parameters to CSV file containing WE2E test info (ufs-community#740) ## DESCRIPTION OF CHANGES: The script/function `get_WE2Etest_names_subdirs_descs.sh` (which is called from `run_WE2E_tests.sh` if needed) creates a CSV (Comma-Separated Value) file named `WE2E_test_info.csv` that contains information about the WE2E tests. Currently, this CSV file contains only 3 columns: the test name, the names of any alternate names for the test, and the test description. In order to have a more complete summary of the WE2E tests, this PR modifies `get_WE2Etest_names_subdirs_descs.sh` so that additional information is included in the CSV file. This additional information consists of the values of the following experiment variables for each test: ``` PREDEF_GRID_NAME CCPP_PHYS_SUITE EXTRN_MDL_NAME_ICS EXTRN_MDL_NAME_LBCS DATE_FIRST_CYCL DATE_LAST_CYCL CYCL_HRS INCR_CYCL_FREQ FCST_LEN_HRS LBC_SPEC_INTVL_HRS NUM_ENS_MEMBERS ``` In addition, the script uses this information to calculate the number of times each test calls the forecast model (e.g. if the test uses 3 different cycle dates, then the forecast model will be called 3 times; if it is an ensemble test for a single cycle, the test will call the forecast model as many times as the number of ensemble members). ## TESTS CONDUCTED: The script `run_WE2E_tests.sh` was called that in turn calls `get_WE2Etest_names_subdirs_descs.sh`. This created a new CSV file that contained the new fields (columns). The CSV file was imported into Google Sheets (using "|" as the field/column separator) and looked correct. ## DOCUMENTATION: The documentation is for the most part already within the `get_WE2Etest_names_subdirs_descs.sh`. This PR slightly modifies that documentation to update it. * Update directory structure of NCO mode (ufs-community#743) * update vertical structure of NCO mode * update sample script for nco * Fix typo on write component of new RRFS CONUS * Default CCPP physics option is FV3_GFS_v16 (ufs-community#746) * Updated the default CCPP physics option to FV3_GFS_v16 * Updated the default CCPP physics option to FV3_GFS_v16 in config_defaults.sh Co-authored-by: Natalie Perlin <Natalie@Natalies-MacBook-Air.local> * Adds an alternative python workflow generation path (ufs-community#698) * Workflow in python starting to work. * Use new python_utils package structure. * Some bug fixes. * Use uppercase TRUE/FALSE in var_dfns * Use config.sh by default. * Minor bug fixes. * Remove config.yaml * Update to the latest develop * Remove quotes from numbers in predef grid. * Minor bug fix. * Move validity checker to the bottom of setup * Add more unit tests. * Update with python_utils changes. * Update to latest develop additions (Need to re-run regression test) * Use set_namelist and fill_jinja_template as python functions. * Replace sed regex searches with python re. * Use python realpath. * Construct settings as dictionary before passing to fill_jinja and set_namelist * Use yaml for setting predefined grid parameters. * Use xml parser for ccpp phys suite definition file. * Remove more run_command calls. * Simplify some func argument processing. * Move different config format parsers to same file. * Use os.path.join for the sake of macosx * Remove remaining func argument processing via os.environ. * Minor bug fix in set_extrn_mdl_params.sh * Add suite defn in test_data. * Minor fixes on unittest on jet. * Simplify boolean condition checks. * Include old in renaming of old directories * Fix conflicting yaml !join tag for paths and strings. * Bug fix with setting sfcperst dict. * Imitate "readlink -m" with os.path.realpath instead of os.readlink * Don't use /tmp as that is shared by multiple users. * Bug fix with cron line, maintain quotes around TRUE/FALSE. * Update to latest develop (untested) * Bug fix with existing cron line and quotes. * Bug fix with case-sensitive MACHINE name, and empty EXPT_DIR. * Update to latest develop * More updates. * Bug fix thanks to @willmayfield! Check both starting/ending characters are brackets for shell variable to be considered an array. * Make empty EXPT_BASEDIR workable. * Update to latest develop * Update in predef grid. * Check f90nml as well. Co-authored-by: Daniel Abdi <dabdi@Orion-login-2.HPC.MsState.Edu> * Fix typo and crontab issue on wcoss dell in workflow python scripts (ufs-community#750) * Fix typo and failure on wcoss * fix new line issue on wcoss dell * remove capture_output * Get USER from environment Co-authored-by: Daniel Abdi <daniel.abdi@noaa.gov> * Add new WE2E configs (ufs-community#748) ## DESCRIPTION OF CHANGES: Added two new WE2E config files for the Sub-CONUS Indianapolis domain to support the upcoming SRW release. In addition, modified the external data used in the `config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh` to match more common datasets used in the WE2E testing process. ## TESTS CONDUCTED: Successfully ran the new WE2E tests (`config.SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_HRRR.sh`, `config.SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta.sh`) and `config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh` on NOAA Parallel Works AWS instance. ## DEPENDENCIES: None. ## DOCUMENTATION: No documentation changes are required. * Added a fixed WoF grid and the python tool to determine the write component parameters (ufs-community#733) * Added a fixed WoF grid and the python tool to determine the write component parameters * Update set_predef_grid_params.sh * Renamed file as recommended and removed unused lines * Modified comment Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com> Co-authored-by: WYH@MBP <yunheng.wang@4374-ywang.winstorm.nssl> * Replace env with modulefiles in scripts (ufs-community#752) * change env to mod * update we2e script * WE2E script improvements for usability (ufs-community#745) ## DESCRIPTION OF CHANGES: * Modifications to `run_WE2E_tests.sh`: * Add examples to help/usage statement * Modifications to `check_expts_status.sh`: * Add arguments list that can be processed by `process_args` * Add new optional arguments: `num_log_lines`, `verbose` * Include a help/usage message ## TESTS CONDUCTED: * Ran `run_WE2E_tests.sh --help` from the command line and got the expected help message. * Ran `check_expts_status.sh --help` from the command line and got the expected help message. * Used `run_WE2E_tests.sh` to run a set of 2 WE2E tests -- works as expected. * Used `check_expts_status` to check on the status of the 2 tests run above and got the expected status message. ## DEPENDENCIES: PR #[241](ufs-community/ufs-srweather-app#241) ## DOCUMENTATION: A lot of this PR is documentation in the scripts. There is an accompanying documentation PR #[241](ufs-community/ufs-srweather-app#241) into ufs-srweather-app. * Standardize static data across Tier-1 platforms; fix and improve IC and LBC data retrieval (ufs-community#744) * Bug fixes (grid size + suppress screen output from module load) (ufs-community#756) ## DESCRIPTION OF CHANGES: 1) Adjust y-direction size of write-component grid of `SUBCONUS_Ind_3km` predefined grid from 195 to 197 (this was just an oversight in PR ufs-community#725 ). 2) Redirect output of module load in launch script (`launch_FV3LAM_wflow.sh`) to `/dev/null` to avoid unwanted screen output (which was introduced in PR #[238](ufs-community/ufs-srweather-app#238) in ufs-srweather-app and is about how to load the `regional_workflow` environment and is not relevant in this context). ## TESTS CONDUCTED: 1) Plotted the `SUBCONUS_Ind_3km` grid to ensure it has correct size (it does). 2) Manually ran `launch_FV3LAM_wflow.sh` from the command line to verify that screen output is suppressed (it is). * Update default SPP ISEED array in config_defaults.sh to use unique values (ufs-community#759) * Modify RRFS North America 3- and 13-km domain configuration and WE2E test. * Modify default ISEED values for SPP * Fix grid in WE2E test * Update workflow python scripts (ufs-community#760) * update python scripts * Change output file name of run_post to meet NCO standards (ufs-community#758) * change output file name * change variable name * update python script * remove duplicates * add a check for empty variables * move variable to common area * clean up unnecessary comments * update scripts * remove duplicate * update python scripts * fix user-staged dir path issue in python script * Add POST_OUTPUT_DOMAIN_NAME to WE2E tests for new grids (ufs-community#763) * Add new var to we2e tests for new grids * rename we2e tests for custom grid * remove unnecessary $ * Modifications to `CODEOWNERS` file (ufs-community#757) * Add @gspetro-NOAA, @natalie-perlin, and @EdwardSnyder-NOAA to CODEOWNERS so they are notified of all PRs and can review them. * Remove duplicates in CODEOWNERS; remove users who will no longer be working with the repo. * Adding a python utility for summarizing compute. (ufs-community#769) Adds a utility that summarizes Rocoto database computational usage information. * Add github actions for python unittests. (ufs-community#747) * Add github actions for python unittests. * Include all python script in ush * Skip defining QUILTING params when it is set to False * Update py_workflow * Update unittest for set_extrn_mdl_params. * Updates from develop. Co-authored-by: Daniel Shawul <dshawul@yahoo.com> * Update sample script for NCO mode (ufs-community#771) * update config.nco.sh * Add comment * Feature/noaacloud (ufs-community#767) * updates for noaacloud * working version * fixes for noaacloud * added extra modules for post * removed cheyenne-specific crontab editing section (ufs-community#773) * Pin down hera miniconda3 module file version. (ufs-community#770) Pin down the version of miniconda3 on Hera, and do not append to the module path. * update staged data dir (ufs-community#774) Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com> Co-authored-by: Mark Potts <33099090+mark-a-potts@users.noreply.github.com> Co-authored-by: michelleharrold <harrold@ucar.edu> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: gsketefian <31046882+gsketefian@users.noreply.github.com> Co-authored-by: BenjaminBlake-NOAA <52074832+BenjaminBlake-NOAA@users.noreply.github.com> Co-authored-by: Benjamin.Blake EMC <Benjamin.Blake@v71a1.ncep.noaa.gov> Co-authored-by: Benjamin.Blake EMC <Benjamin.Blake@v72a1.ncep.noaa.gov> Co-authored-by: Benjamin.Blake EMC <Benjamin.Blake@v71a3.ncep.noaa.gov> Co-authored-by: chan-hoo <chan-hoo.jeon@noaa.gov> Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com> Co-authored-by: Natalie Perlin <68030316+natalie-perlin@users.noreply.github.com> Co-authored-by: Natalie Perlin <Natalie@Natalies-MacBook-Air.local> Co-authored-by: danielabdi-noaa <52012304+danielabdi-noaa@users.noreply.github.com> Co-authored-by: Daniel Abdi <dabdi@Orion-login-2.HPC.MsState.Edu> Co-authored-by: Daniel Abdi <daniel.abdi@noaa.gov> Co-authored-by: EdwardSnyder-NOAA <96196752+EdwardSnyder-NOAA@users.noreply.github.com> Co-authored-by: Yunheng Wang <47898913+ywangwof@users.noreply.github.com> Co-authored-by: WYH@MBP <yunheng.wang@4374-ywang.winstorm.nssl> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> Co-authored-by: Daniel Shawul <dshawul@yahoo.com>

@willmayfield

* Added workflow for RRFS_v1nssl * Renamed FV3_RRFS_v1nssl to FV3_WoFS_v0 and added WE2E tests configuraiton files for suite FV3_WoFS_v0 * Added SUBCONUS test for WoFS suite * water_nc initial value sets to zero for FV3GFS data * Add Gaea as a supported platform for the regional_workflow (#734) * Updates to port regional workflow to gaea * Temp change with -v as batch option * new fixes for gaea/slurm * Updated time for make lbcs * added TEST data directory path * Update gaea.sh * fixes for PR * Add more parameters to CSV file containing WE2E test info (#740) ## DESCRIPTION OF CHANGES: The script/function `get_WE2Etest_names_subdirs_descs.sh` (which is called from `run_WE2E_tests.sh` if needed) creates a CSV (Comma-Separated Value) file named `WE2E_test_info.csv` that contains information about the WE2E tests. Currently, this CSV file contains only 3 columns: the test name, the names of any alternate names for the test, and the test description. In order to have a more complete summary of the WE2E tests, this PR modifies `get_WE2Etest_names_subdirs_descs.sh` so that additional information is included in the CSV file. This additional information consists of the values of the following experiment variables for each test: ``` PREDEF_GRID_NAME CCPP_PHYS_SUITE EXTRN_MDL_NAME_ICS EXTRN_MDL_NAME_LBCS DATE_FIRST_CYCL DATE_LAST_CYCL CYCL_HRS INCR_CYCL_FREQ FCST_LEN_HRS LBC_SPEC_INTVL_HRS NUM_ENS_MEMBERS ``` In addition, the script uses this information to calculate the number of times each test calls the forecast model (e.g. if the test uses 3 different cycle dates, then the forecast model will be called 3 times; if it is an ensemble test for a single cycle, the test will call the forecast model as many times as the number of ensemble members). ## TESTS CONDUCTED: The script `run_WE2E_tests.sh` was called that in turn calls `get_WE2Etest_names_subdirs_descs.sh`. This created a new CSV file that contained the new fields (columns). The CSV file was imported into Google Sheets (using "|" as the field/column separator) and looked correct. ## DOCUMENTATION: The documentation is for the most part already within the `get_WE2Etest_names_subdirs_descs.sh`. This PR slightly modifies that documentation to update it. * Update directory structure of NCO mode (#743) * update vertical structure of NCO mode * update sample script for nco * Fix typo on write component of new RRFS CONUS * Default CCPP physics option is FV3_GFS_v16 (#746) * Updated the default CCPP physics option to FV3_GFS_v16 * Updated the default CCPP physics option to FV3_GFS_v16 in config_defaults.sh Co-authored-by: Natalie Perlin <Natalie@Natalies-MacBook-Air.local> * Adds an alternative python workflow generation path (#698) * Workflow in python starting to work. * Use new python_utils package structure. * Some bug fixes. * Use uppercase TRUE/FALSE in var_dfns * Use config.sh by default. * Minor bug fixes. * Remove config.yaml * Update to the latest develop * Remove quotes from numbers in predef grid. * Minor bug fix. * Move validity checker to the bottom of setup * Add more unit tests. * Update with python_utils changes. * Update to latest develop additions (Need to re-run regression test) * Use set_namelist and fill_jinja_template as python functions. * Replace sed regex searches with python re. * Use python realpath. * Construct settings as dictionary before passing to fill_jinja and set_namelist * Use yaml for setting predefined grid parameters. * Use xml parser for ccpp phys suite definition file. * Remove more run_command calls. * Simplify some func argument processing. * Move different config format parsers to same file. * Use os.path.join for the sake of macosx * Remove remaining func argument processing via os.environ. * Minor bug fix in set_extrn_mdl_params.sh * Add suite defn in test_data. * Minor fixes on unittest on jet. * Simplify boolean condition checks. * Include old in renaming of old directories * Fix conflicting yaml !join tag for paths and strings. * Bug fix with setting sfcperst dict. * Imitate "readlink -m" with os.path.realpath instead of os.readlink * Don't use /tmp as that is shared by multiple users. * Bug fix with cron line, maintain quotes around TRUE/FALSE. * Update to latest develop (untested) * Bug fix with existing cron line and quotes. * Bug fix with case-sensitive MACHINE name, and empty EXPT_DIR. * Update to latest develop * More updates. * Bug fix thanks to @willmayfield! Check both starting/ending characters are brackets for shell variable to be considered an array. * Make empty EXPT_BASEDIR workable. * Update to latest develop * Update in predef grid. * Check f90nml as well. Co-authored-by: Daniel Abdi <dabdi@Orion-login-2.HPC.MsState.Edu> * Fix typo and crontab issue on wcoss dell in workflow python scripts (#750) * Fix typo and failure on wcoss * fix new line issue on wcoss dell * remove capture_output * Get USER from environment Co-authored-by: Daniel Abdi <daniel.abdi@noaa.gov> * Add new WE2E configs (#748) ## DESCRIPTION OF CHANGES: Added two new WE2E config files for the Sub-CONUS Indianapolis domain to support the upcoming SRW release. In addition, modified the external data used in the `config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh` to match more common datasets used in the WE2E testing process. ## TESTS CONDUCTED: Successfully ran the new WE2E tests (`config.SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_HRRR.sh`, `config.SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta.sh`) and `config.specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS.sh` on NOAA Parallel Works AWS instance. ## DEPENDENCIES: None. ## DOCUMENTATION: No documentation changes are required. * Added a fixed WoF grid and the python tool to determine the write component parameters (#733) * Added a fixed WoF grid and the python tool to determine the write component parameters * Update set_predef_grid_params.sh * Renamed file as recommended and removed unused lines * Modified comment Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com> Co-authored-by: WYH@MBP <yunheng.wang@4374-ywang.winstorm.nssl> * Replace env with modulefiles in scripts (#752) * change env to mod * update we2e script * WE2E script improvements for usability (#745) ## DESCRIPTION OF CHANGES: * Modifications to `run_WE2E_tests.sh`: * Add examples to help/usage statement * Modifications to `check_expts_status.sh`: * Add arguments list that can be processed by `process_args` * Add new optional arguments: `num_log_lines`, `verbose` * Include a help/usage message ## TESTS CONDUCTED: * Ran `run_WE2E_tests.sh --help` from the command line and got the expected help message. * Ran `check_expts_status.sh --help` from the command line and got the expected help message. * Used `run_WE2E_tests.sh` to run a set of 2 WE2E tests -- works as expected. * Used `check_expts_status` to check on the status of the 2 tests run above and got the expected status message. ## DEPENDENCIES: PR #[241](ufs-community/ufs-srweather-app#241) ## DOCUMENTATION: A lot of this PR is documentation in the scripts. There is an accompanying documentation PR #[241](ufs-community/ufs-srweather-app#241) into ufs-srweather-app. * Standardize static data across Tier-1 platforms; fix and improve IC and LBC data retrieval (#744) * Bug fixes (grid size + suppress screen output from module load) (#756) ## DESCRIPTION OF CHANGES: 1) Adjust y-direction size of write-component grid of `SUBCONUS_Ind_3km` predefined grid from 195 to 197 (this was just an oversight in PR #725 ). 2) Redirect output of module load in launch script (`launch_FV3LAM_wflow.sh`) to `/dev/null` to avoid unwanted screen output (which was introduced in PR #[238](ufs-community/ufs-srweather-app#238) in ufs-srweather-app and is about how to load the `regional_workflow` environment and is not relevant in this context). ## TESTS CONDUCTED: 1) Plotted the `SUBCONUS_Ind_3km` grid to ensure it has correct size (it does). 2) Manually ran `launch_FV3LAM_wflow.sh` from the command line to verify that screen output is suppressed (it is). * Update default SPP ISEED array in config_defaults.sh to use unique values (#759) * Modify RRFS North America 3- and 13-km domain configuration and WE2E test. * Modify default ISEED values for SPP * Fix grid in WE2E test * Update workflow python scripts (#760) * update python scripts * Change output file name of run_post to meet NCO standards (#758) * change output file name * change variable name * update python script * remove duplicates * add a check for empty variables * move variable to common area * clean up unnecessary comments * update scripts * remove duplicate * update python scripts * fix user-staged dir path issue in python script * Add POST_OUTPUT_DOMAIN_NAME to WE2E tests for new grids (#763) * Add new var to we2e tests for new grids * rename we2e tests for custom grid * remove unnecessary $ * Modifications to `CODEOWNERS` file (#757) * Add @gspetro-NOAA, @natalie-perlin, and @EdwardSnyder-NOAA to CODEOWNERS so they are notified of all PRs and can review them. * Remove duplicates in CODEOWNERS; remove users who will no longer be working with the repo. * Adding a python utility for summarizing compute. (#769) Adds a utility that summarizes Rocoto database computational usage information. * Add github actions for python unittests. (#747) * Add github actions for python unittests. * Include all python script in ush * Skip defining QUILTING params when it is set to False * Update py_workflow * Update unittest for set_extrn_mdl_params. * Updates from develop. Co-authored-by: Daniel Shawul <dshawul@yahoo.com> * Update sample script for NCO mode (#771) * update config.nco.sh * Add comment * Feature/noaacloud (#767) * updates for noaacloud * working version * fixes for noaacloud * added extra modules for post * removed cheyenne-specific crontab editing section (#773) * Pin down hera miniconda3 module file version. (#770) Pin down the version of miniconda3 on Hera, and do not append to the module path. * update staged data dir (#774) * Changed to smaller SUBCONUS_Ind_3km domain Co-authored-by: Mark Potts <33099090+mark-a-potts@users.noreply.github.com> Co-authored-by: gsketefian <31046882+gsketefian@users.noreply.github.com> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: Natalie Perlin <68030316+natalie-perlin@users.noreply.github.com> Co-authored-by: Natalie Perlin <Natalie@Natalies-MacBook-Air.local> Co-authored-by: danielabdi-noaa <52012304+danielabdi-noaa@users.noreply.github.com> Co-authored-by: Daniel Abdi <dabdi@Orion-login-2.HPC.MsState.Edu> Co-authored-by: Daniel Abdi <daniel.abdi@noaa.gov> Co-authored-by: EdwardSnyder-NOAA <96196752+EdwardSnyder-NOAA@users.noreply.github.com> Co-authored-by: JeffBeck-NOAA <55201531+JeffBeck-NOAA@users.noreply.github.com> Co-authored-by: WYH@MBP <yunheng.wang@4374-ywang.winstorm.nssl> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> Co-authored-by: Christina Holt <56881914+christinaholtNOAA@users.noreply.github.com> Co-authored-by: Daniel Shawul <dshawul@yahoo.com>

change output file name

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chan-hoo requested review from mkavulich, gsketefian, JeffBeck-NOAA, RatkoVasic-NOAA, BenjaminBlake-NOAA, ywangwof, panll, christinaholtNOAA, christopherwharrop-noaa, danielabdi-noaa, mark-a-potts, jkbk2004, willmayfield, jwolff-ncar and dmwright526 as code owners May 5, 2022 18:08

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chan-hoo added 2 commits May 6, 2022 11:01

change variable name

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update python script

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chan-hoo added 2 commits May 6, 2022 17:13

remove duplicates

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add a check for empty variables

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chan-hoo added 2 commits May 6, 2022 19:04

move variable to common area

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clean up unnecessary comments

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gsketefian approved these changes May 9, 2022

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update scripts

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chan-hoo added 3 commits May 9, 2022 17:56

Merge branch 'develop' of https://github.com/ufs-community/regional_w…

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…orkflow into feature/filename_nco

remove duplicate

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update python scripts

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danielabdi-noaa approved these changes May 9, 2022

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fix user-staged dir path issue in python script

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chan-hoo merged commit 1ec6851 into ufs-community:develop May 10, 2022

chan-hoo deleted the feature/filename_nco branch May 10, 2022 08:03

danielabdi-noaa mentioned this pull request May 10, 2022

new_ESGgrid doesn't run #761

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Change output file name of run_post to meet NCO standards #758

Change output file name of run_post to meet NCO standards #758

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Change output file name of run_post to meet NCO standards #758

Change output file name of run_post to meet NCO standards #758

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DESCRIPTION OF CHANGES:

TESTS CONDUCTED:

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