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emcbot/gdas_prepoceanobs.log

Created April 7, 2025 14:45
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error log file from CI run PR_3549
Raw
gdas_prepoceanobs.log
Begin prepoceanobs.sh at Mon Apr 7 14:38:40 UTC 2025
+ prepoceanobs.sh[8]. /work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/ush/load_ufsda_modules.sh
++ load_ufsda_modules.sh[4][[ hxB == *x* ]]
++ load_ufsda_modules.sh[5]set_x=YES
++ load_ufsda_modules.sh[10][[ NO == \N\O ]]
++ load_ufsda_modules.sh[11]echo 'Loading modules quietly...'
Loading modules quietly...
++ load_ufsda_modules.sh[12]set +x
Running "module reset". Resetting modules to system default. The following $MODULEPATH directories have been removed: None
-------------------------------------------------------------------------------
The following dependent module(s) are not currently loaded: py-numpy/1.22.3 (required by: bufr/12.0.1), python/3.10.13 (required by: boost/1.84.0, bufr/12.0.1, fckit/0.11.0, atlas/0.36.0, py-pybind11/2.11.0)
-------------------------------------------------------------------------------
Currently Loaded Modules:
1) intel-oneapi-compilers/2023.1.0 34) openblas/0.3.24
2) stack-intel/2021.9.0 35) eckit/1.24.5
3) intel-oneapi-mpi/2021.9.0 36) fftw/3.3.10
4) stack-intel-oneapi-mpi/2021.9.0 37) fckit/0.11.0
5) zlib-ng/2.1.5 38) fiat/1.2.0
6) cmake/3.23.1 39) ectrans/1.2.0
7) nghttp2/1.57.0 40) fms/2023.04
8) curl/8.4.0 41) esmf/8.6.1
9) zlib/1.2.13 42) qhull/2020.2
10) git/2.31.1 43) atlas/0.36.0
11) hdf5/1.14.3 44) sp/2.5.0
12) parallel-netcdf/1.12.3 45) gsl-lite/0.37.0
13) snappy/1.1.10 46) libjpeg/2.1.0
14) zstd/1.5.2 47) krb5/1.20.1
15) c-blosc/1.21.5 48) libtirpc/1.3.3
16) netcdf-c/4.9.2 49) hdf/4.2.15
17) nccmp/1.9.0.1 50) jedi-cmake/1.4.0
18) netcdf-fortran/4.6.1 51) libpng/1.6.37
19) antlr/2.7.7 52) libxt/1.3.0
20) gsl/2.7.1 53) libxmu/1.1.4
21) nco/5.1.6 54) libxpm/3.5.17
22) parallelio/2.6.2 55) libxaw/1.0.15
23) wget/1.21.1 56) udunits/2.2.28
24) pigz/2.8 57) ncview/2.1.9
25) tar/1.34 58) netcdf-cxx4/4.3.1
26) gettext/0.21.1 59) py-pybind11/2.11.0
27) boost/1.84.0 60) contrib/0.1
28) bufr/12.0.1 61) noaatools/3.1
29) git-lfs/3.1.2 62) rocoto/1.3.7
30) ecbuild/3.7.2 63) hpc/1.2.0
31) openjpeg/2.3.1 64) miniconda3/4.6.14
32) eccodes/2.33.0 65) gdasapp/1.0.0
33) eigen/3.4.0 66) GDAS/hercules.intel
++ load_ufsda_modules.sh[74]pip list
Package Version
------------------ ---------
attrs 21.4.0
autopep8 1.6.0
boto3 1.21.23
botocore 1.24.23
Bottleneck 1.3.2
certifi 2022.6.15
cftime 1.5.1.1
click 8.1.7
Cython 0.29.28
f90nml 1.4.3
h5py 2.10.0
importlib-metadata 4.8.2
iniconfig 1.1.1
Jinja2 3.1.2
jmespath 1.0.0
Markdown 3.4.1
MarkupSafe 2.1.2
mkl-fft 1.3.1
mkl-random 1.2.2
mkl-service 2.4.0
mpi4py 3.1.5
netCDF4 1.4.2
numexpr 2.8.1
numpy 1.21.6
packaging 21.3
pandas 1.3.5
pip 21.2.2
pluggy 1.0.0
py 1.11.0
py-ncepbufr 12.0.1
pybind11 2.11.0
pycodestyle 2.8.0
pygrib 2.1.4
pygw 0.0.1
pyparsing 3.0.4
pyproj 1.9.6
pytest 6.2.5
python-dateutil 2.8.2
pytz 2021.3
PyYAML 6.0
r2d2 1.0.0
s3transfer 0.5.2
scipy 1.7.3
setuptools 58.0.4
six 1.16.0
solo 1.0.0
toml 0.10.2
typing-extensions 3.10.0.2
urllib3 1.26.9
wheel 0.37.1
wxflow 0.1.0
xarray 0.20.1
zipp 3.7.0
+ Unknown[1]uname -p
++ load_ufsda_modules.sh[77]wxflowPATH=/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/ush/python
++ load_ufsda_modules.sh[78]PYTHONPATH=/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.7.0/envs/ue-intel/install/intel/2021.9.0/py-pybind11-2.11.0-bxoo6yn/lib/python3.10/site-packages:/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.7.0/envs/ue-intel/install/intel/2021.9.0/bufr-12.0.1-h7wq5ai/lib64/python3.10/site-packages:/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.7.0/envs/ue-intel/install/intel/2021.9.0/bufr-12.0.1-h7wq5ai/lib/python3.10/site-packages:/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/ush:/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/ush/python
++ load_ufsda_modules.sh[79]export PYTHONPATH
++ load_ufsda_modules.sh[82]ulimit -S -s 16384
++ load_ufsda_modules.sh[83]unset ulimit_s
+ prepoceanobs.sh[9]status=0
+ prepoceanobs.sh[10][[ 0 -ne 0 ]]
+ prepoceanobs.sh[14]export job=prepoceanobs
+ prepoceanobs.sh[14]job=prepoceanobs
+ prepoceanobs.sh[15]export jobid=prepoceanobs.2555623
+ prepoceanobs.sh[15]jobid=prepoceanobs.2555623
++ prepoceanobs.sh[20]detect_py_ver
++ bash_utils.sh[113]regex='[0-9]+\.[0-9]+'
+++ bash_utils.sh[115]python --version
++ bash_utils.sh[115][[ Python 3.7.12 =~ [0-9]+\.[0-9]+ ]]
++ bash_utils.sh[116]echo 3.7
+ prepoceanobs.sh[20]pyiodaPATH=/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/sorc/gdas.cd/build/lib/python3.7/
+ prepoceanobs.sh[21]PYTHONPATH=/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/sorc/gdas.cd/build/lib/python3.7/:/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.7.0/envs/ue-intel/install/intel/2021.9.0/py-pybind11-2.11.0-bxoo6yn/lib/python3.10/site-packages:/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.7.0/envs/ue-intel/install/intel/2021.9.0/bufr-12.0.1-h7wq5ai/lib64/python3.10/site-packages:/work/noaa/epic/role-epic/spack-stack/hercules/spack-stack-1.7.0/envs/ue-intel/install/intel/2021.9.0/bufr-12.0.1-h7wq5ai/lib/python3.10/site-packages:/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/ush:/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/ush/python
+ prepoceanobs.sh[22]export PYTHONPATH
+ prepoceanobs.sh[26]/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/jobs/JGLOBAL_PREP_OCEAN_OBS
+ bash[8]'[' -z '' ']'
+ bash[9]case "$-" in
+ bash[12]__lmod_vx=x
+ bash[16]'[' -n x ']'
+ bash[16]set +x
Shell debugging temporarily silenced: export LMOD_SH_DBG_ON=1 for this output (/apps/other/lmod/lmod/init/bash)
Shell debugging restarted
+ bash[224]unset __lmod_vx
+ JGLOBAL_PREP_OCEAN_OBS[2]source /work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/ush/jjob_header.sh -e prepoceanobs -c 'base prepoceanobs'
++ jjob_header.sh[43]_calling_script=/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/jobs/JGLOBAL_PREP_OCEAN_OBS
++ jjob_header.sh[44]source /work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/ush/preamble.sh
+++ preamble.sh[20]set +x
Begin /work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/global-workflow/jobs/JGLOBAL_PREP_OCEAN_OBS at Mon Apr 7 14:39:21 UTC 2025
++ jjob_header.sh[46]OPTIND=1
++ jjob_header.sh[47]getopts c:e: option
++ jjob_header.sh[48]case "${option}" in
++ jjob_header.sh[50]env_job=prepoceanobs
++ jjob_header.sh[47]getopts c:e: option
++ jjob_header.sh[48]case "${option}" in
++ jjob_header.sh[49]read -ra configs
++ jjob_header.sh[47]getopts c:e: option
++ jjob_header.sh[61]shift 4
++ jjob_header.sh[63][[ -z prepoceanobs ]]
++ jjob_header.sh[71]export DATA=/work2/noaa/stmp/role-global/HERCULES/RUNDIRS/C48mx500_hybAOWCDA_e1a089c0/gdas.2021032500/prepoceanobs.2555623
++ jjob_header.sh[71]DATA=/work2/noaa/stmp/role-global/HERCULES/RUNDIRS/C48mx500_hybAOWCDA_e1a089c0/gdas.2021032500/prepoceanobs.2555623
++ jjob_header.sh[72][[ YES == \Y\E\S ]]
++ jjob_header.sh[73]rm -rf /work2/noaa/stmp/role-global/HERCULES/RUNDIRS/C48mx500_hybAOWCDA_e1a089c0/gdas.2021032500/prepoceanobs.2555623
++ jjob_header.sh[75]mkdir -p /work2/noaa/stmp/role-global/HERCULES/RUNDIRS/C48mx500_hybAOWCDA_e1a089c0/gdas.2021032500/prepoceanobs.2555623
++ jjob_header.sh[76]cd /work2/noaa/stmp/role-global/HERCULES/RUNDIRS/C48mx500_hybAOWCDA_e1a089c0/gdas.2021032500/prepoceanobs.2555623
++ jjob_header.sh[85]export cycle=t00z
++ jjob_header.sh[85]cycle=t00z
++ jjob_header.sh[86]setpdy.sh
+ setpdy.sh[21][[ ! t00z =~ t??z ]]
+ setpdy.sh[26]case $# in
+ setpdy.sh[27]dates_before_PDY=7
+ setpdy.sh[28]dates_after_PDY=7
+ setpdy.sh[46]COMDATEROOT=/work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/RUNTESTS/COMROOT
+ setpdy.sh[49]'[' -z 20210325 ']'
+ setpdy.sh[53]sed 's/[0-9]\{8\}/20210325/' /work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/RUNTESTS/COMROOT/date/t00z
sed: can't read /work2/noaa/global/role-global/GFS_CI_CD/HERCULES/CI/3549/RUNTESTS/COMROOT/date/t00z: No such file or directory
++ setpdy.sh[58]finddate.sh 20210325 s-7
+++ finddate.sh[27]set +x
/apps/contrib/NCEP/libs/hpc-stack/intel-2018.4/prod_util/1.2.2/bin/finddate.sh: line 263: pdstr: unbound variable
+ setpdy.sh[58]DATElne_minus=
+ setpdy.sh[59]export err=1
+ setpdy.sh[59]err=1
+ setpdy.sh[59]err_chk
+ err_chk[14]COREROOT=/gpfs/hps/ptmp/production.core/prepoceanobs.2555623
+ err_chk[16]'[' -z 1 ']'
+ err_chk[18]'[' 1 -ne 0 ']'
+ err_chk[21]'[' 1 -eq 139 ']'
+ err_chk[33]err_exit
+ environment[0]set +eux
-------------------------------------------------------------
-- FATAL ERROR: Job prepoceanobs.2555623 failed RETURN CODE 1
-- ABNORMAL EXIT at Mon Apr 7 09:39:22 CDT 2025 on hercules-03-45
-------------------------------------------------------------
Currently Loaded Modules:
1) intel-oneapi-compilers/2023.1.0 34) openblas/0.3.24
2) stack-intel/2021.9.0 35) eckit/1.24.5
3) intel-oneapi-mpi/2021.9.0 36) fftw/3.3.10
4) stack-intel-oneapi-mpi/2021.9.0 37) fckit/0.11.0
5) zlib-ng/2.1.5 38) fiat/1.2.0
6) cmake/3.23.1 39) ectrans/1.2.0
7) nghttp2/1.57.0 40) fms/2023.04
8) curl/8.4.0 41) esmf/8.6.1
9) zlib/1.2.13 42) qhull/2020.2
10) git/2.31.1 43) atlas/0.36.0
11) hdf5/1.14.3 44) sp/2.5.0
12) parallel-netcdf/1.12.3 45) gsl-lite/0.37.0
13) snappy/1.1.10 46) libjpeg/2.1.0
14) zstd/1.5.2 47) krb5/1.20.1
15) c-blosc/1.21.5 48) libtirpc/1.3.3
16) netcdf-c/4.9.2 49) hdf/4.2.15
17) nccmp/1.9.0.1 50) jedi-cmake/1.4.0
18) netcdf-fortran/4.6.1 51) libpng/1.6.37
19) antlr/2.7.7 52) libxt/1.3.0
20) gsl/2.7.1 53) libxmu/1.1.4
21) nco/5.1.6 54) libxpm/3.5.17
22) parallelio/2.6.2 55) libxaw/1.0.15
23) wget/1.21.1 56) udunits/2.2.28
24) pigz/2.8 57) ncview/2.1.9
25) tar/1.34 58) netcdf-cxx4/4.3.1
26) gettext/0.21.1 59) py-pybind11/2.11.0
27) boost/1.84.0 60) contrib/0.1
28) bufr/12.0.1 61) noaatools/3.1
29) git-lfs/3.1.2 62) rocoto/1.3.7
30) ecbuild/3.7.2 63) hpc/1.2.0
31) openjpeg/2.3.1 64) miniconda3/4.6.14
32) eccodes/2.33.0 65) gdasapp/1.0.0
33) eigen/3.4.0 66) GDAS/hercules.intel
Job prepoceanobs.2555623 failed RETURN CODE 1
/work2/noaa/stmp/role-global/HERCULES/RUNDIRS/C48mx500_hybAOWCDA_e1a089c0/gdas.2021032500/prepoceanobs.2555623
total 0
-rw-r----- 1 role-global stmp 0 Apr 7 09:39 ncepdate
slurmstepd: error: *** JOB 4989605 ON hercules-03-45 CANCELLED AT 2025-04-07T09:39:22 ***
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