Reenable Orion Cycling Support #2877

DavidHuber-NOAA · 2024-08-29T15:28:02Z

Description

This updates the model hash to include the UPP update needed to be able to run the post processor on Orion, thus reenabling support on that system.

A note on the UPP: it is using a newer version of g2tmpl that requires a separate spack-stack 1.6.0 installation. This version of g2tmpl will be standard in spack-stack 1.8.0, but for now requires loading separate modules for the UPP.

A note on running analyses on Orion: due to a yet-unknown issue causing the BUFR library to run much slower on Orion when compared with Rocky 8, the GSI and GDASApp are expected to run significantly slower than on any other platform (on the order of an hour longer).

Lastly, I made adjustments to the build_all.sh script to send more cores to compiling the UFS and GDASApp. Under this configuration, the GSI, UPP, UFS_Utils, and WW3 pre/post executables finish compiling before the UFS when run with 20 cores.

Resolves #2694
Resolves #2851

Type of change

Maintenance (code refactor, clean-up, new CI test, etc.)

Change characteristics

Is this a breaking change (a change in existing functionality)? NO
Does this change require a documentation update? NO
Does this change require an update to any of the following submodules? YES (If YES, please add a link to any PRs that are pending.)
- EMC verif-global
- GDAS
- GFS-utils
- GSI
- GSI-monitor
- GSI-utils
- UFS-utils
- UFS-weather-model
- wxflow

How has this been tested?

Build on Orion
C48_ATM on Orion
C48_S2SW on Orion
C96C48_hybatmDA on Orion

Checklist

Any dependent changes have been merged and published
My code follows the style guidelines of this project
I have performed a self-review of my own code
I have commented my code, particularly in hard-to-understand areas
My changes generate no new warnings
New and existing tests pass with my changes

sorc/link_workflow.sh

jobs/rocoto/upp.sh

DavidHuber-NOAA · 2024-08-29T18:50:18Z

@WenMeng-NOAA

The spack-stack environment used by the UPP (upp-addon) does not include xarray and uses older versions of numpy (v1.22.3) and jinja2 (3.0.3) than the gsi-addon environment. To make this work, I had to add a kludge to ush/python/pygfs/__init.py__ so that the marine Tasks' importing of xarray does not cause the UPP to fail. This can be removed once we get to spack-stack v1.8.0.

With these changes, the gdasatmanlupp and gfsatmanlupp jobs ran to completion. Wen, would you be able to look at the output files and verify they are OK? You can find a pair of examples here:

/work/noaa/global/dhuber/para/orion/COMROOT/c96_4denvar/gdas.20211221/00/model/atmos/master/gdas.t00z.master.grb2anl
/work/noaa/global/dhuber/para/orion/COMROOT/c96_4denvar/gfs.20211221/00/model/atmos/master/gfs.t00z.master.grb2anl

WenMeng-NOAA · 2024-08-29T19:01:08Z

@DavidHuber-NOAA Can you change the access permission of /work/noaa/global/dhuber/para/orion/COMROOT/c96_4denvar/gdas.20211221/00/model/atmos/master/?

DavidHuber-NOAA · 2024-08-29T19:03:44Z

@WenMeng-NOAA Yes, done.

…/global-workflow into feature/orion_upp_update

sorc/link_workflow.sh

WenMeng-NOAA · 2024-08-29T21:33:08Z

@WenMeng-NOAA

The spack-stack environment used by the UPP (upp-addon) does not include xarray and uses older versions of numpy (v1.22.3) and jinja2 (3.0.3) than the gsi-addon environment. To make this work, I had to add a kludge to ush/python/pygfs/__init.py__ so that the marine Tasks' importing of xarray does not cause the UPP to fail. This can be removed once we get to spack-stack v1.8.0.

With these changes, the gdasatmanlupp and gfsatmanlupp jobs ran to completion. Wen, would you be able to look at the output files and verify they are OK? You can find a pair of examples here:
/work/noaa/global/dhuber/para/orion/COMROOT/c96_4denvar/gdas.20211221/00/model/atmos/master/gdas.t00z.master.grb2anl
/work/noaa/global/dhuber/para/orion/COMROOT/c96_4denvar/gfs.20211221/00/model/atmos/master/gfs.t00z.master.grb2anl

@DavidHuber-NOAA Somehow, the 6 aerosol fields (ATOK) are missing in both gfs and gdas master files. To output them from UPP, itag should be set as:

&nampgb
  kpo = 57,
  po = 1000.0, 975.0, 950.0, 925.0, 900.0, 875.0, 850.0, 825.0, 800.0, 775.0, 750.0, 725.0, 700.0, 675.0, 650.0, 625.0, 600.0, 575.0, 550.0, 525.0, 500.0, 475.0, 450.0, 425.0, 400.0, 375.0, 350.0, 325.0, 300.0, 275.0, 250.0, 225.0, 200.0, 175.0, 150.0, 125.0, 100.0, 70.0, 50.0, 40.0, 30.0, 20.0, 15.0, 10.0, 7.0, 5.0, 3.0, 2.0, 1.0, 0.7, 0.4, 0.2, 0.1, 0.07, 0.04, 0.02, 0.01,
  rdaod = .true.

DavidHuber-NOAA · 2024-08-30T12:00:36Z

@WenMeng-NOAA Here are the contents of the nampgb namelist used to generate the master file:

&nampgb
  kpo = 57,
  po = 1000.0, 975.0, 950.0, 925.0, 900.0, 875.0, 850.0, 825.0, 800.0, 775.0, 750.0, 725.0, 700.0, 675.0, 650.0, 625.0, 600.0, 575.0, 550.0, 525.0, 500.0, 475.0, 450.0, 425.0, 400.0, 375.0, 350.0, 325.0, 300.0, 275.0, 250.0, 225.0, 200.0, 175.0, 150.0, 125.0, 100.0, 70.0, 50.0, 40.0, 30.0, 20.0, 15.0, 10.0, 7.0, 5.0, 3.0, 2.0, 1.0, 0.7, 0.4, 0.2, 0.1, 0.07, 0.04, 0.02, 0.01,
  rdaod = .true.

These appear to be the same. The experiment that I was running was ATM-only, so that may be why the aerosol fields were not present. I will try running the C96C48_hybatmaerosnowDA test case and let you know when I have an analysis master grib2 file ready.

…update

DavidHuber-NOAA · 2024-08-30T18:00:06Z

@WenMeng-NOAA I have finished running the C96C48_hybatmaerosnowDA test case. The analysis grib2 file can be found here: /work/noaa/global/dhuber/para/orion/COMROOT/hybaerosnow/gdas.20211221/00/model/atmos/master/gdas.t00z.master.grb2anl. Running wgrib2 | grep ATOK returned no entries. Is this a feature that requires a new g2 or g2tmpl module? Or is there perhaps a change in another namelist elsewhere?

emcbot · 2024-09-05T21:21:38Z

Automated global-workflow Testing Results:

Machine: Wcoss2
Start: Thu Sep  5 20:39:48 UTC 2024 on dlogin03
---------------------------------------------------
Build: Completed at 09/05/24 09:21:14 PM
Case setup: Completed for experiment C48_ATM_c8710fe9
Case setup: Skipped for experiment C48mx500_3DVarAOWCDA_c8710fe9
Case setup: Skipped for experiment C48_S2SWA_gefs_c8710fe9
Case setup: Completed for experiment C48_S2SW_c8710fe9
Case setup: Completed for experiment C96_atm3DVar_extended_c8710fe9
Case setup: Skipped for experiment C96_atm3DVar_c8710fe9
Case setup: Completed for experiment C96C48_hybatmaerosnowDA_c8710fe9
Case setup: Completed for experiment C96C48_hybatmDA_c8710fe9
Case setup: Completed for experiment C96C48_ufs_hybatmDA_c8710fe9

emcbot · 2024-09-05T22:36:32Z

Experiment C96_atm3DVar_extended_c8710fe9 FAIL on Wcoss2 at 09/05/24 10:36:32 PM

Error logs:

/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/logs/2021122100/gfsgoesupp_f000.log
/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/logs/2021122100/gfsgoesupp_f001.log
/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/logs/2021122100/gfsgoesupp_f002.log
/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/logs/2021122100/gfsgoesupp_f003.log
/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/logs/2021122100/gfsgoesupp_f004.log
/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/logs/2021122100/gfsgoesupp_f005.log
/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/logs/2021122100/gfsgoesupp_f006.log
/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/logs/2021122100/gfsgoesupp_f007.log

Follow link here to view the contents of the above file(s): (link)

WalterKolczynski-NOAA · 2024-09-05T22:44:33Z

The index file isn't being created in the GOES UPP job. I checked $DATA and it isn't there (GFSGOES.GrbF00 is there).

�[38;21m2024-09-05 22:30:49,031 - INFO     - upp         : Copy 'goes' processed data to COM/ directory�[0m
�[38;21m2024-09-05 22:30:49,034 - INFO     - file_utils  : Copied /lfs/h2/emc/stmp/terry.mcguinness/RUNDIRS/C96_atm3DVar_extended_c8710fe9/gfs.2021122100/upp.161988/GFSGOES.GrbF00 to /lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/RUNTESTS/COMROOT/C96_atm3DVar_extended_c8710fe9/gfs.20211221/00//model/atmos/master/gfs.t00z.special.grb2f000�[0m
Traceback (most recent call last):
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/ush/python/wxflow/fsutils.py", line 85, in cp
    shutil.copy2(source, target)
  File "/apps/spack/python/3.8.6/intel/19.1.3.304/pjn2nzkjvqgmjw4hmyz43v5x4jbxjzpk/lib/python3.8/shutil.py", line 432, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/apps/spack/python/3.8.6/intel/19.1.3.304/pjn2nzkjvqgmjw4hmyz43v5x4jbxjzpk/lib/python3.8/shutil.py", line 261, in copyfile
    with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/lfs/h2/emc/stmp/terry.mcguinness/RUNDIRS/C96_atm3DVar_extended_c8710fe9/gfs.2021122100/upp.161988/GFSGOES.GrbF00.idx'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/scripts/exglobal_atmos_upp.py", line 48, in <module>
    main()
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/ush/python/wxflow/logger.py", line 266, in wrapper
    retval = func(*args, **kwargs)
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/scripts/exglobal_atmos_upp.py", line 44, in main
    upp.finalize(upp_dict.upp_run, upp_yaml)
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/ush/python/wxflow/logger.py", line 266, in wrapper
    retval = func(*args, **kwargs)
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/ush/python/pygfs/task/upp.py", line 264, in finalize
    FileHandler(upp_yaml[upp_run].data_out).sync()
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/ush/python/wxflow/file_utils.py", line 43, in sync
    sync_factory[action](files)
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/ush/python/wxflow/file_utils.py", line 63, in _copy_files
    cp(src, dest)
  File "/lfs/h2/emc/global/noscrub/globalworkflow.ci/GFS_CI_ROOT/PR/2877/global-workflow/ush/python/wxflow/fsutils.py", line 87, in cp
    raise OSError(f"unable to copy {source} to {target}")
OSError: unable to copy /lfs/h2/emc/stmp/terry.mcguinness/RUNDIRS/C96_atm3DVar_extended_c8710fe9/gfs.2021122100/upp.161988/GFSGOES.GrbF00.idx to

emcbot · 2024-09-06T00:10:30Z

CI Passed on Orion in Build# 5
Built and ran in directory /work2/noaa/stmp/CI/ORION/2877


Experiment C48_ATM_c8710fe9 Completed 1 Cycles: *SUCCESS* at Thu Sep  5 05:32:18 PM CDT 2024
Experiment C96C48_hybatmDA_c8710fe9 Completed 3 Cycles: *SUCCESS* at Thu Sep  5 06:52:35 PM CDT 2024
Experiment C96_atm3DVar_c8710fe9 Completed 3 Cycles: *SUCCESS* at Thu Sep  5 06:52:43 PM CDT 2024
Experiment C48_S2SWA_gefs_c8710fe9 Completed 1 Cycles: *SUCCESS* at Thu Sep  5 06:59:03 PM CDT 2024
Experiment C48_S2SW_c8710fe9 Completed 1 Cycles: *SUCCESS* at Thu Sep  5 07:10:15 PM CDT 2024

aerorahul · 2024-09-06T00:22:20Z

Let's disable the GOES product generation and merge this PR.
Something has changed unintentionally in there that needs to be further investigated.
HR4 needs to commence immediately.

aerorahul · 2024-09-06T00:27:07Z

NOAA-EMC/UPP@97ea655
here GFSGOES was renamed in the post_gfs_goes control file.

https://github.com/NOAA-EMC/global-workflow/blob/develop/ush/python/pygfs/task/upp.py#L203-L207
The index file is created from GFSPRS and GFSFLX files. The above change in from GFSPRS to GFSGOES broke this part of the workflow.

aerorahul · 2024-09-06T00:29:54Z

@DavidHuber-NOAA

global-workflow/ush/python/pygfs/task/upp.py

Line 205 in 2e4f4b7

for ftype in ['PRS', 'FLX']:

Can you add GOES to the list here?
['PRS', 'FLX', 'GOES']
This should be done properly, but this will do in a pinch.

emcbot · 2024-09-06T12:29:08Z

CI Update on Wcoss2 at 09/06/24 12:29:07 PM
============================================
Cloning and Building global-workflow PR: 2877
with PID: 216532 on host: dlogin03

emcbot · 2024-09-06T13:13:49Z

Automated global-workflow Testing Results:

Machine: Wcoss2
Start: Fri Sep  6 12:32:39 UTC 2024 on dlogin03
---------------------------------------------------
Build: Completed at 09/06/24 01:13:16 PM
Case setup: Completed for experiment C48_ATM_8f7bbc44
Case setup: Skipped for experiment C48mx500_3DVarAOWCDA_8f7bbc44
Case setup: Skipped for experiment C48_S2SWA_gefs_8f7bbc44
Case setup: Completed for experiment C48_S2SW_8f7bbc44
Case setup: Completed for experiment C96_atm3DVar_extended_8f7bbc44
Case setup: Skipped for experiment C96_atm3DVar_8f7bbc44
Case setup: Completed for experiment C96C48_hybatmaerosnowDA_8f7bbc44
Case setup: Completed for experiment C96C48_hybatmDA_8f7bbc44
Case setup: Completed for experiment C96C48_ufs_hybatmDA_8f7bbc44

emcbot · 2024-09-07T03:15:24Z

All CI Test Cases Passed on Wcoss2:

Experiment C48_ATM_8f7bbc44 *** SUCCESS *** at 09/06/24 02:36:12 PM
Experiment C48_S2SW_8f7bbc44 *** SUCCESS *** at 09/06/24 02:51:12 PM
Experiment C96C48_hybatmDA_8f7bbc44 *** SUCCESS *** at 09/06/24 03:48:26 PM
Experiment C96C48_hybatmaerosnowDA_8f7bbc44 *** SUCCESS *** at 09/06/24 04:48:41 PM
Experiment C96C48_ufs_hybatmDA_8f7bbc44 *** SUCCESS *** at 09/06/24 05:42:35 PM
Experiment C96_atm3DVar_extended_8f7bbc44 *** SUCCESS *** at 09/07/24 03:12:49 AM

* origin/develop: Create JEDI class (NOAA-EMC#2805) Restructure the bufr sounding job (NOAA-EMC#2853) Add an archive task to GEFS system to archive files locally (NOAA-EMC#2816) Reenable Orion Cycling Support (NOAA-EMC#2877) Eliminate race conditions and remove DATAROOT last in cleanup (NOAA-EMC#2893) Update aerosol climatology to 2013-2024 mean (NOAA-EMC#2888) Add ability to run CI test C96_atm3DVar.yaml to Gaea-C5 (NOAA-EMC#2885) Support global-workflow GEFS C48 on Google Cloud (NOAA-EMC#2861) Add 3 and 9 hr increment files to IC staging (NOAA-EMC#2876) Add diffusion/diag B for aerosol DA and some other needed changes (NOAA-EMC#2738) Correct ocean `MOM.res_#` stage copy (NOAA-EMC#2868) Support coupling on AWS (NOAA-EMC#2859) Add JEDI ATM lgetkf observer and solver jobs (NOAA-EMC#2833) Fix gdas build on Gaea and add Gaea to available CI list (NOAA-EMC#2857) Support ATM forecast only on Google (NOAA-EMC#2832) Add GEFS C48 support on AWS (NOAA-EMC#2818) Update omega calculation (NOAA-EMC#2751) Add snow DA update and recentering for the EnKF forecasts (NOAA-EMC#2690) support ATM forecast only on Azure (NOAA-EMC#2827) Convert staging job to python and yaml (NOAA-EMC#2651) Fixed test on UNAVAILBLE in python Rocoto check (NOAA-EMC#2842)

Update model hash, reenable Orion cycling support

22ae367

DavidHuber-NOAA requested review from aerorahul, WalterKolczynski-NOAA and WenMeng-NOAA August 29, 2024 15:28

Adjust walltime for eobs, rename walltime variables

9b270f9

WalterKolczynski-NOAA requested changes Aug 29, 2024

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WalterKolczynski-NOAA requested review from CatherineThomas-NOAA and RuiyuSun August 29, 2024 17:18

DavidHuber-NOAA added 2 commits August 29, 2024 13:28

Link gfs and gefs upp parm directories instead of files

878dc4a

Load more modules for the UPP

210acb9

WalterKolczynski-NOAA reviewed Aug 29, 2024

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jobs/rocoto/upp.sh Outdated Show resolved Hide resolved

Merge branch 'develop' into feature/orion_upp_update

58674bb

DavidHuber-NOAA added 4 commits August 29, 2024 14:10

Update path to post_tag_gfs*

42e8d3a

Merge branch 'feature/orion_upp_update' of github.com:davidhuber-noaa…

e8d0837

…/global-workflow into feature/orion_upp_update

Update UPP parm paths

4c21543

Revert UPP modules

6a802ca

WalterKolczynski-NOAA previously approved these changes Aug 29, 2024

View reviewed changes

Remove extra whitespace

7243745

DavidHuber-NOAA dismissed WalterKolczynski-NOAA’s stale review via 7243745 August 29, 2024 20:03

WalterKolczynski-NOAA previously approved these changes Aug 29, 2024

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WenMeng-NOAA reviewed Aug 29, 2024

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sorc/link_workflow.sh Show resolved Hide resolved

Link post_tag files to parm/post

04c4835

DavidHuber-NOAA dismissed WalterKolczynski-NOAA’s stale review via 04c4835 August 30, 2024 13:07

Merge remote-tracking branch 'origin/develop' into feature/orion_upp_…

200cf26

…update

emcbot added CI-Wcoss2-Failed **Bot use only** CI testing on WCOSS for this PR has failed and removed CI-Wcoss2-Running **Bot use only** CI testing on WCOSS for this PR is in-progress labels Sep 5, 2024

emcbot added CI-Orion-Passed **Bot use only** CI testing on Orion for this PR has completed successfully and removed CI-Orion-Running **Bot use only** CI testing on Orion for this PR is in-progress labels Sep 6, 2024

Add GOES to the list of indexable file types.

8f7bbc4

emcbot added CI-Wcoss2-Building **Bot use only** CI testing is cloning/building on WCOSS and removed CI-Wcoss2-Ready **CM use only** PR is ready for CI testing on WCOSS labels Sep 6, 2024

emcbot added CI-Wcoss2-Running **Bot use only** CI testing on WCOSS for this PR is in-progress and removed CI-Wcoss2-Building **Bot use only** CI testing is cloning/building on WCOSS labels Sep 6, 2024

aerorahul mentioned this pull request Sep 6, 2024

Create JEDI class #2805

Merged

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emcbot added CI-Wcoss2-Passed **Bot use only** CI testing on WCOSS for this PR has completed successfully and removed CI-Wcoss2-Running **Bot use only** CI testing on WCOSS for this PR is in-progress labels Sep 7, 2024

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WalterKolczynski-NOAA merged commit ac93a9b into NOAA-EMC:develop Sep 7, 2024
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Reenable Orion Cycling Support #2877

Reenable Orion Cycling Support #2877

DavidHuber-NOAA commented Aug 29, 2024 •

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Reenable Orion Cycling Support #2877

Reenable Orion Cycling Support #2877

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DavidHuber-NOAA commented Aug 29, 2024 • edited Loading

Description

Type of change

Change characteristics

How has this been tested?

Checklist

DavidHuber-NOAA commented Aug 29, 2024

WenMeng-NOAA commented Aug 29, 2024

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