Add Hercules build capability to GDASApp #774

RussTreadon-NOAA · 2023-11-28T16:47:33Z

MSU Hercules is available for use. This PR adds hercules.lua to GDASApp modulefiles/GDAS.

Fixes #773

CoryMartin-NOAA

DavidHuber-NOAA · 2024-01-09T13:03:39Z

Just a heads up that GSI-based cycling support in the global workflow has been ported to Hercules, with the exception of the GSI-monitor.

RussTreadon-NOAA · 2024-01-09T19:07:48Z

Install RussTreadon-NOAA:feature/hercules at 23453d7 on Hercules. Run GDASApp ctests. All 32 tests pass.

(gdasapp) hercules-login-4:/work2/noaa/da/rtreadon/git/GDASApp/hercules/build$ ctest -R test_gdasapp
Test project /work2/noaa/da/rtreadon/git/GDASApp/hercules/build
      Start 1324: test_gdasapp_util_coding_norms
 1/32 Test #1324: test_gdasapp_util_coding_norms .............   Passed    0.98 sec
      Start 1325: test_gdasapp_util_ioda_example
 2/32 Test #1325: test_gdasapp_util_ioda_example .............   Passed    4.55 sec
      Start 1326: test_gdasapp_util_prepdata
 3/32 Test #1326: test_gdasapp_util_prepdata .................   Passed    3.27 sec
      Start 1327: test_gdasapp_util_rads2ioda
 4/32 Test #1327: test_gdasapp_util_rads2ioda ................   Passed    0.28 sec
      Start 1328: test_gdasapp_util_ghrsst2ioda
 5/32 Test #1328: test_gdasapp_util_ghrsst2ioda ..............   Passed    0.07 sec
      Start 1329: test_gdasapp_util_smap2ioda
 6/32 Test #1329: test_gdasapp_util_smap2ioda ................   Passed    0.07 sec
      Start 1330: test_gdasapp_util_smos2ioda
 7/32 Test #1330: test_gdasapp_util_smos2ioda ................   Passed    0.18 sec
      Start 1331: test_gdasapp_util_viirsaod2ioda
 8/32 Test #1331: test_gdasapp_util_viirsaod2ioda ............   Passed    0.07 sec
      Start 1332: test_gdasapp_util_icecamsr2ioda
 9/32 Test #1332: test_gdasapp_util_icecamsr2ioda ............   Passed    0.08 sec
      Start 1664: test_gdasapp_check_python_norms
10/32 Test #1664: test_gdasapp_check_python_norms ............   Passed    1.33 sec
      Start 1665: test_gdasapp_check_yaml_keys
11/32 Test #1665: test_gdasapp_check_yaml_keys ...............   Passed    0.52 sec
      Start 1666: test_gdasapp_jedi_increment_to_fv3
12/32 Test #1666: test_gdasapp_jedi_increment_to_fv3 .........   Passed    8.36 sec
      Start 1667: test_gdasapp_convert_ewok_yaml
13/32 Test #1667: test_gdasapp_convert_ewok_yaml .............   Passed    1.64 sec
      Start 1668: test_gdasapp_convert_bufr_temp_dbuoy
14/32 Test #1668: test_gdasapp_convert_bufr_temp_dbuoy .......   Passed    0.99 sec
      Start 1669: test_gdasapp_convert_bufr_salt_dbuoy
15/32 Test #1669: test_gdasapp_convert_bufr_salt_dbuoy .......   Passed    0.92 sec
      Start 1670: test_gdasapp_convert_bufr_temp_mbuoyb
16/32 Test #1670: test_gdasapp_convert_bufr_temp_mbuoyb ......   Passed    8.08 sec
      Start 1671: test_gdasapp_convert_bufr_salt_mbuoyb
17/32 Test #1671: test_gdasapp_convert_bufr_salt_mbuoyb ......   Passed   12.62 sec
      Start 1672: test_gdasapp_convert_bufr_tesacprof
18/32 Test #1672: test_gdasapp_convert_bufr_tesacprof ........   Passed    1.82 sec
      Start 1673: test_gdasapp_convert_bufr_trkobprof
19/32 Test #1673: test_gdasapp_convert_bufr_trkobprof ........   Passed    0.76 sec
      Start 1674: test_gdasapp_convert_bufr_sfcships
20/32 Test #1674: test_gdasapp_convert_bufr_sfcships .........   Passed    0.22 sec
      Start 1675: test_gdasapp_convert_bufr_sfcshipsu
21/32 Test #1675: test_gdasapp_convert_bufr_sfcshipsu ........   Passed    0.15 sec
      Start 1676: test_gdasapp_soca_obsdb
22/32 Test #1676: test_gdasapp_soca_obsdb ....................   Passed   12.99 sec
      Start 1677: test_gdasapp_soca_nsst_increment_to_mom6
23/32 Test #1677: test_gdasapp_soca_nsst_increment_to_mom6 ...   Passed   42.32 sec
      Start 1678: test_gdasapp_land_create_ens
24/32 Test #1678: test_gdasapp_land_create_ens ...............   Passed    1.82 sec
      Start 1679: test_gdasapp_land_imsproc
25/32 Test #1679: test_gdasapp_land_imsproc ..................   Passed    8.21 sec
      Start 1680: test_gdasapp_land_apply_jediincr
26/32 Test #1680: test_gdasapp_land_apply_jediincr ...........   Passed   22.63 sec
      Start 1681: test_gdasapp_land_letkfoi_snowda
27/32 Test #1681: test_gdasapp_land_letkfoi_snowda ...........   Passed   74.13 sec
      Start 1682: test_gdasapp_convert_bufr_adpsfc_snow
28/32 Test #1682: test_gdasapp_convert_bufr_adpsfc_snow ......   Passed    2.96 sec
      Start 1683: test_gdasapp_convert_bufr_adpsfc
29/32 Test #1683: test_gdasapp_convert_bufr_adpsfc ...........   Passed    5.56 sec
      Start 1684: test_gdasapp_convert_gsi_satbias
30/32 Test #1684: test_gdasapp_convert_gsi_satbias ...........   Passed   17.84 sec
      Start 1685: test_gdasapp_store_gsi_satbias
31/32 Test #1685: test_gdasapp_store_gsi_satbias .............   Passed    0.49 sec
      Start 1686: test_gdasapp_aero_gen_3dvar_yaml
32/32 Test #1686: test_gdasapp_aero_gen_3dvar_yaml ...........   Passed    0.25 sec

100% tests passed, 0 tests failed out of 32

Label Time Summary:
gdas-utils    =   9.54 sec*proc (9 tests)
script        =   9.54 sec*proc (9 tests)

Total Test time (real) = 236.47 sec

Install RussTreadon-NOAA:feature/hercules at 23453d7 inside working copy of g-w develop @ b056b53. Run GDASApp ctests. Several soca and atm_jjob tests fail.

The atm_jjob tests failed because driver scripts in test/atm/global-workflow did not include Hercules as a valid $machine. Add Hercules as a valid $machine. Also found it necessary to specify the target file on soft links in the atm_jjob driver scripts. With these changes the atm_jjob tests pass. The following soca tests fail

(gdasapp) hercules-login-4:/work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/build$ ctest -R test_gdasapp
Test project /work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/build
      Start 1324: test_gdasapp_util_coding_norms
 1/55 Test #1324: test_gdasapp_util_coding_norms ........................   Passed    0.79 sec
      Start 1325: test_gdasapp_util_ioda_example
 2/55 Test #1325: test_gdasapp_util_ioda_example ........................   Passed    6.93 sec
      Start 1326: test_gdasapp_util_prepdata
 3/55 Test #1326: test_gdasapp_util_prepdata ............................   Passed    0.50 sec
      Start 1327: test_gdasapp_util_rads2ioda
 4/55 Test #1327: test_gdasapp_util_rads2ioda ...........................   Passed    0.47 sec
      Start 1328: test_gdasapp_util_ghrsst2ioda
 5/55 Test #1328: test_gdasapp_util_ghrsst2ioda .........................   Passed    0.09 sec
      Start 1329: test_gdasapp_util_smap2ioda
 6/55 Test #1329: test_gdasapp_util_smap2ioda ...........................   Passed    0.09 sec
      Start 1330: test_gdasapp_util_smos2ioda
 7/55 Test #1330: test_gdasapp_util_smos2ioda ...........................   Passed    0.09 sec
      Start 1331: test_gdasapp_util_viirsaod2ioda
 8/55 Test #1331: test_gdasapp_util_viirsaod2ioda .......................   Passed    0.09 sec
      Start 1332: test_gdasapp_util_icecamsr2ioda
 9/55 Test #1332: test_gdasapp_util_icecamsr2ioda .......................   Passed    0.08 sec
      Start 1664: test_gdasapp_check_python_norms
10/55 Test #1664: test_gdasapp_check_python_norms .......................   Passed    1.15 sec
      Start 1665: test_gdasapp_check_yaml_keys
11/55 Test #1665: test_gdasapp_check_yaml_keys ..........................   Passed    0.06 sec
      Start 1666: test_gdasapp_jedi_increment_to_fv3
12/55 Test #1666: test_gdasapp_jedi_increment_to_fv3 ....................   Passed    0.31 sec
      Start 1667: test_gdasapp_convert_ewok_yaml
13/55 Test #1667: test_gdasapp_convert_ewok_yaml ........................   Passed    0.17 sec
      Start 1668: test_gdasapp_setup_cycled_exp
14/55 Test #1668: test_gdasapp_setup_cycled_exp .........................   Passed    0.36 sec
      Start 1669: test_gdasapp_convert_bufr_temp_dbuoy
15/55 Test #1669: test_gdasapp_convert_bufr_temp_dbuoy ..................   Passed    0.60 sec
      Start 1670: test_gdasapp_convert_bufr_salt_dbuoy
16/55 Test #1670: test_gdasapp_convert_bufr_salt_dbuoy ..................   Passed    0.19 sec
      Start 1671: test_gdasapp_convert_bufr_temp_mbuoyb
17/55 Test #1671: test_gdasapp_convert_bufr_temp_mbuoyb .................   Passed    0.20 sec
      Start 1672: test_gdasapp_convert_bufr_salt_mbuoyb
18/55 Test #1672: test_gdasapp_convert_bufr_salt_mbuoyb .................   Passed    0.20 sec
      Start 1673: test_gdasapp_convert_bufr_tesacprof
19/55 Test #1673: test_gdasapp_convert_bufr_tesacprof ...................   Passed    0.20 sec
      Start 1674: test_gdasapp_convert_bufr_trkobprof
20/55 Test #1674: test_gdasapp_convert_bufr_trkobprof ...................   Passed    0.19 sec
      Start 1675: test_gdasapp_convert_bufr_sfcships
21/55 Test #1675: test_gdasapp_convert_bufr_sfcships ....................   Passed    0.20 sec
      Start 1676: test_gdasapp_convert_bufr_sfcshipsu
22/55 Test #1676: test_gdasapp_convert_bufr_sfcshipsu ...................   Passed    0.19 sec
      Start 1677: test_gdasapp_soca_obsdb
23/55 Test #1677: test_gdasapp_soca_obsdb ...............................   Passed    0.88 sec
      Start 1678: test_gdasapp_soca_nsst_increment_to_mom6
24/55 Test #1678: test_gdasapp_soca_nsst_increment_to_mom6 ..............   Passed    5.31 sec
      Start 1679: test_gdasapp_soca_prep
25/55 Test #1679: test_gdasapp_soca_prep ................................   Passed    4.09 sec
      Start 1680: test_gdasapp_soca_concatioda
26/55 Test #1680: test_gdasapp_soca_concatioda ..........................   Passed    1.01 sec
      Start 1681: test_gdasapp_soca_run_clean
27/55 Test #1681: test_gdasapp_soca_run_clean ...........................   Passed    0.10 sec
      Start 1682: test_gdasapp_soca_setup_obsproc
28/55 Test #1682: test_gdasapp_soca_setup_obsproc .......................   Passed    0.33 sec
      Start 1683: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
29/55 Test #1683: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP ....***Failed    0.58 sec
      Start 1684: test_gdasapp_soca_JGLOBAL_PREP_OCEAN_OBS
30/55 Test #1684: test_gdasapp_soca_JGLOBAL_PREP_OCEAN_OBS ..............***Failed    0.12 sec
      Start 1685: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT
31/55 Test #1685: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT ....***Failed    0.12 sec
      Start 1686: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
32/55 Test #1686: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN .....***Failed    0.12 sec
      Start 1687: test_gdasapp_soca_copy_scratch
33/55 Test #1687: test_gdasapp_soca_copy_scratch ........................***Failed    0.05 sec
      Start 1688: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
34/55 Test #1688: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT ...***Failed    0.12 sec
      Start 1689: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
35/55 Test #1689: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_POST ....***Failed    0.12 sec
      Start 1690: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY
36/55 Test #1690: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY ....***Failed    0.12 sec
      Start 1691: test_gdasapp_soca_socahybridweights
37/55 Test #1691: test_gdasapp_soca_socahybridweights ...................***Failed    0.10 sec
      Start 1692: test_gdasapp_soca_incr_handler
38/55 Test #1692: test_gdasapp_soca_incr_handler ........................***Failed    0.10 sec
      Start 1693: test_gdasapp_soca_ens_handler
39/55 Test #1693: test_gdasapp_soca_ens_handler .........................***Failed    0.10 sec
      Start 1694: test_gdasapp_land_create_ens
40/55 Test #1694: test_gdasapp_land_create_ens ..........................   Passed    0.64 sec
      Start 1695: test_gdasapp_land_imsproc
41/55 Test #1695: test_gdasapp_land_imsproc .............................   Passed    2.05 sec
      Start 1696: test_gdasapp_land_apply_jediincr
42/55 Test #1696: test_gdasapp_land_apply_jediincr ......................   Passed    3.60 sec
      Start 1697: test_gdasapp_land_letkfoi_snowda
43/55 Test #1697: test_gdasapp_land_letkfoi_snowda ......................   Passed   27.79 sec
      Start 1698: test_gdasapp_convert_bufr_adpsfc_snow
44/55 Test #1698: test_gdasapp_convert_bufr_adpsfc_snow .................   Passed    2.28 sec
      Start 1699: test_gdasapp_convert_bufr_adpsfc
45/55 Test #1699: test_gdasapp_convert_bufr_adpsfc ......................   Passed    3.07 sec
      Start 1700: test_gdasapp_convert_gsi_satbias
46/55 Test #1700: test_gdasapp_convert_gsi_satbias ......................   Passed    3.38 sec
      Start 1701: test_gdasapp_store_gsi_satbias
47/55 Test #1701: test_gdasapp_store_gsi_satbias ........................   Passed    0.40 sec
      Start 1702: test_gdasapp_setup_atm_cycled_exp
48/55 Test #1702: test_gdasapp_setup_atm_cycled_exp .....................   Passed    0.55 sec
      Start 1703: test_gdasapp_atm_jjob_var_init
49/55 Test #1703: test_gdasapp_atm_jjob_var_init ........................   Passed   12.62 sec
      Start 1704: test_gdasapp_atm_jjob_var_run
50/55 Test #1704: test_gdasapp_atm_jjob_var_run .........................   Passed   79.17 sec
      Start 1705: test_gdasapp_atm_jjob_var_final
51/55 Test #1705: test_gdasapp_atm_jjob_var_final .......................   Passed   10.04 sec
      Start 1706: test_gdasapp_atm_jjob_ens_init
52/55 Test #1706: test_gdasapp_atm_jjob_ens_init ........................   Passed   11.51 sec
      Start 1707: test_gdasapp_atm_jjob_ens_run
53/55 Test #1707: test_gdasapp_atm_jjob_ens_run .........................   Passed  253.19 sec
      Start 1708: test_gdasapp_atm_jjob_ens_final
54/55 Test #1708: test_gdasapp_atm_jjob_ens_final .......................   Passed   14.23 sec
      Start 1709: test_gdasapp_aero_gen_3dvar_yaml
55/55 Test #1709: test_gdasapp_aero_gen_3dvar_yaml ......................   Passed    0.21 sec

80% tests passed, 11 tests failed out of 55

Label Time Summary:
gdas-utils    =   9.13 sec*proc (9 tests)
script        =   9.13 sec*proc (9 tests)

Total Test time (real) = 451.50 sec

The following tests FAILED:
        1683 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP (Failed)
        1684 - test_gdasapp_soca_JGLOBAL_PREP_OCEAN_OBS (Failed)
        1685 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT (Failed)
        1686 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN (Failed)
        1687 - test_gdasapp_soca_copy_scratch (Failed)
        1688 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT (Failed)
        1689 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_POST (Failed)
        1690 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY (Failed)
        1691 - test_gdasapp_soca_socahybridweights (Failed)
        1692 - test_gdasapp_soca_incr_handler (Failed)
        1693 - test_gdasapp_soca_ens_handler (Failed)
Errors while running CTest

The test_gdasapp_soca failures appear to be similar to the $machine problem with test_gdasapp_jjob_atm. test/soca/gw/CMakeLists.txt sets MACHINE based on a directory

# Identify machine
set(MACHINE "container")
IF (IS_DIRECTORY /work2/noaa/da)
  set(MACHINE "orion")
  set(PARTITION "orion")
ENDIF()
IF (IS_DIRECTORY /scratch2/NCEPDEV/)
  set(MACHINE "hera")
  set(PARTITION "hera")
ENDIF()

Hercules and Orion share the same filesets. /work2/noaa/da is a valid directory on Hercules and Orion. We need a different way to distinguish between Hercules and Orion.

ush/soca/run_jjobs.py does not include hercules in the list of valid machines

machines = {"container", "hera", "orion"}

While it is necessary to add hercules to the machine list, this alone is not sufficient. The yaml file processed by run_jjobs.py contains machine: orion. This traces back to test/soca/CMakeLists.txt.

Tagging @guillaumevernieres for awareness.

DavidHuber-NOAA · 2024-01-09T19:13:48Z

@RussTreadon-NOAA The directory I suggest using to differentiate the two is /apps/other, which only exists on Hercules. You can start by checking for /work2/noaa/da to ensure you are testing just Hercules and Orion and limit the possibility of misidentifying another machine added in the future. This is how I did it in the global-workflow.

RussTreadon-NOAA · 2024-01-09T21:27:33Z

Thank you @DavidHuber-NOAA for sharing your experience. test/soca/gw/CMakeLists.txt was updated following your example. GDASApp was rebuilt and ctests rerun. The number of soca failures was reduced to

        1685 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT (Failed)
        1686 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN (Failed)
        1688 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT (Failed)
        1689 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_POST (Failed)
        1690 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY (Failed)
        1692 - test_gdasapp_soca_incr_handler (Failed)

I see that g-w jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT sources the wrong config files.

-source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalrun" -c "base ocnanal ocnanalrun"
+source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalbmat" -c "base ocnanal ocnanalbmat"

After the above correction test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT passed.

Unfortunately, test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN failed with

+ exgdas_global_marine_analysis_run.sh[44]: srun -l --export=ALL -n 16 --cpus-per-task=2 /work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/../../sorc/gdas.cd/build/bin/soca_var.x var.yaml
srun: error: Unable to create step for job 373792: More processors requested than permitted
+ exgdas_global_marine_analysis_run.sh[45]: export err=1

I see that g-w parm/config/gfs/config.resources specifies 2 threads. I changed this to one

     export npe_ocnanalrun=${npes}
-    export nth_ocnanalrun=2
+    export nth_ocnanalrun=1
     export is_exclusive=True

With this change test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN successfully ran to completion but I do not understand why 2 threads didn't work. 16 tasks with 2 threads per task fits on a Hercules node.

The remaining failed test_gdasapp_soca jobs successfully completed after getting test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN to pass.

The only exception is test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY. This job still failed. A check of the log file shows this job fails with

/work2/noaa/da/python/opt/core/miniconda3/4.6.14/envs/eva/lib/python3.9/site-packages/cartopy/io/__init__.py:241: DownloadWarning: Downloading: https://naturalearth.s3.amazonaws.com/110m_physical/ne_110m_coastline.zip
  warnings.warn(f'Downloading: {url}', DownloadWarning)
slurmstepd: error: *** JOB 373844 ON hercules-01-19 CANCELLED AT 2024-01-09T15:14:36 DUE TO TIME LIMIT ***

The GDASApp changes needed to get atm and soca ctests to run were committed to RussTreadon-NOAA:feature/hercules at 8e67f9b.

The following g-w changes have also been made

        modified:   jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT
        modified:   parm/config/gfs/config.resources
        modified:   sorc/build_all.sh

The change to sorc/build.sh was to allow GDASApp to be built on hercules.

 if [[ "${_build_ufsda}" == "YES" ]]; then
-   if [[ "${MACHINE_ID}" != "orion" && "${MACHINE_ID}" != "hera" ]]; then
+   if [[ "${MACHINE_ID}" != "orion" && "${MACHINE_ID}" != "hera" && "${MACHINE_ID}" != "hercules"]]; then
       echo "NOTE: The GDAS App is not supported on ${MACHINE_ID}.  Disabling build."
    else

The above g-w changes remain local to my working copy of g-w on hercules. Look in /work2/noaa/da/rtreadon/git/global-workflow/hercules

Running RussTreadon-NOAA:feature/hercules at 8e67f9b with the above local g-w changes yields the following ctest results

(gdasapp) hercules-login-4:/work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/build$ ctest -R test_gdasapp
Test project /work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/build
      Start 1324: test_gdasapp_util_coding_norms
 1/55 Test #1324: test_gdasapp_util_coding_norms ........................   Passed    0.78 sec
      Start 1325: test_gdasapp_util_ioda_example
 2/55 Test #1325: test_gdasapp_util_ioda_example ........................   Passed    0.14 sec
      Start 1326: test_gdasapp_util_prepdata
 3/55 Test #1326: test_gdasapp_util_prepdata ............................   Passed    0.90 sec
      Start 1327: test_gdasapp_util_rads2ioda
 4/55 Test #1327: test_gdasapp_util_rads2ioda ...........................   Passed    0.10 sec
      Start 1328: test_gdasapp_util_ghrsst2ioda
 5/55 Test #1328: test_gdasapp_util_ghrsst2ioda .........................   Passed    0.48 sec
      Start 1329: test_gdasapp_util_smap2ioda
 6/55 Test #1329: test_gdasapp_util_smap2ioda ...........................   Passed    0.11 sec
      Start 1330: test_gdasapp_util_smos2ioda
 7/55 Test #1330: test_gdasapp_util_smos2ioda ...........................   Passed    0.09 sec
      Start 1331: test_gdasapp_util_viirsaod2ioda
 8/55 Test #1331: test_gdasapp_util_viirsaod2ioda .......................   Passed    0.24 sec
      Start 1332: test_gdasapp_util_icecamsr2ioda
 9/55 Test #1332: test_gdasapp_util_icecamsr2ioda .......................   Passed    0.24 sec
      Start 1664: test_gdasapp_check_python_norms
10/55 Test #1664: test_gdasapp_check_python_norms .......................   Passed    1.08 sec
      Start 1665: test_gdasapp_check_yaml_keys
11/55 Test #1665: test_gdasapp_check_yaml_keys ..........................   Passed    0.06 sec
      Start 1666: test_gdasapp_jedi_increment_to_fv3
12/55 Test #1666: test_gdasapp_jedi_increment_to_fv3 ....................   Passed    0.28 sec
      Start 1667: test_gdasapp_convert_ewok_yaml
13/55 Test #1667: test_gdasapp_convert_ewok_yaml ........................   Passed    0.17 sec
      Start 1668: test_gdasapp_setup_cycled_exp
14/55 Test #1668: test_gdasapp_setup_cycled_exp .........................   Passed    0.44 sec
      Start 1669: test_gdasapp_convert_bufr_temp_dbuoy
15/55 Test #1669: test_gdasapp_convert_bufr_temp_dbuoy ..................   Passed    3.01 sec
      Start 1670: test_gdasapp_convert_bufr_salt_dbuoy
16/55 Test #1670: test_gdasapp_convert_bufr_salt_dbuoy ..................   Passed    0.18 sec
      Start 1671: test_gdasapp_convert_bufr_temp_mbuoyb
17/55 Test #1671: test_gdasapp_convert_bufr_temp_mbuoyb .................   Passed    0.18 sec
      Start 1672: test_gdasapp_convert_bufr_salt_mbuoyb
18/55 Test #1672: test_gdasapp_convert_bufr_salt_mbuoyb .................   Passed    0.18 sec
      Start 1673: test_gdasapp_convert_bufr_tesacprof
19/55 Test #1673: test_gdasapp_convert_bufr_tesacprof ...................   Passed    0.19 sec
      Start 1674: test_gdasapp_convert_bufr_trkobprof
20/55 Test #1674: test_gdasapp_convert_bufr_trkobprof ...................   Passed    0.18 sec
      Start 1675: test_gdasapp_convert_bufr_sfcships
21/55 Test #1675: test_gdasapp_convert_bufr_sfcships ....................   Passed    0.34 sec
      Start 1676: test_gdasapp_convert_bufr_sfcshipsu
22/55 Test #1676: test_gdasapp_convert_bufr_sfcshipsu ...................   Passed    0.18 sec
      Start 1677: test_gdasapp_soca_obsdb
23/55 Test #1677: test_gdasapp_soca_obsdb ...............................   Passed    0.78 sec
      Start 1678: test_gdasapp_soca_nsst_increment_to_mom6
24/55 Test #1678: test_gdasapp_soca_nsst_increment_to_mom6 ..............   Passed    5.02 sec
      Start 1679: test_gdasapp_soca_prep
25/55 Test #1679: test_gdasapp_soca_prep ................................   Passed    6.71 sec
      Start 1680: test_gdasapp_soca_concatioda
26/55 Test #1680: test_gdasapp_soca_concatioda ..........................   Passed    1.52 sec
      Start 1681: test_gdasapp_soca_run_clean
27/55 Test #1681: test_gdasapp_soca_run_clean ...........................   Passed    0.17 sec
      Start 1682: test_gdasapp_soca_setup_obsproc
28/55 Test #1682: test_gdasapp_soca_setup_obsproc .......................   Passed    0.38 sec
      Start 1683: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
29/55 Test #1683: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP ....   Passed  173.83 sec
      Start 1684: test_gdasapp_soca_JGLOBAL_PREP_OCEAN_OBS
30/55 Test #1684: test_gdasapp_soca_JGLOBAL_PREP_OCEAN_OBS ..............   Passed   42.15 sec
      Start 1685: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT
31/55 Test #1685: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT ....   Passed   42.15 sec
      Start 1686: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN
32/55 Test #1686: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN .....   Passed   42.16 sec
      Start 1687: test_gdasapp_soca_copy_scratch
33/55 Test #1687: test_gdasapp_soca_copy_scratch ........................   Passed    6.42 sec
      Start 1688: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
34/55 Test #1688: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT ...   Passed   42.15 sec
      Start 1689: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_POST
35/55 Test #1689: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_POST ....   Passed   42.15 sec
      Start 1690: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY
36/55 Test #1690: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY ....***Failed  650.29 sec
      Start 1691: test_gdasapp_soca_socahybridweights
37/55 Test #1691: test_gdasapp_soca_socahybridweights ...................   Passed   10.13 sec
      Start 1692: test_gdasapp_soca_incr_handler
38/55 Test #1692: test_gdasapp_soca_incr_handler ........................   Passed    2.11 sec
      Start 1693: test_gdasapp_soca_ens_handler
39/55 Test #1693: test_gdasapp_soca_ens_handler .........................   Passed   10.12 sec
      Start 1694: test_gdasapp_land_create_ens
40/55 Test #1694: test_gdasapp_land_create_ens ..........................   Passed    1.78 sec
      Start 1695: test_gdasapp_land_imsproc
41/55 Test #1695: test_gdasapp_land_imsproc .............................   Passed    2.36 sec
      Start 1696: test_gdasapp_land_apply_jediincr
42/55 Test #1696: test_gdasapp_land_apply_jediincr ......................   Passed    4.90 sec
      Start 1697: test_gdasapp_land_letkfoi_snowda
43/55 Test #1697: test_gdasapp_land_letkfoi_snowda ......................   Passed   13.60 sec
      Start 1698: test_gdasapp_convert_bufr_adpsfc_snow
44/55 Test #1698: test_gdasapp_convert_bufr_adpsfc_snow .................   Passed    2.32 sec
      Start 1699: test_gdasapp_convert_bufr_adpsfc
45/55 Test #1699: test_gdasapp_convert_bufr_adpsfc ......................   Passed    3.03 sec
      Start 1700: test_gdasapp_convert_gsi_satbias
46/55 Test #1700: test_gdasapp_convert_gsi_satbias ......................   Passed    6.03 sec
      Start 1701: test_gdasapp_store_gsi_satbias
47/55 Test #1701: test_gdasapp_store_gsi_satbias ........................   Passed    0.41 sec
      Start 1702: test_gdasapp_setup_atm_cycled_exp
48/55 Test #1702: test_gdasapp_setup_atm_cycled_exp .....................   Passed    0.86 sec
      Start 1703: test_gdasapp_atm_jjob_var_init
49/55 Test #1703: test_gdasapp_atm_jjob_var_init ........................   Passed   44.35 sec
      Start 1704: test_gdasapp_atm_jjob_var_run
50/55 Test #1704: test_gdasapp_atm_jjob_var_run .........................   Passed   74.13 sec
      Start 1705: test_gdasapp_atm_jjob_var_final
51/55 Test #1705: test_gdasapp_atm_jjob_var_final .......................   Passed   42.12 sec
      Start 1706: test_gdasapp_atm_jjob_ens_init
52/55 Test #1706: test_gdasapp_atm_jjob_ens_init ........................   Passed   44.16 sec
      Start 1707: test_gdasapp_atm_jjob_ens_run
53/55 Test #1707: test_gdasapp_atm_jjob_ens_run .........................   Passed  330.15 sec
      Start 1708: test_gdasapp_atm_jjob_ens_final
54/55 Test #1708: test_gdasapp_atm_jjob_ens_final .......................   Passed   42.14 sec
      Start 1709: test_gdasapp_aero_gen_3dvar_yaml
55/55 Test #1709: test_gdasapp_aero_gen_3dvar_yaml ......................   Passed    0.22 sec

98% tests passed, 1 tests failed out of 55

Label Time Summary:
gdas-utils    =   3.08 sec*proc (9 tests)
script        =   3.08 sec*proc (9 tests)

Total Test time (real) = 1700.68 sec

The following tests FAILED:
        1690 - test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY (Failed)
Errors while running CTest

RussTreadon-NOAA · 2024-01-10T11:24:07Z

@guillaumevernieres, @AndrewEichmann-NOAA, @CoryMartin-NOAA , and @DavidHuber-NOAA : this PR is ready for merger into develop apart from three items:

test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY fails because the cartopy download of ne_110m_coastline.zip fails (hangs). Should we download and install this file somewhere on Hercules?
execution of soca_var.x in test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN fails when executing srun -l --export=ALL -n 16 --cpus-per-task=2 with error message More processors requested than permitted
config.resources specifies two threads for ocnanalrun. Changing this to one thread allows test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN to successfully run. Good, but why did srun complain about 2 threads? 16 tasks with 2 threads per task fits on a Hercules node.
To fully enable the GDASApp build from g-w, we need to update two, possibly three, g-w files

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_BMAT - source correct config files
parm/config/gfs/config.resources - change ocnanalrun to 1 thread
sorc/build_all.sh - add hercules as valid platform for GDASApp build

An additional change would be to update the hash for the gdas.cd submodule. A g-w issue and PR are needed to get these changes into g-w develop.

RussTreadon-NOAA · 2024-01-10T14:07:57Z

test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN

The srun error is due to a mismatch between how the job is configured via #SBATCH lines in the submitted run script and the srun options used to execute soca_var.x.

Script ush/soca/run_jjobs.py creates and submits local file run_jjob.sh to run JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN. The #SBATCH preamble in run_jjobs.sh is

#!/usr/bin/env bash
# Running on hercules
#SBATCH --account=da-cpu
#SBATCH --qos=batch
#SBATCH --output=JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN.out
#SBATCH --nodes=1
#SBATCH --ntasks=16
#SBATCH --partition=hercules
#SBATCH --time=00:10:00

whereas the srun command executed by exgdas_global_marine_analysis_run.sh is srun -l --export=ALL -n 16 --cpus-per-task=2. The line #SBATCH --cpus-per-task=2 is missing from run_jjobs.sh.

Manually add the line #SBATCH --cpus-per-task=2 to run_jjobs.sh and resubmit. The script successfully ran soca_var.x via srun -l --export=ALL -n 16 --cpus-per-task=2.

It is not yet clear to me how to modify run_jjobs.py such that it inserts the correct #SBATCH --cpus-per-task line for each job for which it creates and submits run_jjobs.sh. Most jobs which run_jjobs.py launches run with one thread. config.resources specifies two threads for JGDAS_GLOBAL_OCEAN_ANALYSIS_RUN

CoryMartin-NOAA · 2024-01-10T14:35:57Z

the download warning must mean that the home directories are not shared between orion and hercules. If you copy the shapefiles from ~/.local/cartopy on orion to the same path on hercules (or run cartopy once in a login shell), then it should pass

RussTreadon-NOAA · 2024-01-10T14:57:53Z

Thank you @CoryMartin-NOAA . I rsync'd shapefiles from my Orion cartopy directory to Hercules. Does every user their own snapshot of the shapefiles? Can we have the shape files installed in single publicly shared location?

I reran test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY. The job got past the previous cartopy download failure. @guillaumevernieres and @AndrewEichmann-NOAA , the VRFY job now fails with the message

2024-01-10 14:52:08:ERROR:Error occurred when attempting to load: /work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gd\
as.cd/../../sorc/gdas.cd/build/test/soca/gw/testrun/testjjobs/ROTDIRS/gdas_test/gdas.20180415/12//analysis/ocean/yaml/var_orig\
inal.yaml, error: while scanning for the next token
found character '%' that cannot start any token
  in "/work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/../../sorc/gdas.cd/build/test/soca/gw/testrun/testjjob\
s/ROTDIRS/gdas_test/gdas.20180415/12//analysis/ocean/yaml/var_original.yaml", line 135, column 20
Traceback (most recent call last):
  File "/work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/../../sorc/gdas.cd/scripts/exgdas_global_marine_anal\
ysis_vrfy.py", line 219, in <module>
    gen_eva_obs_yaml.gen_eva_obs_yaml(varyaml, marinetemplate, 'preevayamls')
  File "/work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/ush/eva/gen_eva_obs_yaml.py", line 20, in gen_eva_obs_yaml
    if 'cost function' in jedi_yaml_dict:
UnboundLocalError: local variable 'jedi_yaml_dict' referenced before assignment

Line 135 of var_original.yaml is the pattern line below

            - hsnon
          pattern: %mem%
          nmembers: 4

How do we fix this?

CoryMartin-NOAA · 2024-01-10T17:10:06Z

I think there's an env var one can set, @ShastriPaturi did this on Hera I think for role.jedipara.
See a familiar face here: SciTools/cartopy#1827

RussTreadon-NOAA · 2024-01-10T20:17:51Z

I think there's an env var one can set, @ShastriPaturi did this on Hera I think for role.jedipara. See a familiar face here: SciTools/cartopy#1827

Thanks, @CoryMartin-NOAA . Two questions

Are cartopy shapefiles installed in a central location on Orion and Hercules? If so, where?
@ShastriPaturi , where did you set CARTOPY_DATA_DIR in the Hera role.jedipara environment?

CoryMartin-NOAA · 2024-01-10T20:23:14Z

@RussTreadon-NOAA I've copied mine to /work2/noaa/da/cmartin/GDASApp/fix/cartopy (from ~/.local/share/cartopy) but I'm not sure exacty which subdirectory the env var should be set to to find these properly.

RussTreadon-NOAA · 2024-01-11T19:34:24Z

Thank you @CoryMartin-NOAA . I rsync'd shapefiles from my Orion cartopy directory to Hercules. Does every user their own snapshot of the shapefiles? Can we have the shape files installed in single publicly shared location?

I reran test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY. The job got past the previous cartopy download failure. @guillaumevernieres and @AndrewEichmann-NOAA , the VRFY job now fails with the message

2024-01-10 14:52:08:ERROR:Error occurred when attempting to load: /work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gd\
as.cd/../../sorc/gdas.cd/build/test/soca/gw/testrun/testjjobs/ROTDIRS/gdas_test/gdas.20180415/12//analysis/ocean/yaml/var_orig\
inal.yaml, error: while scanning for the next token
found character '%' that cannot start any token
  in "/work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/../../sorc/gdas.cd/build/test/soca/gw/testrun/testjjob\
s/ROTDIRS/gdas_test/gdas.20180415/12//analysis/ocean/yaml/var_original.yaml", line 135, column 20
Traceback (most recent call last):
  File "/work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/../../sorc/gdas.cd/scripts/exgdas_global_marine_anal\
ysis_vrfy.py", line 219, in <module>
    gen_eva_obs_yaml.gen_eva_obs_yaml(varyaml, marinetemplate, 'preevayamls')
  File "/work2/noaa/da/rtreadon/git/global-workflow/hercules/sorc/gdas.cd/ush/eva/gen_eva_obs_yaml.py", line 20, in gen_eva_obs_yaml
    if 'cost function' in jedi_yaml_dict:
UnboundLocalError: local variable 'jedi_yaml_dict' referenced before assignment

Line 135 of var_original.yaml is the pattern line below

            - hsnon
          pattern: %mem%
          nmembers: 4

How do we fix this?

@CoryMartin-NOAA suggested adding quotes around %mem%. I did so in the local copy of var_original.yaml so that it reads

            - hsnon
          pattern: '%mem%'
          nmembers: 4

The rerun of test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY passed

1/1 Test #1690: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY ...   Passed  362.35 sec

The following tests passed:
        test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY

100% tests passed, 0 tests failed out of 1

Total Test time (real) = 362.70 sec

As a test remove the quotes and rerun the VRFY test. Once again the test failed with the same error message as above.

1/1 Test #1690: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY ...***Failed  330.51 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 330.88 sec

The pattern section of var_original.yaml is from parm/soca/berror/saber_blocks.yaml. Interestingly, quotes are present in saber_blocks.yaml.

        state variables: [tocn, socn, ssh, uocn, vocn, cicen, hicen, hsnon]
      pattern: '%mem%'
      nmembers: ${ENS_SIZE}

Quotes must be removed in the process of combining various source yamls into var_original.yaml.

@CoryMartin-NOAA and @guillaumevernieres , is there a way to construct var_original.yaml such that the quotes in saber_blocks.yaml are retained?

RussTreadon-NOAA · 2024-01-11T19:53:51Z

I am fine with merging this PR into develop.

Most soca ctests failures can be resolved by updating global-workflow. Doing so requires a separate issue and PR in g-w. How best to resolve the yaml quote issue in the soca VRFY ctest can be addressed in a future GDASApp issue.

CoryMartin-NOAA · 2024-01-11T19:56:25Z

I'm perplexed by this '%mem%' issue since that seems like it has been there for 8 months. Why is it only an issue on Hercules?

RussTreadon-NOAA · 2024-01-11T21:07:44Z

I'm perplexed by this '%mem%' issue since that seems like it has been there for 8 months. Why is it only an issue on Hercules?

Out of curiosity I installed the current head of GDASApp develop at 4846a7f on Orion inside the current head of g-w develop at 4cb5802. test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY passed Orion.

      Start 1689: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY
34/52 Test #1689: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY ....   Passed  654.63 sec

A check of var_original.yaml on Orion shows that quotes are retained!

            - hsnon
          pattern: '%mem%'
          nmembers: '4'

This prompted me to rerun all test_gdasapp on Hercules. This time the Hercules var_original.yaml retains quotes and the VRFY job passes

      Start 1690: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY
36/55 Test #1690: test_gdasapp_soca_JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY ....   Passed  330.59 sec

The following section of scripts/exgdas_global_marine_analysis_run.sh removes quotes when creating var.yaml.

function clean_yaml()
{
    mv $1 tmp_yaml;
    sed -e "s/'//g" tmp_yaml > $1
}

################################################################################
# run 3DVAR FGAT
cp var.yaml var_original.yaml
clean_yaml var.yaml

I can not explain the previous failure on Hercules apart from user (ie, me) error.

initial commit for hercules GDASApp build (NOAA-EMC#773)

7df82e1

RussTreadon-NOAA self-assigned this Nov 28, 2023

Merge branch 'NOAA-EMC:develop' into feature/hercules

7a24ca7

RussTreadon-NOAA marked this pull request as ready for review November 28, 2023 17:20

Merge branch 'NOAA-EMC:develop' into feature/hercules

fa4ab8d

RussTreadon-NOAA mentioned this pull request Nov 30, 2023

Upgrade subcomponents and the global workflow to use spack-stack NOAA-EMC/global-workflow#1868

Closed

Merge branch 'develop' into feature/hercules

cdb4e58

CoryMartin-NOAA previously approved these changes Nov 30, 2023

View reviewed changes

Merge branch 'NOAA-EMC:develop' into feature/hercules

4d8b257

DavidHuber-NOAA mentioned this pull request Dec 6, 2023

Port to Hercules NOAA-EMC/global-workflow#1588

Closed

17 tasks

Merge branch 'NOAA-EMC:develop' into feature/hercules

4bb1fbf

DavidHuber-NOAA mentioned this pull request Jan 5, 2024

Port to Hercules NOAA-EMC/global-workflow#2196

Merged

6 tasks

Merge branch 'NOAA-EMC:develop' into feature/hercules

23453d7

add hercules to atm and soca ctests (NOAA-EMC#773)

8e67f9b

RussTreadon-NOAA dismissed CoryMartin-NOAA’s stale review via 8e67f9b January 9, 2024 21:15

RussTreadon-NOAA mentioned this pull request Jan 10, 2024

Use submodules rather than ecbuild_bundle git #811

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Merge branch 'develop' into feature/hercules

4cd27bf

CoryMartin-NOAA approved these changes Jan 11, 2024

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CoryMartin-NOAA merged commit cc4c940 into NOAA-EMC:develop Jan 11, 2024
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Add Hercules build capability to GDASApp #774

Add Hercules build capability to GDASApp #774

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Add Hercules build capability to GDASApp #774

Add Hercules build capability to GDASApp #774

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