Feature/cheyenne fix#258
Merged
mark-a-potts merged 10 commits intoMay 18, 2022
Merged
Conversation
Update develop to head at ufs-community
mark-a-potts
requested review from
BenjaminBlake-NOAA,
EdwardSnyder-NOAA,
JeffBeck-NOAA,
RatkoVasic-NOAA,
chan-hoo,
christinaholtNOAA,
christopherwharrop-noaa,
danielabdi-noaa,
dmwright526,
gsketefian,
gspetro-NOAA,
jkbk2004,
mkavulich,
natalie-perlin,
panll,
willmayfield and
ywangwof
as code owners
willmayfield
approved these changes
May 16, 2022
Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com>
Collaborator
|
@mark-a-potts I am having trouble testing this fix for GNU on Cheyenne because there appears to be a bug in the crontab generation of the WE2E tests that overwrites the crontab rather than appending to it. Is this a known problem in the NOAA-EPIC repository? I did not encounter it when testing from develop in ufs-community a couple weeks ago, but there have been some commits since then, so I'm not sure when this problem started. |
Contributor
Author
|
@mkavulich, unfortunately, that sounds like a new bug. I am not sure what might be causing that. Will have to investigate... |
JeffBeck-NOAA
approved these changes
May 17, 2022
christinaholtNOAA
referenced
this pull request
in NOAA-GSL/ufs-srweather-app
Jun 7, 2022
* Add support on NSSL/Odin (#227) * Add support on NSSL/Odin * Add wlfow_odin.env and modify detect_machine.sh * update comment * Detect explicitly odin1/odin2 * Add python module to cheyenne build environments (#232) * Update SRW Documentation (#212) * 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 Co-authored-by: gspetro <gillian.s.petro@gmail.com> * Update hashes of all components to latest versions (#233) * Add a Contributor's Guide feature to the docs (#228) * create contributor's guide * add guidelines for making good PR * good pull request edits * 1st Draft of COntributor's Guide * minor formatting edits * Add instructions for srw_common module load * fix module files guidance * fix typo * update Intro & BuildRunSRW based on Mark's feedback * minor intro updates * add info on documentation requirements * 1st round of J. Beck's edits * add textonly issue template + minor typo-type fixes * minor edits/formatting * remove pylintrc requirement * fixed .yaml & other minor Co-authored-by: gspetro <gillian.s.petro@gmail.com> * Updates to parameters in config_defaults .rst files (#237) * edit config intro & platform environment sections * edit sections on cron & directory parameters, platform & parameters for running without a workflow manager * edit NCO, file-separator, filename params, add some METplus and model config params * ConfigWorkflow.rst revisions, added METplus to Components, grid info * add grid config details * changes to readme.md * RTD readme.md edits * create MacOS install/build instructions * update task run and grid parameters * fixed file params & workflow task params * 1st draft of ConfigParameters.inc * minor edits * add stochastic physics var details * update FVCOM, thread affinity params * halo_blend, ens, crtm, custom post, subhourly updates * update HPC-Stack submodule/docs * Rocoto WF tasks & params * workflow tasks/params, debug, verbose, pre-existing dir, predefined grid * move Stochastic physics to CCP section; write component edits * comp'l forecast, grid gen, NOMADS, user-staged files * METplus, model config & forecast params, separator * 2nd draft complete * physics updates * remove MacInstall empty file * undo hpc-stack submodule update (save for separate PR) * undo hpc-stack install doc update (save for separate PR) * revisions to SPP & LSM physics * minor edits * update comments in LAM Grid chapter * update LSM_SPP_EACH_STEP * revert LSM_SPP_EACH_STEP to original definition * combine config info into one doc instead of two Co-authored-by: gspetro <gillian.s.petro@gmail.com> * Added functionality for MacOS X (#242) * Added functionality for MacOS X Functionality for MacOS, updated module list in srw_common * Update build_macos_gnu.env * Update srw_common * Update build_macos_gnu.env The env/build_mac_gnu.env does not load srw_common module, but instead loads individual HPC-stack modules built locally on the Mac that contain higher-versions of some packages. This avoids conflicts with SRW builds for other platforms. * Update srw_common corrected the version of the gftl-shared * Update build_macos_gnu.env No need to load libpng module found in srw_common, as this is not being built as a part of the hpc-stack on MacOS X, rather installed system-wide. Co-authored-by: Natalie Perlin <Natalie@Natalies-MacBook-Air.local> * Add gaea to supported platforms (#236) * fixes for gaea * updates for gaea * tweak for build env * 2nd tweak for build env * Fixes for slurm * another fix for env * added version for cmake * Update Externals.cfg * Update wflow_gaea.env * tweak * pulling Externals.cfg explicitly from develop * temporarily removing externals * Checked out directly from develop * Bug fix with singularity env files (#245) * Replace bash env files with modules (#238) * Pass machine name to build scripts. * Use modules environment instead of shell scripts. * Leave conda activation to the user. * Remove set_machine script. * Rename env to modulefiles * Minor fix. * Minor fix * Take out *module purge* from modufiles and put it in devbuild.sh * Activate conda directly in signularity modulefile. * Minor fixes. * Add Gaea modulefiles. * Restore odin env files. * Bug fixes in singularity modulefiles. * Move activation of Lmod to devbuild.sh * Don't do 'module purge' on cray systems * Put Lmod initialization code in separate script. * Go back to using modulefile for odin. * Optionally pass machine name to lmod-setup.sh * Modify odin wflow modulefile. * Allow unknown platforms in devbuild.sh * Update documentation. * Move cmake init out of lmod-setup.sh on odin * Also update markup language build documentation. * Lmod setup script for both bash and tcsh login shells. * Some fixes for tcsh login shell. * Add singularity platform to lmod-setup * update hash of regional workflow (#247) * Update WE2E documentation (#241) ## DESCRIPTION OF CHANGES: This updates the documentation for how to use the WE2E testing system. ## TESTS CONDUCTED: Compiled the documentation using `sphinx-build` and viewed the resulting html. ## DEPENDENCIES: PR #[745](ufs-community/regional_workflow#745) in regional_workflow. ## CONTRIBUTORS: @gspetro * fixes for gaea modules (#248) * Update regional_workflow hash, add shortcuts for common devbuild.sh options (#251) * Modifications to `CODEOWNERS` file (#252) ## DESCRIPTION OF CHANGES: Make the following modifications to the github `CODEOWNERS` file: 1) Add several EPIC staff (@gspetro-NOAA, @natalie-perlin, and @EdwardSnyder-NOAA) so they are notified of all PRs and can review them. 2) Remove duplicate entries. 3) Remove users who will no longer be working with the repo (thus far only @jwolff-ncar) . ## TESTS CONDUCTED: None. * Add verification tasks to documentation (#243) * METplus, model config & forecast params, separator * remove MacInstall empty file * undo hpc-stack submodule update (save for separate PR) * undo hpc-stack install doc update (save for separate PR) * combine config info into one doc instead of two * remove ConfigParameters.inc (contents now appear in ConfigWorkflow.rst) * add VX tables, config info, & Rocoto output tables * add module use/load statements, fix typos * varied minor details * add workflow svg diagram * condense VX task table using ## * update README * add png and revert hpc-stack commits until PR#240 (mac docs) is approved * jwolff edits * add info on run_vx.local Co-authored-by: gspetro <gillian.s.petro@gmail.com> * Add NOAA cloud platforms to SRW (#221) * updates for noaacloud * working version * pointing to noaa-epic for testing * changes for noaacloud * switched to load-any * fix for regional_workflow pointer (#260) * update hash of regional workflow (#261) * Feature/cheyenne fix (#258) * Adding a github action to build on cheyenne with intel * fixing yml * fixes for missing load-any on cheyenne * added pio as well * Update .github/workflows/build.yml Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com> Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com> * tweaks for build/run on gaea (#254) * tweaks for build/run on gaea * fixed path * Updates for PR * Check-in Jenkinsfile and unified scripts (#253) * Add Jenkinsfile that includes a build and test pipeline, which leverages the unified build and test scripts * Supported platforms are Cheyenne, Gaea, and Orion * Supported compilers are GNU and Intel * Fix for miniconda3 load on Hera (#257) Pin down the version of miniconda3 on Hera, and do not append to the module path * Updates to Remaining Chapters (6 & 8-12) of SRW Docs/User's Guide (#255) * 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 * edit config intro & platform environment sections * edit sections on cron & directory parameters, platform & parameters for running without a workflow manager * edit NCO, file-separator, filename params, add some METplus and model config params * ConfigWorkflow.rst revisions, added METplus to Components, grid info * add grid config details * changes to readme.md * RTD readme.md edits * create MacOS install/build instructions * update task run and grid parameters * fixed file params & workflow task params * 1st draft of ConfigParameters.inc * minor edits * add stochastic physics var details * update FVCOM, thread affinity params * halo_blend, ens, crtm, custom post, subhourly updates * update HPC-Stack submodule/docs * remove extra macinstall document * Rocoto WF tasks & params * workflow tasks/params, debug, verbose, pre-existing dir, predefined grid * move Stochastic physics to CCP section; write component edits * comp'l forecast, grid gen, NOMADS, user-staged files * METplus, model config & forecast params, separator * 2nd draft complete * physics updates * remove MacInstall empty file * undo hpc-stack submodule update (save for separate PR) * undo hpc-stack install doc update (save for separate PR) * revert hpc-stack submodule update * revisions to SPP & LSM physics * minor edits * update comments in LAM Grid chapter * update LSM_SPP_EACH_STEP * revert LSM_SPP_EACH_STEP to original definition * combine config info into one doc instead of two * remove ConfigParameters.inc (contents now appear in ConfigWorkflow.rst) * update hpc-stack docs submodule * odds & ends * add VX tables, config info, & Rocoto output tables * add module use/load statements, fix typos * varied minor details * add workflow svg diagram * edits to rocoto ch * updates to Rocoto chapter * fix minor formatting/wording issues * updates to LAMgrid chapter * LAM Grid edits * LAM ch: user-defined grid section * add UPP Product tables ch 6 * I/O edits & glossary terms * I/O Pt2 * I/O changes * include updated images * update docs to reflect changes in PR #238 * Graphics Ch-1st pass * minor updates to Graphics * minor updates to Graphics * edit ConfigNewPlatform sections 1-4 * ConfigNewPlatform edits * resolve merge conflicts * I/O ch edits * I/O edits * more I/O edits * hpc-stack submodule updates * add HPC-Stack MacOs info * WE2E edits & tables * fix typo * minor grammar/typos * merge conflict resolution * merge conflict resolution * fix grid name * remove resolved comments * add compact grids * file path updates & info for HPC-Stack * add SRW prereqs to Intro * change ConfigNewPlatform to a non-container quickstart * clean up non-container quickstart * update build options for non-container QS * update file paths & WE2E * minor fixes * update I/O & Gaea file paths * update error in non-container QS * add warning for users w/o Rocoto * add UPP Satellite Product instructions * Xlink for UPP satellite output info Co-authored-by: gspetro <gillian.s.petro@gmail.com> * Update compiler prerequisite in docs (#267) * 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 * edit config intro & platform environment sections * edit sections on cron & directory parameters, platform & parameters for running without a workflow manager * edit NCO, file-separator, filename params, add some METplus and model config params * ConfigWorkflow.rst revisions, added METplus to Components, grid info * add grid config details * changes to readme.md * RTD readme.md edits * create MacOS install/build instructions * update task run and grid parameters * fixed file params & workflow task params * 1st draft of ConfigParameters.inc * minor edits * add stochastic physics var details * update FVCOM, thread affinity params * halo_blend, ens, crtm, custom post, subhourly updates * update HPC-Stack submodule/docs * remove extra macinstall document * Rocoto WF tasks & params * workflow tasks/params, debug, verbose, pre-existing dir, predefined grid * move Stochastic physics to CCP section; write component edits * comp'l forecast, grid gen, NOMADS, user-staged files * METplus, model config & forecast params, separator * 2nd draft complete * physics updates * remove MacInstall empty file * undo hpc-stack submodule update (save for separate PR) * undo hpc-stack install doc update (save for separate PR) * revert hpc-stack submodule update * revisions to SPP & LSM physics * minor edits * update comments in LAM Grid chapter * update LSM_SPP_EACH_STEP * revert LSM_SPP_EACH_STEP to original definition * combine config info into one doc instead of two * remove ConfigParameters.inc (contents now appear in ConfigWorkflow.rst) * update hpc-stack docs submodule * odds & ends * add VX tables, config info, & Rocoto output tables * add module use/load statements, fix typos * varied minor details * add workflow svg diagram * edits to rocoto ch * updates to Rocoto chapter * fix minor formatting/wording issues * updates to LAMgrid chapter * LAM Grid edits * LAM ch: user-defined grid section * add UPP Product tables ch 6 * I/O edits & glossary terms * I/O Pt2 * I/O changes * include updated images * update docs to reflect changes in PR #238 * Graphics Ch-1st pass * minor updates to Graphics * minor updates to Graphics * edit ConfigNewPlatform sections 1-4 * ConfigNewPlatform edits * resolve merge conflicts * I/O ch edits * I/O edits * more I/O edits * hpc-stack submodule updates * add HPC-Stack MacOs info * WE2E edits & tables * fix typo * minor grammar/typos * merge conflict resolution * merge conflict resolution * fix grid name * remove resolved comments * add compact grids * file path updates & info for HPC-Stack * add SRW prereqs to Intro * change ConfigNewPlatform to a non-container quickstart * clean up non-container quickstart * update build options for non-container QS * update file paths & WE2E * minor fixes * update I/O & Gaea file paths * update error in non-container QS * add warning for users w/o Rocoto * add UPP Satellite Product instructions * Xlink for UPP satellite output info * clarify compiler prereqs Co-authored-by: gspetro <gillian.s.petro@gmail.com> Co-authored-by: Yunheng Wang <47898913+ywangwof@users.noreply.github.com> Co-authored-by: Will Mayfield <59745143+willmayfield@users.noreply.github.com> Co-authored-by: Gillian Petro <96886803+gspetro-NOAA@users.noreply.github.com> Co-authored-by: gspetro <gillian.s.petro@gmail.com> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> 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: Mark Potts <33099090+mark-a-potts@users.noreply.github.com> Co-authored-by: danielabdi-noaa <52012304+danielabdi-noaa@users.noreply.github.com> 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: Jesse McFarland <jesse@mcfarland.sh>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
4 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Cheyenne's version of LMOD does not support the "load-any" option, so the recent changes to srw_common have broken the build. A request has been made to CISL to update LMOD, but until that is completed, these changes will load the missing modules for both intel and gnu builds.