Bugfix: Pass domain name to python plotting scripts #783
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…ipts in order to be able to form the proper UPP output file names. Edit/add to comments.
gsketefian
requested review from
mkavulich,
JeffBeck-NOAA,
RatkoVasic-NOAA,
BenjaminBlake-NOAA,
ywangwof,
chan-hoo,
panll,
christinaholtNOAA,
christopherwharrop-noaa,
danielabdi-noaa,
mark-a-potts,
jkbk2004,
willmayfield,
dmwright526,
gspetro-NOAA,
natalie-perlin and
EdwardSnyder-NOAA
as code owners
|
@chan-hoo, is inclusion of the domain name within the grib2 output files acceptable to NCO? We hadn't done that before, so just wanted to make sure. @mark-a-potts, @gsketefian, I don't mean to hold up this PR, just want to see if we need a follow-up PR in the future, so please continue! |
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@gsketefian The looks good to me. The qsub_job*.sh and sq_job*.sh are also going to need to be updated with the new variable. Since we source the var_defns.sh in those job scripts, we should just need to add ${POST_OUTPUT_DOMAIN_NAME} to the last line. |
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@JeffBeck-NOAA Having the domain name in the grib2 files is acceptable to NCO. For the HRRR Alaska grib2 files, they have "ak" in them, and the NAM nest grib2 files also have domain-specific labels in the filenames. |
BenjaminBlake-NOAA
approved these changes
Jun 2, 2022
|
@JeffBeck-NOAA, as Ben mentioned above, it is a new requirement of the NCO standards (Ver. 11.0.0, Jan 19, 2022, pp. 6) "Filename format for files in com: model.tHHz.var_info.f###.domain.format". |
chan-hoo
approved these changes
Jun 2, 2022
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Thanks, @chan-hoo and @BenjaminBlake-NOAA ! |
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@dmwright526 Thanks for pointing that out. I fixed the batch scripts as well and tested the slurm ones on Hera (didn't test the PBS ones on Cheyenne though). |
gsketefian
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that referenced
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Jun 2, 2022
## DESCRIPTION OF CHANGES: This PR updates the RST documentation files to accompany changes in PR #[783](ufs-community/regional_workflow#783) in `regional_workflow`. ## DEPENDENCIES: PR #[783](ufs-community/regional_workflow#783) in `regional_workflow`. ## ISSUE (optional): Partially resolves issue #[781](ufs-community/regional_workflow#781) (still need to introduce tests in `regional_workflow` that run the plotting scripts). ## CONTRIBUTORS: @mark-a-potts
gsketefian
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Jun 7, 2022
## DESCRIPTION OF CHANGES: PR #[763](ufs-community#763) introduced the experiment variable `POST_OUTPUT_DOMAIN_NAME` and used it to modify the names of the UPP output files. This PR adds `POST_OUTPUT_DOMAIN_NAME` as an argument to the python plotting scripts to enable those scripts to form the proper UPP output file names to read in. It also modifies the batch scripts (`qsub_job.sh`, `qsub_job_diff.sh`, `sq_job.sh`, and `sq_job_diff.sh`) to add the new argument to the calls to the python plotting scripts that are called. ## TESTS CONDUCTED: Both python plotting scripts `plot_allvars.py` and `plot_allvars_diff.py` were run on Hera on preexisting UPP output files and completed successfully. The batch scripts `sq_job.sh` and `sq_job_diff.sh` were also run successfully on Hera (`qsub_job.sh` and `qsub_job_diff.sh` were not run on e.g. Cheyenne). ## DEPENDENCIES: PR # in `ufs-srweather-app`. ## DOCUMENTATION: Modifications to the documentation are in PR #. ## ISSUE: Partially resolves issue ufs-community#781 (still need to introduce tests in `regional_workflow` that run the plotting scripts). ## CONTRIBUTORS: @mark-a-potts pointed out the problem and first made the necessary fixes in the `NOAA-EPIC` fork of `regional_workflow`; @gsketefian introduced those changes to this PR and made edits to the comments and documentation.
This was referenced Jun 8, 2022
gsketefian
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Jun 8, 2022
…ts (#788) ## DESCRIPTION OF CHANGES: This is the counterpart of PR #[783](#783) but to be merged into the `release/public-v2` branch instead of `develop`. See that PR for details. ## DEPENDENCIES: PR #[298](ufs-community/ufs-srweather-app#298) in `ufs-srweather-app`.
EdwardSnyder-NOAA
added a commit
that referenced
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Jun 10, 2022
* update IC/LBC file paths to match new IC/LBC file structure (#766) * update IC/LBC file paths to match new IC/LBC file structure * change forecast length * Update config.community.sh These changes reflects the SRW team's preference for a 12-hours forecast. The gfs.t18z.pgrb2.0p25.f012 file will need to be added to all Level 1 systems. Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> * add a machine file for MacOS (#777) Co-authored-by: Natalie Perlin <perlin.natalie@gmail.com> * Add columns for relative test and time step to CSV file containing WE2E test info (#776) ## DESCRIPTION OF CHANGES: This PR modifies the script `get_WE2Etest_names_subdirs_descs.sh` that creates the CSV file containing test information the columns for relative cost and time step (`DT_ATMOS`). This allows users to have a better idea of what the cost of each test is (the relative cost is defined such that 1 unit represents the cost of running a single 6-hour forecast on the `RRFS_CONUS_25km` grid). Other related changes: * Add the flag `generate_csv_file` to the `run_WE2E_tests.sh` script to allow users to skip the CSV file generation step (since it can take a while). * Use arguments for the function `set_predef_grid_params()` so that it can be called not just from the experiment generation scripts but also others (in this case from `get_WE2Etest_names_subdirs_descs.sh`). Necessary for this PR. * Move some constants (`NH0`, `NH3`, `NH4`) from `config_defaults.sh` to `constants.sh` to make it easier to access them. * Place the contents of `constants.sh` at the start of each experiment's `var_defns.sh` so that these constants are available to the j-jobs and ex-scripts when `var_defns.sh` is sourced. * Use variable `valid_vals_BOOLEAN` in many more places (which allows many other `valid_vals_...` variables in `valid_param_vals.sh` and `setup.sh` to be removed). * Several other bug fixes. ## TESTS CONDUCTED: The following tests (with results) were conducted on Hera. There were only three (previously existing) failures. ``` * grid_CONUS_25km_GFDLgrid_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_2017_gfdlmp: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_2017_gfdlmp_regional: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v15p2: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16: SUCCESS * grid_RRFS_CONUS_25km_ics_FV3GFS_lbcs_RAP_suite_HRRR: SUCCESS * grid_RRFS_CONUS_25km_ics_GSMGFS_lbcs_GSMGFS_suite_GFS_2017_gfdlmp: SUCCESS * grid_RRFS_CONUS_25km_ics_GSMGFS_lbcs_GSMGFS_suite_GFS_v15p2: SUCCESS * grid_RRFS_CONUS_25km_ics_GSMGFS_lbcs_GSMGFS_suite_GFS_v16: FAILURE * grid_RRFS_CONUS_25km_ics_NAM_lbcs_NAM_suite_HRRR: SUCCESS * grid_RRFS_CONUS_25km_ics_NAM_lbcs_NAM_suite_RRFS_v1beta: SUCCESS * grid_RRFS_CONUScompact_25km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_HRRR_suite_HRRR: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_HRRR_suite_RRFS_v1beta: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_HRRR: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_RRFS_v1alpha: SUCCESS * grid_RRFS_CONUScompact_25km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta: SUCCESS * grid_SUBCONUS_Ind_3km_ics_FV3GFS_lbcs_FV3GFS_suite_GFS_v16: SUCCESS * grid_SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_HRRR: SUCCESS * grid_SUBCONUS_Ind_3km_ics_HRRR_lbcs_RAP_suite_RRFS_v1beta: SUCCESS * GST_release_public_v1: SUCCESS * MET_ensemble_verification: SUCCESS * MET_verification: SUCCESS * community_ensemble_008mems: SUCCESS * community_ensemble_2mems: SUCCESS * custom_ESGgrid: SUCCESS * custom_GFDLgrid: SUCCESS * custom_GFDLgrid__GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES_eq_FALSE: SUCCESS * custom_GFDLgrid__GFDLgrid_USE_GFDLgrid_RES_IN_FILENAMES_eq_TRUE: SUCCESS * deactivate_tasks: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2019061200: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2019101818: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2020022518: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2020022600: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_grib2_2021010100: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2019061200: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2019101818: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2020022518: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2020022600: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio_2021010100: SUCCESS * get_from_HPSS_ics_FV3GFS_lbcs_FV3GFS_fmt_netcdf_2021062000: SUCCESS * get_from_HPSS_ics_GSMGFS_lbcs_GSMGFS: SUCCESS * get_from_HPSS_ics_HRRR_lbcs_RAP: SUCCESS * get_from_HPSS_ics_RAP_lbcs_RAP: SUCCESS * get_from_NOMADS_ics_FV3GFS_lbcs_FV3GFS_fmt_nemsio: SUCCESS * inline_post: SUCCESS * nco_ensemble: SUCCESS * nco_inline_post: SUCCESS * pregen_grid_orog_sfc_climo: SUCCESS * specify_DOT_OR_USCORE: SUCCESS * specify_DT_ATMOS_LAYOUT_XY_BLOCKSIZE: SUCCESS * specify_EXTRN_MDL_SYSBASEDIR_ICS_LBCS: SUCCESS * specify_RESTART_INTERVAL: SUCCESS * specify_template_filenames: SUCCESS * subhourly_post: FAILURE * subhourly_post_ensemble_2mems: FAILURE ``` ## DOCUMENTATION: Documentation is updated via PR #[278](ufs-community/ufs-srweather-app#278) in the ``ufs-srweather-app`` repo. * Bug fix for calculation of number of time steps for a given WE2E test. (#782) ## DESCRIPTION OF CHANGES: This PR fixes a bug in the way the number of time steps (`num_time_steps` in `get_WE2Etest_names_subdirs_descs.sh`) is calculated for each WE2E test when creating the CSV file containing information about the available WE2E tests. ## TESTS CONDUCTED: Reran the `run_WE2E_tests.sh` script (which in turn calls `get_WE2Etest_names_subdirs_descs.sh`), and a CSV file containing the adjusted numbers was successfully created. ## DOCUMENTATION: None needed. * Bugfix: Pass domain name to python plotting scripts (#783) ## DESCRIPTION OF CHANGES: PR #[763](#763) introduced the experiment variable `POST_OUTPUT_DOMAIN_NAME` and used it to modify the names of the UPP output files. This PR adds `POST_OUTPUT_DOMAIN_NAME` as an argument to the python plotting scripts to enable those scripts to form the proper UPP output file names to read in. It also modifies the batch scripts (`qsub_job.sh`, `qsub_job_diff.sh`, `sq_job.sh`, and `sq_job_diff.sh`) to add the new argument to the calls to the python plotting scripts that are called. ## TESTS CONDUCTED: Both python plotting scripts `plot_allvars.py` and `plot_allvars_diff.py` were run on Hera on preexisting UPP output files and completed successfully. The batch scripts `sq_job.sh` and `sq_job_diff.sh` were also run successfully on Hera (`qsub_job.sh` and `qsub_job_diff.sh` were not run on e.g. Cheyenne). ## DEPENDENCIES: PR # in `ufs-srweather-app`. ## DOCUMENTATION: Modifications to the documentation are in PR #. ## ISSUE: Partially resolves issue #781 (still need to introduce tests in `regional_workflow` that run the plotting scripts). ## CONTRIBUTORS: @mark-a-potts pointed out the problem and first made the necessary fixes in the `NOAA-EPIC` fork of `regional_workflow`; @gsketefian introduced those changes to this PR and made edits to the comments and documentation. * created new non-compact grids * fixed typo * Update scripts to work with the latest hashes of UFS_UTILS and UPP (#775) * update input namelist of chgres_cube * update diag_table templates * update scripts * back to original * specify miniconda version on Jet Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> Co-authored-by: Natalie Perlin <68030316+natalie-perlin@users.noreply.github.com> Co-authored-by: Natalie Perlin <perlin.natalie@gmail.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>
mark-a-potts
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Jun 12, 2022
* Fix artifact creation for branches with / in name (#275) The slash in branch names such as release/.* and feature/.* is interpreted as a directory separator. This change replaces the "/" character with a "_". * Include documentation for building/running SRW App on Mac (#240) * updated docs * added git submodule * fix formatting * added new submodule commits * fixed ref links * finished Intro * finish Components & Intro edits * edited Rocoto workflow section of Quickstart * added minor hpc submodule commits * Updates to Rocoto Workflow in Quick Start * add to HPC-stack intro * submodule updates * added submodule docs edits * hpc-stack updates & formatting fixes * hpc-stack intro edits * bibtex attempted fix * add hpc-stack module edits * update sphinxcontrib version * add .readthedocs.yaml file * update .readthedocs.yaml file * update .readthedocs.yaml file * update conf.py * updates .readthedocs.yaml with submodules * updates .readthedocs.yaml with submodules * submodule updates * submodule updates * minor Intro edits * minor Intro edits * minor Intro edits * submodule updates * fixed typos in QS * QS updates * QS updates * QS updates * updates to InputOutput and QS * fix I/O doc typos * pull updates to hpc-stack docs * pull updates to hpc-stack docs * fix table wrapping * updates to QS for cloud * fix QS export statements * fix QS export statements * QS edits on bind, config * add bullet points to notes * running without rocoto * add HPC-Stack submodule w/docs * split QS into container/non-container approaches * added filepath changes for running in container on Orion, et al. * edits to overview and container QS * moved CodeReposAndDirs.rst info to the Introduction & deleted file * continued edits to SRWAppOverview * combine overview w/non-container docs * finish merging non-container guide & SRWOverview, rename/remove files, update FAQ * minor edits for Intro & QS * updates to BuildRun doc through 3.8.1 * edits to Build/Run and Components * remove .gitignore * fix Ch 3 title, 4 supported platform levels note * fix typos, add term links * other minor fixes/suggestions implemented * updated Intro based on feedback; changed SRW to SRW App throughout * update comment to Intro citation * add user-defined vertical levels to future work * Add instructions for srw_common module load * fix typo * update Intro & BuildRunSRW based on Mark's feedback * minor intro updates * 1st round of jwolff's edits * 2nd round of jwolff updates * update QS intro * fix minor physics details * update citation and physics suite name * add compute node allocation info to QS * add authoritative hpc-stack docs to Intro * create MacOS install/build instructions * add MacOS Build/Run instructions * fix MacOS Build/Run details * add MacOS info directly to Build/Run SRW chapter * minor details * minor edits * update Include-HPCInstall with mac installation docs * add note re: Terminal.app & bash shell in MacOS section * remove MacInstall file-contents added to BuildRunSRW * update hpc-stack submodule to include mac installation info * add MacOS config details * add MacOS config & run details * minor MacOS note * mention need to verify software library version #'s * update hpc-stack-mod * align MacDetails section with PR #238 info * remove gsed & alter related commands * update hpc-stack submodule * typos * switch from env to module load Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com> * Update BuildRunSRW.rst * update hpc-stack module docs & MacOS config.sh * update machine file instructions * updates to BuildRun chapter * fix typo Co-authored-by: gspetro <gillian.s.petro@gmail.com> Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com> * Update documentation for CSV file containing WE2E test info (#278) * Edits to documentation to match latest in code. * Edits to documentation to match latest in code. * Minor changes to documentation. * Port SRW App to WCOSS2 (#270) * port to wcoss2 * update scripts * ensure platform name from variance * update scripts * remove wcoss2 from lmod-setup * Fix --ccpp option in devbuild.sh (#280) * fix ccpp issue * update script * Print usage if machine name is not passed to `lmod-setup.sh/csh`. (#262) * Print usage() message if machine name is not passed. * Bug fix with macos modulefiles. * Back to original hashes (#287) * Updated the Introduction, build for MacOS (#281) * Updated the Introduction, build for MacOS * Update Introduction.rst Some comments removed * Update Introduction.rst Updated data storage requirements for the SRW * Update documentation for python plotting scripts (#289) ## DESCRIPTION OF CHANGES: This PR updates the RST documentation files to accompany changes in PR #[783](ufs-community/regional_workflow#783) in `regional_workflow`. ## DEPENDENCIES: PR #[783](ufs-community/regional_workflow#783) in `regional_workflow`. ## ISSUE (optional): Partially resolves issue #[781](ufs-community/regional_workflow#781) (still need to introduce tests in `regional_workflow` that run the plotting scripts). ## CONTRIBUTORS: @mark-a-potts * Updating for testing with updated ufs weather model * added version to wflow for jet * switched to epic repo for testing * Updates to modules for cheyenne * updated module path * changed hash to branch for testing * updated to use ufs-community version of WM * Pointing to PR-branch of regional_workflow for testing * Updating module files for cheyenne for testing * Added png explicitly under gaea. * Update build_cheyenne_intel Corrected loading system modules (load intel/2022.1, mpt/2.25), updated package versions if newer modules are built. * Updated pointer to model for testing * fixed repos * updated to point at my regional_workflow branch * updated regional_workflow to release/public-v2 Co-authored-by: Jesse McFarland <jesse@mcfarland.sh> Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> Co-authored-by: gspetro <gillian.s.petro@gmail.com> Co-authored-by: Will Mayfield <59745143+willmayfield@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: danielabdi-noaa <52012304+danielabdi-noaa@users.noreply.github.com> Co-authored-by: Natalie Perlin <68030316+natalie-perlin@users.noreply.github.com> Co-authored-by: Mark Potts <mpotts@redlineperf.com>
danielabdi-noaa
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Jun 15, 2022
PR #[763](ufs-community#763) introduced the experiment variable `POST_OUTPUT_DOMAIN_NAME` and used it to modify the names of the UPP output files. This PR adds `POST_OUTPUT_DOMAIN_NAME` as an argument to the python plotting scripts to enable those scripts to form the proper UPP output file names to read in. It also modifies the batch scripts (`qsub_job.sh`, `qsub_job_diff.sh`, `sq_job.sh`, and `sq_job_diff.sh`) to add the new argument to the calls to the python plotting scripts that are called. Both python plotting scripts `plot_allvars.py` and `plot_allvars_diff.py` were run on Hera on preexisting UPP output files and completed successfully. The batch scripts `sq_job.sh` and `sq_job_diff.sh` were also run successfully on Hera (`qsub_job.sh` and `qsub_job_diff.sh` were not run on e.g. Cheyenne). PR # in `ufs-srweather-app`. Modifications to the documentation are in PR #. Partially resolves issue ufs-community#781 (still need to introduce tests in `regional_workflow` that run the plotting scripts). @mark-a-potts pointed out the problem and first made the necessary fixes in the `NOAA-EPIC` fork of `regional_workflow`; @gsketefian introduced those changes to this PR and made edits to the comments and documentation.
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DESCRIPTION OF CHANGES:
PR #763 introduced the experiment variable
POST_OUTPUT_DOMAIN_NAMEand used it to modify the names of the UPP output files. This PR addsPOST_OUTPUT_DOMAIN_NAMEas an argument to the python plotting scripts to enable those scripts to form the proper UPP output file names to read in. It also modifies the batch scripts (qsub_job.sh,qsub_job_diff.sh,sq_job.sh, andsq_job_diff.sh) to add the new argument to the calls to the python plotting scripts that are called.TESTS CONDUCTED:
Both python plotting scripts
plot_allvars.pyandplot_allvars_diff.pywere run on Hera on preexisting UPP output files and completed successfully. The batch scriptssq_job.shandsq_job_diff.shwere also run successfully on Hera (qsub_job.shandqsub_job_diff.shwere not run on e.g. Cheyenne).DEPENDENCIES:
PR #289 in
ufs-srweather-app.DOCUMENTATION:
Modifications to the documentation are in PR #289.
ISSUE:
Partially resolves issue #781 (still need to introduce tests in
regional_workflowthat run the plotting scripts).CONTRIBUTORS:
@mark-a-potts pointed out the problem and first made the necessary fixes in the
NOAA-EPICfork ofregional_workflow; @gsketefian introduced those changes to this PR and made edits to the comments and documentation.