guillaumevernieres
commented
6 months ago Thanks for testing @GeorgeVandenberghe-NOAA . @CoryMartin-NOAA reported the issue (GDASApp/issues/812) a while back too. I'll try to work on a fix this week.
Open GeorgeVandenberghe-NOAA opened 6 months ago
guillaumevernieres
commented
6 months ago Thanks for testing @GeorgeVandenberghe-NOAA . @CoryMartin-NOAA reported the issue (GDASApp/issues/812) a while back too. I'll try to work on a fix this week.
guillaumevernieres
commented
6 months ago It's failing because it's not finding filesystem, which is part of c++17. Could that be an indication that the standard library and compiler were not installed properly?
GeorgeVandenberghe-NOAA
commented
6 months ago I found a gcc-mixed module that does not unload intel and I am trying that. Default gcc is 7.x and the mixed one loads 11.2
Otherwise I will have to report it to admins and wait for a correction.
On Tue, Jan 9, 2024 at 8:01 PM Guillaume Vernieres @.***> wrote:
It's failing because it's not finding filesystem, which is part of c++17. Could that be an indication that the standard library and compiler were not installed properly?
— Reply to this email directly, view it on GitHub https://github.com/NOAA-EMC/GDASApp/issues/841#issuecomment-1883697440, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANDS4FTPTEPWNRDU3S7R2W3YNWOZPAVCNFSM6AAAAABBTSTSTWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBTGY4TONBUGA . You are receiving this because you were mentioned.Message ID: @.***>
--
George W Vandenberghe
Lynker Technologies at NOAA/NWS/NCEP/EMC
5830 University Research Ct., Rm. 2141
College Park, MD 20740
@.***
301-683-3769(work) 3017751547(cell)
GeorgeVandenberghe-NOAA
commented
6 months ago Different error when I load gcc-mixed
cd /u/george.vandenberghe/w/workflow/w0106/sorc/ gdas.cd/build/ioda/src/engines/ioda && /opt/cray/pe/craype/2.7.13/bin/CC -DH5_BUILT_AS_DYNAMIC_LIB -DNDEBUG -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -Dioda_EXPORTING -Dioda_SHARED=1 -Dioda_engines_EXPORTS -I/u/george.vandenberghe/w/workflow/w0106/sorc/ gdas.cd/ioda/src/engines/ioda/private -I/u/george.vandenberghe/w/workflow/w0106/sorc/ gdas.cd/build/ioda/src/engines/ioda/config -I/u/george.vandenberghe/w/workflow/w0106/sorc/ gdas.cd/ioda/src/engines/ioda/include -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/oops/include -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/oops/src -I/u/george.vandenberghe/w/workflow/w0106/sorc/ gdas.cd/build/module/oops/Intel/2021.6.0.20220226 -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/gsl-lite-0.37.0-tgxiry7/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/udunits-2.2.28-ofptt3d/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/odc-1.4.6-z4ps66c/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/odc-1.4.6-z4ps66c/include/odc -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit/sql -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/netcdf-fortran-4.6.0-e4gh24r/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/netcdf-c-4.9.2-agt6ew3/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/fckit-0.11.0-7cqugu5/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/fckit-0.11.0-7cqugu5/module/fckit -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/fckit-0.11.0-7cqugu5/include/fckit -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/ecmwf-atlas-0.35.0-wp4cu3i/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/ecmwf-atlas-0.35.0-wp4cu3i/module/atlas -isystem /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/hdf5-1.14.0-w5vslqn/include -isystem /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/boost-1.78.0-2nmo377/include -isystem /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eigen-3.4.0-s5vmmkg/include/eigen3 -g -traceback -g -traceback -O2 -DNDEBUG -fPIC -qopenmp -std=c++17 -MD -MT ioda/src/engines/ioda/CMakeFiles/ioda_engines.dir/src/ioda/Attribute.cpp.o -MF CMakeFiles/ioda_engines.dir/src/ioda/Attribute.cpp.o.d -o CMakeFiles/ioda_engines.dir/src/ioda/Attribute.cpp.o -c /u/george.vandenberghe/w/workflow/w0106/sorc/ gdas.cd/ioda/src/engines/ioda/src/ioda/Attribute.cpp I
*n file included from /opt/cray/pe/gcc/12.1.0/snos/include/g++/random(49), from /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eigen-3.4.0-s5vmmkg/include/eigen3/unsupported/Eigen/CXX11/Tensor(41), from /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/ioda/src/engines/ioda/include/ioda/Misc/Eigen_Compat.h(27) http://gdas.cd/ioda/src/engines/ioda/include/ioda/Misc/Eigen_Compat.h(27), from /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/ioda/src/engines/ioda/include/ioda/Attributes/Attribute.h(26) http://gdas.cd/ioda/src/engines/ioda/include/ioda/Attributes/Attribute.h(26), from /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/ioda/src/engines/ioda/src/ioda/Attribute.cpp(7) http://gdas.cd/ioda/src/engines/ioda/src/ioda/Attribute.cpp(7):/opt/cray/pe/gcc/12.1.0/snos/include/g++/bits/random.h(104): error: expected a declaration { extension using type = unsigned __int128; }; ^/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/ioda/src/engines/ioda/src/ioda/Attribute.cpp(131) http://gdas.cd/ioda/src/engines/ioda/src/ioda/Attribute.cpp(131): warning
/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/ioda/src/engines/ioda/src/ioda/Attribute.cpp http://gdas.cd/ioda/src/engines/ioda/src/ioda/Attribute.cpp (code 2)make[2]: [ioda/src/engines/ioda/CMakeFiles/ioda_engines.dir/build.make:76: ioda/src/engines/ioda/CMakeFiles/ioda_engines.dir/src/ioda/Attribute.cpp.o] Error 2make[2]: Leaving directory '/lfs/h1/emc/ptmp/gwv/workflow/w0106/sorc/gdas.cd/build http://gdas.cd/build'make[1]: [CMakeFiles/Makefile2:15554: ioda/src/engines/ioda/CMakeFiles/ioda_engines.dir/all] Error 2* make[1]: Leaving directory '/lfs/h1/emc/ptmp/gwv/workflow/w0106/sorc/ gdas.cd/build' make: *** [Makefile:166: all] Error 2
On Tue, Jan 9, 2024 at 8:01 PM Guillaume Vernieres @.***> wrote:
It's failing because it's not finding filesystem, which is part of c++17. Could that be an indication that the standard library and compiler were not installed properly?
— Reply to this email directly, view it on GitHub https://github.com/NOAA-EMC/GDASApp/issues/841#issuecomment-1883697440, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANDS4FTPTEPWNRDU3S7R2W3YNWOZPAVCNFSM6AAAAABBTSTSTWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBTGY4TONBUGA . You are receiving this because you were mentioned.Message ID: @.***>
--
George W Vandenberghe
Lynker Technologies at NOAA/NWS/NCEP/EMC
5830 University Research Ct., Rm. 2141
College Park, MD 20740
@.***
301-683-3769(work) 3017751547(cell)
The following setup to compile gdasapp fails on acorn
module use /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/modulefiles/Core module load stack-intel/2022.0.2.262 stack-cray-mpich/8.1.9 module load jedi-base-env/1.0.0
then
cd $workflow_root/sorc/gdas.cd
rm -rf build ; mkdir build ; cd build cmake -DMPIEXEC_EXECUTABLE=/apps/slurm/default/bin/srun -DMPIEXEC_NUMPROC_FLAG=-n -DBUILD_GSIBEC=ON -DCLONE_JCSDADATA=NO -DWORKFLOW_TESTS=ON .. time make -j 8 VERBOSE=1
The failure is
[ 97%] Built target test_soca_convertstate_soca2cice.x make -f gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/build.make gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/depend make[2]: Entering directory '/lfs/h1/emc/ptmp/gwv/workflow/w0106/sorc/gdas.cd/build' cd /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build && /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/cmake-3.23.1-hghxkax/bin/cmake -E cmake_depends "Unix Makefiles" /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/gdas-utils/soca /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/gdas-utils/soca /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/DependInfo.cmake --color= Dependencies file "gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/gdas_incr_handler.cc.o.d" is newer than depends file "/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/compiler_depend.internal". Consolidate compiler generated dependencies of target gdas_incr_handler.x make[2]: Leaving directory '/lfs/h1/emc/ptmp/gwv/workflow/w0106/sorc/gdas.cd/build' make -f gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/build.make gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/build make[2]: Entering directory '/lfs/h1/emc/ptmp/gwv/workflow/w0106/sorc/gdas.cd/build' [ 97%] Building CXX object gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/gdas_incr_handler.cc.o cd /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/gdas-utils/soca && /opt/cray/pe/craype/2.7.13/bin/CC -DGSW_FOUND -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -Dioda_SHARED=1 -Dioda_fortran_SHARED=1 -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/oops/include -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/oops/src -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/module/oops/Intel/2021.6.0.20220226 -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/soca/src/soca/.. -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/soca/module -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/fms/module -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/fms/include -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/gsw/module -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/module/mom6/Intel/2021.6.0.20220226 -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/mom6/config_src/memory/dynamic_nonsymmetric -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/mom6/src/framework -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/saber/src/saber/.. -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/module/saber/Intel/2021.6.0.20220226 -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/gsibec/src/gsibec/.. -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/module/gsibec/Intel/2021.6.0.20220226 -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/vader/src -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/ioda/include -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/module/ioda/Intel/2021.6.0.20220226 -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/ioda/src/engines/ioda/include -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/ioda/src/engines/ioda/fortran -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/ioda/src/engines/ioda/fortran -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/ioda/src/engines/ioda/config -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/ufo/src -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/ufo/module -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/module/crtm/Intel/2021.6.0.20220226 -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/build/module/icepack/Intel/2021.6.0.20220226 -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/icepack/configuration -I/u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/icepack/columnphysics -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/netcdf-cxx4-4.3.1-t2m6f4y/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/netcdf-fortran-4.6.0-e4gh24r/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/netcdf-c-4.9.2-agt6ew3/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/fckit-0.11.0-7cqugu5/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/fckit-0.11.0-7cqugu5/module/fckit -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/fckit-0.11.0-7cqugu5/include/fckit -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/ecmwf-atlas-0.35.0-wp4cu3i/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/ecmwf-atlas-0.35.0-wp4cu3i/module/atlas -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/ecmwf-atlas-0.35.0-wp4cu3i/include/atlas -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit/geometry -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit/linalg -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit/maths -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit/mpi -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit/option -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/ecmwf-atlas-0.35.0-wp4cu3i/include/atlas_io -I/apps/ops/prod/libs/intel/19.1.3.304/sp/2.3.3/include_d -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/gsl-lite-0.37.0-tgxiry7/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/udunits-2.2.28-ofptt3d/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/odc-1.4.6-z4ps66c/include -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/odc-1.4.6-z4ps66c/include/odc -I/lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eckit-1.24.4-lk2oupj/include/eckit/sql -isystem /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/boost-1.78.0-2nmo377/include -isystem /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/eigen-3.4.0-s5vmmkg/include/eigen3 -isystem /lfs/h1/emc/nceplibs/noscrub/spack-stack/spack-stack-1.5.1/envs/unified-env/install/intel/2022.0.2.262/hdf5-1.14.0-w5vslqn/include -O2 -g -DNDEBUG -fPIE -qopenmp -std=c++17 -MD -MT gdas-utils/soca/CMakeFiles/gdas_incr_handler.x.dir/gdas_incr_handler.cc.o -MF CMakeFiles/gdas_incr_handler.x.dir/gdas_incr_handler.cc.o.d -o CMakeFiles/gdas_incr_handler.x.dir/gdas_incr_handler.cc.o -c /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/gdas-utils/soca/gdas_incr_handler.cc In file included from /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/gdas-utils/soca/gdas_incr_handler.cc(1): /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/gdas-utils/soca/gdas_incr_handler.h(3): catastrophic error: cannot open source file "filesystem"
include
compilation aborted for /u/george.vandenberghe/w/workflow/w0106/sorc/gdas.cd/gdas-utils/soca/gdas_incr_handler.cc (code
This works on jet, gaeaC5, hercules, orion, and hera only failing on Acorn. It cannot be attempted on WCOSS2 of course because of lack of supporting libraries there