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emcbot/build_gdas.log

Created June 27, 2024 19:38
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error log file from CI run PR_BUILD_2729
Raw
build_gdas.log
+ OPTIND=1
+ _opts='-f '
+ getopts :j:dv option
+ case "${option}" in
+ BUILD_JOBS=8
+ getopts :j:dv option
+ shift 2
+ BUILD_JOBS=8
+ WORKFLOW_BUILD=ON
+ ./gdas.cd/build.sh -f -f
Building GDASApp on hera
Currently Loaded Modules:
1) intel/2022.1.2 20) netcdf-fortran/4.6.1 39) openblas/0.3.24 58) libxaw/1.0.13 77) py-bottleneck/1.3.7
2) stack-intel/2021.5.0 21) antlr/2.7.7 40) eckit/1.24.5 59) udunits/2.2.28 78) py-numexpr/2.8.4
3) impi/2022.1.2 22) gsl/2.7.1 41) fftw/3.3.10 60) ncview/2.1.9 79) py-et-xmlfile/1.0.1
4) stack-intel-oneapi-mpi/2021.5.1 23) nco/5.0.6 42) fckit/0.11.0 61) netcdf-cxx4/4.3.1 80) py-openpyxl/3.1.2
5) cmake/3.23.1 24) parallelio/2.5.10 43) fiat/1.2.0 62) json/3.10.5 81) py-six/1.16.0
6) gettext/0.19.8.1 25) wget/1.14 44) ectrans/1.2.0 63) rocoto/1.3.6 82) py-python-dateutil/2.8.2
7) pcre2/10.42 26) libxcrypt/4.4.35 45) qhull/2020.2 64) bacio/2.4.1 83) py-pytz/2023.3
8) nghttp2/1.57.0 27) sqlite/3.43.2 46) atlas/0.35.1 65) w3emc/2.10.0 84) py-pyxlsb/1.0.10
9) curl/8.4.0 28) util-linux-uuid/2.38.1 47) sp/2.5.0 66) prod_util/2.1.1 85) py-xlrd/2.0.1
10) zlib/1.2.13 29) python/3.10.13 48) gsl-lite/0.37.0 67) py-markupsafe/2.1.3 86) py-xlsxwriter/3.1.7
11) git/2.18.0 30) boost/1.83.0 49) libjpeg/2.1.0 68) py-jinja2/3.0.3 87) py-xlwt/1.3.0
12) pkg-config/0.27.1 31) py-setuptools/63.4.3 50) krb5/1.20.1 69) py-cftime/1.0.3.4 88) py-pandas/1.5.3
13) hdf5/1.14.0 32) py-numpy/1.22.3 51) libtirpc/1.3.3 70) py-netcdf4/1.5.8 89) py-xarray/2023.7.0
14) parallel-netcdf/1.12.2 33) bufr/12.0.1 52) hdf/4.2.15 71) py-pybind11/2.11.0 90) py-f90nml/1.4.3
15) snappy/1.1.10 34) git-lfs/2.10.0 53) jedi-cmake/1.4.0 72) py-pycodestyle/2.11.0 91) py-pip/23.1.2
16) zstd/1.5.2 35) ecbuild/3.7.2 54) libpng/1.6.37 73) libyaml/0.2.5 92) GDAS/hera.intel
17) c-blosc/1.21.5 36) openjpeg/2.3.1 55) libxt/1.1.5 74) py-pyyaml/6.0
18) netcdf-c/4.9.2 37) eccodes/2.32.0 56) libxmu/1.1.4 75) py-scipy/1.11.3
19) nccmp/1.9.0.1 38) eigen/3.4.0 57) libxpm/4.11.0 76) py-packaging/23.1
Configuring ...
+ cmake -DMPIEXEC_EXECUTABLE=/apps/slurm/default/bin/srun -DMPIEXEC_NUMPROC_FLAG=-n -DBUILD_GSIBEC=ON -DCLONE_JCSDADATA=NO -DWORKFLOW_TESTS=ON /scratch1/NCEPDEV/global/CI/2729/gfs/sorc/gdas.cd/bundle
-- The C compiler identification is Intel 2021.5.0.20211109
-- The CXX compiler identification is Intel 2021.5.0.20211109
-- The Fortran compiler identification is Intel 2021.5.0.20211109
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /apps/oneapi/mpi/2021.5.1/bin/mpiicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /apps/oneapi/mpi/2021.5.1/bin/mpiicpc - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /apps/oneapi/mpi/2021.5.1/bin/mpiifort - skipped
-- ecbuild 3.7.2 /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/ecbuild-3.7.2-7yxdhug/share/ecbuild/cmake
-- cmake 3.23.1 /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/cmake-3.23.1-qjplcak/bin/cmake
-- ---------------------------------------------------------
-- Found Git: /usr/bin/git (found version "2.39.3")
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of void*
-- Check size of void* - done
-- Check size of off_t
-- Check size of off_t - done
-- ---------------------------------------------------------
-- ---------------------------------------------------------
-- [GDAS-bundle] (1.0.0)
-- Feature TESTS enabled
-- Found Python3: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/python-3.10.13-2p2rady/bin/python3.10 (found version "3.10.13") found components: Interpreter
-- Feature TESTS enabled
-- ---------------------------------------------------------
-- Adding bundle project jedicmake
-- ---------------------------------------------------------
-- Skipping bundle project eckit
-- ---------------------------------------------------------
-- Skipping bundle project fckit
-- ---------------------------------------------------------
-- Skipping bundle project atlas
-- ---------------------------------------------------------
-- Adding bundle project crtm
-- ---------------------------------------------------------
-- [crtm] (2.4.1)
-- Feature TESTS enabled
-- Found OpenMP_Fortran: -qopenmp (found version "5.0")
-- Found OpenMP: TRUE (found version "5.0") found components: Fortran
-- Found NetCDF: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv/include (found version "4.9.2") found components: Fortran
-- FindNetCDF defines targets:
-- - NetCDF::NetCDF_Fortran [/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv/lib/libnetcdff.so]
-- ---------------------------------------------------------
-- [CRTM_Tests] (1.0.1)
-- Feature TESTS enabled
-- use LOCAL_PATH_JEDI_TESTFILES: /scratch1/NCEPDEV/global/CI/2729/gfs/sorc/gdas.cd/bundle/fix
Using existing local fix directory instead of downloading.
-- Hostname: hfe08
-- Host FQDN: hfe08-ib
-- Git Branch (set CDASH_OVERRIDE_GIT_BRANCH to force): GIT_BRANCH_UNSPECIFIED
-- System ID: Rocky_8.8
-- Compilers: Intel_2021.5.0.20211109
-- Build: GIT_BRANCH_UNSPECIFIED;Rocky_8.8;Intel_2021.5.0.20211109;RelWithDebInfo
-- Site: hfe08-ib
-- ---------------------------------------------------------
-- Adding bundle project gsibec
-- Found ecbuild: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/ecbuild-3.7.2-7yxdhug/share/ecbuild/cmake (found suitable version "3.7.2", minimum required is "3.3.2")
-- ---------------------------------------------------------
-- [gsibec] (1.2.1)
-- Feature TESTS enabled
-- Found MKL: /apps/oneapi/mkl/2022.0.2/lib/intel64/libmkl_intel_lp64.so;/apps/oneapi/mkl/2022.0.2/lib/intel64/libmkl_sequential.so;/apps/oneapi/mkl/2022.0.2/lib/intel64/libmkl_core.so
-- Found MPI_Fortran: /apps/oneapi/mpi/2021.5.1/bin/mpiifort (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: Fortran
-- Found MPI_C: /apps/oneapi/mpi/2021.5.1/bin/mpiicc (found version "3.1")
-- Found MPI_CXX: /apps/oneapi/mpi/2021.5.1/bin/mpiicpc (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found NetCDF: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-c-4.9.2-ejp7j3k/include;/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv/include (found version "4.9.2") found components: Fortran
-- FindNetCDF defines targets:
-- - NetCDF_VERSION [4.9.2]
-- - NetCDF_PARALLEL [TRUE]
-- - NetCDF_C_CONFIG_EXECUTABLE [/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-c-4.9.2-ejp7j3k/bin/nc-config]
-- - NetCDF::NetCDF_C [SHARED] [Root: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-c-4.9.2-ejp7j3k] Lib: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-c-4.9.2-ejp7j3k/lib/libnetcdf.so
-- - NetCDF_Fortran_CONFIG_EXECUTABLE [/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv/bin/nf-config]
-- - NetCDF::NetCDF_Fortran [SHARED] [Root: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv] Lib: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv/lib/libnetcdff.so
-- Found sp: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/sp-2.5.0-2pqzhuv/lib64/libsp_4.a (found version "2.5.0")
-- ---------------------------------------------------------
-- Adding bundle project gsw
-- ---------------------------------------------------------
-- [gsw] (3.0.8)
-- Feature TESTS enabled
-- ---------------------------------------------------------
-- Adding bundle project oops
-- ---------------------------------------------------------
-- [oops] (1.10.0)
-- Feature TESTS enabled
-- Found OpenMP_CXX: -qopenmp (found version "5.0")
-- Found OpenMP: TRUE (found version "5.0") found components: CXX Fortran
-- Found MPI: TRUE (found version "3.1") found components: C CXX Fortran
-- Found MPI: TRUE (found version "3.1")
-- Found NetCDF: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-c-4.9.2-ejp7j3k/include;/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv/include (found version "4.9.2") found components: C Fortran
-- FindNetCDF defines targets:
-- - NetCDF_VERSION [4.9.2]
-- - NetCDF_PARALLEL [TRUE]
-- - NetCDF_C_CONFIG_EXECUTABLE [/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-c-4.9.2-ejp7j3k/bin/nc-config]
-- - NetCDF::NetCDF_C [SHARED] [Root: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-c-4.9.2-ejp7j3k] Lib: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-c-4.9.2-ejp7j3k/lib/libnetcdf.so
-- - NetCDF_Fortran_CONFIG_EXECUTABLE [/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv/bin/nf-config]
-- - NetCDF::NetCDF_Fortran [SHARED] [Root: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv] Lib: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/netcdf-fortran-4.6.1-ifhqcwv/lib/libnetcdff.so
-- Found Boost: /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/boost-1.83.0-a2avo2q/lib/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.64.0")
-- Found OpenMP_CXX: -qopenmp (found version "5.0")
-- Found OpenMP: TRUE (found version "5.0") found components: CXX
-- Found addr2line at /usr/bin/addr2line.
-- Performing Test OOPS_STACKTRACE_AVAILABLE_addr2line
-- Performing Test OOPS_STACKTRACE_AVAILABLE_addr2line - Failed
-- Performing Test OOPS_STACKTRACE_AVAILABLE_addr2line_nognus
-- Performing Test OOPS_STACKTRACE_AVAILABLE_addr2line_nognus - Failed
-- Performing Test OOPS_STACKTRACE_AVAILABLE_addr2line_gnus
-- Performing Test OOPS_STACKTRACE_AVAILABLE_addr2line_gnus - Failed
-- Performing Test OOPS_STACKTRACE_AVAILABLE_default
-- Performing Test OOPS_STACKTRACE_AVAILABLE_default - Success
-- Using this provider for stacktraces: default.
-- ---------------------------------------------------------
-- Adding bundle project vader
CMake Error at /scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/ecbuild-3.7.2-7yxdhug/share/ecbuild/cmake/ecbuild_log.cmake:190 (message):
CRITICAL - Source directory
'/scratch1/NCEPDEV/global/CI/2729/gfs/sorc/gdas.cd/bundle/vader' for
subproject 'vader' does not exist or does not contain a CMakeLists.txt
file.
Call Stack (most recent call first):
/scratch1/NCEPDEV/nems/role.epic/spack-stack/spack-stack-1.6.0/envs/unified-env-rocky8/install/intel/2021.5.0/ecbuild-3.7.2-7yxdhug/share/ecbuild/cmake/ecbuild_bundle.cmake:166 (ecbuild_critical)
CMakeLists.txt:80 (ecbuild_bundle)
-- Configuring incomplete, errors occurred!
See also "/scratch1/NCEPDEV/global/CI/2729/gfs/sorc/gdas.cd/build/CMakeFiles/CMakeOutput.log".
See also "/scratch1/NCEPDEV/global/CI/2729/gfs/sorc/gdas.cd/build/CMakeFiles/CMakeError.log".
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