*** palmmrun will be executed. Please wait ... *** INFORMATIVE: additional source code directory "/mnt/lustre/scratch/nlsas/home/otras/oom/rfa/PALM/palm_model_system-v22.04/JOBS/madeira_airport_50m_offline_nesting_2020-07-13/USER_CODE" does not exist or is not a directory. No source code will be used from this directory! #------------------------------------------------------------------------# | palmrun Tue Aug 2 16:23:55 CEST 2022 | | Version: PALM 22.04 | | | | called on: c203-33 | | config. identifier: debug (execute on IP: 127.0.0.1) | | running in: interactive run mode | | number of cores: 50 | | tasks per node: 50 (number of nodes: 1) | | | | cpp directives: -cpp -D__intel_compiler -D__parallel -DMPI_RE | | AL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUB | | LE_PRECISION -D__netcdf -D__fftw -D__rrtmg | | compiler options: -fpp -fpe0 -O0 -check -check nooutput_convers | | ion -traceback -g -I /opt/cesga/2020/software | | /MPI/intel/2021.3.0/impi/2021.3.0/netcdf-fort | | ran/4.5.3/include -I /mnt/netapp1/Optcesga_FT | | 2_RHEL7/2020/gentoo/22072020/usr/include -I / | | mnt/lustre/scratch/nlsas/home/otras/oom/rfa/P | | ALM/palm_model_system-v22.04/rrtmg/include | | linker options: -O3 -fp-model source -fno-alias -fpe0 -ftz -n | | o-prec-div -no-prec-sqrt -ip -nbs -diag-disab | | le 8290,8291 /opt/cesga/2020/software/MPI/int | | el/2021.3.0/impi/2021.3.0/netcdf-fortran/4.5. | | 3/lib/libnetcdff.so /mnt/netapp1/Optcesga_FT2 | | _RHEL7/2020/gentoo/22072020/usr/lib/libfftw3. | | so /mnt/lustre/scratch/nlsas/home/otras/oom/r | | fa/PALM/palm_model_system-v22.04/rrtmg/lib/li | | brrtmg.so | | | | run identifier: madeira_airport_50m_offline_nesting_2020-07-13 | | activation string list: d3# | #------------------------------------------------------------------------# *** creating executable and other sources for the local host *** nothing to compile for this run *** executable and other sources created *** changed to temporary directory: /mnt/lustre/scratch/nlsas/home/otras/oom/rfa/PALM/palm_model_system-v22.04/tmp/madeira_airport_50m_offline_nesting_2020-07-13.28304 *** providing INPUT-files: ---------------------------------------------------------------------------- >>> INPUT: /mnt/lustre/scratch/nlsas/home/otras/oom/rfa/PALM/palm_model_system-v22.04/JOBS/madeira_airport_50m_offline_nesting_2020-07-13/INPUT/madeira_airport_50m_offline_nesting_2020-07-13_p3d to PARIN >>> INPUT: /mnt/lustre/scratch/nlsas/home/otras/oom/rfa/PALM/palm_model_system-v22.04/JOBS/madeira_airport_50m_offline_nesting_2020-07-13/INPUT/madeira_airport_50m_offline_nesting_2020-07-13_static to PIDS_STATIC >>> INPUT: /mnt/lustre/scratch/nlsas/home/otras/oom/rfa/PALM/palm_model_system-v22.04/JOBS/madeira_airport_50m_offline_nesting_2020-07-13/INPUT/madeira_airport_50m_offline_nesting_2020-07-13_dynamic to PIDS_DYNAMIC >>> INPUT: /mnt/lustre/scratch/nlsas/home/otras/oom/rfa/PALM/palm_model_system-v22.04/JOBS/madeira_airport_50m_offline_nesting_2020-07-13/INPUT/madeira_airport_50m_offline_nesting_2020-07-13_rlw to RRTMG_LW >>> INPUT: /mnt/lustre/scratch/nlsas/home/otras/oom/rfa/PALM/palm_model_system-v22.04/JOBS/madeira_airport_50m_offline_nesting_2020-07-13/INPUT/madeira_airport_50m_offline_nesting_2020-07-13_rsw to RRTMG_SW *** INFORMATIVE: some optional INPUT-files are not present ---------------------------------------------------------------------------- *** all INPUT-files provided *** execution of INPUT-commands: ---------------------------------------------------------------------------- >>> ulimit -s unlimited ---------------------------------------------------------------------------- *** execution starts in directory "/mnt/lustre/scratch/nlsas/home/otras/oom/rfa/PALM/palm_model_system-v22.04/tmp/madeira_airport_50m_offline_nesting_2020-07-13.28304" ---------------------------------------------------------------------------- *** execute command: "mpirun -n 50 ./palm" MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found [0] MPI startup(): Intel(R) MPI Library, Version 2021.3 Build 20210601 (id: 6f90181f1) [0] MPI startup(): Copyright (C) 2003-2021 Intel Corporation. All rights reserved. [0] MPI startup(): library kind: release MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found MPI startup(): Warning: I_MPI_PMI_LIBRARY will be ignored since the hydra process manager was found [0] MPI startup(): libfabric version: 1.12.1-impi [0] MPI startup(): libfabric provider: mlx [0] MPI startup(): Load tuning file: "/opt/cesga/2020/software/Compiler/intel/2021.3.0/impi/2021.3.0/mpi/latest/etc/tuning_icx_shm-ofi_mlx.dat" [0] MPI startup(): Rank Pid Node name Pin cpu [0] MPI startup(): 0 1612277 c203-33 0 [0] MPI startup(): 1 1612278 c203-33 1 [0] MPI startup(): 2 1612279 c203-33 2 [0] MPI startup(): 3 1612280 c203-33 3 [0] MPI startup(): 4 1612281 c203-33 4 [0] MPI startup(): 5 1612282 c203-33 5 [0] MPI startup(): 6 1612283 c203-33 6 [0] MPI startup(): 7 1612284 c203-33 7 [0] MPI startup(): 8 1612285 c203-33 8 [0] MPI startup(): 9 1612286 c203-33 9 [0] MPI startup(): 10 1612287 c203-33 10 [0] MPI startup(): 11 1612288 c203-33 11 [0] MPI startup(): 12 1612289 c203-33 12 [0] MPI startup(): 13 1612290 c203-33 13 [0] MPI startup(): 14 1612291 c203-33 14 [0] MPI startup(): 15 1612292 c203-33 15 [0] MPI startup(): 16 1612293 c203-33 16 [0] MPI startup(): 17 1612294 c203-33 17 [0] MPI startup(): 18 1612295 c203-33 18 [0] MPI startup(): 19 1612296 c203-33 19 [0] MPI startup(): 20 1612297 c203-33 20 [0] MPI startup(): 21 1612298 c203-33 21 [0] MPI startup(): 22 1612299 c203-33 22 [0] MPI startup(): 23 1612300 c203-33 23 [0] MPI startup(): 24 1612301 c203-33 24 [0] MPI startup(): 25 1612302 c203-33 25 [0] MPI startup(): 26 1612303 c203-33 26 [0] MPI startup(): 27 1612304 c203-33 27 [0] MPI startup(): 28 1612305 c203-33 28 [0] MPI startup(): 29 1612306 c203-33 29 [0] MPI startup(): 30 1612307 c203-33 30 [0] MPI startup(): 31 1612308 c203-33 31 [0] MPI startup(): 32 1612309 c203-33 32 [0] MPI startup(): 33 1612310 c203-33 33 [0] MPI startup(): 34 1612311 c203-33 34 [0] MPI startup(): 35 1612312 c203-33 35 [0] MPI startup(): 36 1612313 c203-33 36 [0] MPI startup(): 37 1612314 c203-33 37 [0] MPI startup(): 38 1612315 c203-33 38 [0] MPI startup(): 39 1612316 c203-33 39 [0] MPI startup(): 40 1612317 c203-33 40 [0] MPI startup(): 41 1612318 c203-33 41 [0] MPI startup(): 42 1612319 c203-33 42 [0] MPI startup(): 43 1612320 c203-33 43 [0] MPI startup(): 44 1612321 c203-33 44 [0] MPI startup(): 45 1612322 c203-33 45 [0] MPI startup(): 46 1612323 c203-33 46 [0] MPI startup(): 47 1612324 c203-33 47 [0] MPI startup(): 48 1612325 c203-33 48 [0] MPI startup(): 49 1612326 c203-33 49 [0] MPI startup(): I_MPI_LIBRARY_KIND=release_mt [0] MPI startup(): I_MPI_ROOT=/opt/cesga/2020/software/Compiler/intel/2021.3.0/impi/2021.3.0/mpi/latest [0] MPI startup(): I_MPI_MPIRUN=mpirun [0] MPI startup(): I_MPI_HYDRA_TOPOLIB=hwloc [0] MPI startup(): I_MPI_HYDRA_BOOTSTRAP=slurm [0] MPI startup(): I_MPI_INTERNAL_MEM_POLICY=default [0] MPI startup(): I_MPI_DEBUG=5 [0] MPI startup(): I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so 16:24:04 -start---- reading environment parameters from ENVPAR 16:24:04 -finished- reading environment parameters from ENVPAR 16:24:04 -start---- reading NAMELIST parameters from PARIN 16:24:04 -finished- reading NAMELIST parameters from PARIN 16:24:04 -start---- creating virtual PE grids + MPI derived data types +++ warning message --- ID: PA0648 generated by routine: poismg No grid coarsening possible, multigrid approach effectively reduces to a Gauss-Seidel scheme. Further information can be found at http://palm.muk.uni-hannover.de/trac/wiki/doc/app/errmsg#PA0648 16:24:04 -finished- creating virtual PE grids + MPI derived data types 16:24:04 -start---- Setup topography --- informative message --- ID: PA0430 generated by routine: topography_mod Topography was filtered, i.e. holes resolved by only one grid point were filled during initialization. Further information can be found at http://palm.muk.uni-hannover.de/trac/wiki/doc/app/errmsg#PA0430 16:24:16 -finished- Setup topography 16:24:16 -start---- checking parameters 16:24:16 -finished- checking parameters 16:24:16 -start---- model initialization 16:24:22 -start---- initializing surface layer 16:24:22 -finished- initializing surface layer 16:24:28 -finished- model initialization +++ warning message --- ID: PA0773 generated by routine: do_topo_and_surface_setup Topography and surface-setup output requires parallel netCDF. No output file will be created. Further information can be found at http://palm.muk.uni-hannover.de/trac/wiki/doc/app/errmsg#PA0773 forrtl: warning (406): fort: (1): In call to DEFINE_GEO_COORDINATES, an array temporary was created for argument #2 Image PC Routine Line Source palm 00000000044082DF Unknown Unknown Unknown palm 0000000002644060 netcdf_interface_ 2454 netcdf_interface_mod.f90 palm 0000000000AA5958 check_open_ 550 check_open.f90 palm 0000000000E8C1EC data_output_2d_ 196 data_output_2d.f90 palm 000000000286E5B6 MAIN__ 338 palm.f90 palm 00000000004140A2 Unknown Unknown Unknown libc-2.31.so 000014E974DA5CCA __libc_start_main Unknown Unknown palm 0000000000413FAA Unknown Unknown Unknown forrtl: warning (406): fort: (1): In call to DEFINE_GEO_COORDINATES, an array temporary was created for argument #3 Image PC Routine Line Source palm 00000000044082DF Unknown Unknown Unknown palm 0000000002644319 netcdf_interface_ 2454 netcdf_interface_mod.f90 palm 0000000000AA5958 check_open_ 550 check_open.f90 palm 0000000000E8C1EC data_output_2d_ 196 data_output_2d.f90 palm 000000000286E5B6 MAIN__ 338 palm.f90 palm 00000000004140A2 Unknown Unknown Unknown libc-2.31.so 000014E974DA5CCA __libc_start_main Unknown Unknown palm 0000000000413FAA Unknown Unknown Unknown forrtl: warning (406): fort: (1): In call to DEFINE_GEO_COORDINATES, an array temporary was created for argument #2 Image PC Routine Line Source palm 00000000044082DF Unknown Unknown Unknown palm 0000000002664A7B netcdf_interface_ 3334 netcdf_interface_mod.f90 palm 0000000000AA6486 check_open_ 611 check_open.f90 palm 0000000000E8D985 data_output_2d_ 226 data_output_2d.f90 palm 000000000286E5D8 MAIN__ 339 palm.f90 palm 00000000004140A2 Unknown Unknown Unknown libc-2.31.so 000014E974DA5CCA __libc_start_main Unknown Unknown palm 0000000000413FAA Unknown Unknown Unknown forrtl: warning (406): fort: (1): In call to DEFINE_GEO_COORDINATES, an array temporary was created for argument #3 Image PC Routine Line Source palm 00000000044082DF Unknown Unknown Unknown palm 0000000002664D34 netcdf_interface_ 3334 netcdf_interface_mod.f90 palm 0000000000AA6486 check_open_ 611 check_open.f90 palm 0000000000E8D985 data_output_2d_ 226 data_output_2d.f90 palm 000000000286E5D8 MAIN__ 339 palm.f90 palm 00000000004140A2 Unknown Unknown Unknown libc-2.31.so 000014E974DA5CCA __libc_start_main Unknown Unknown palm 0000000000413FAA Unknown Unknown Unknown forrtl: warning (406): fort: (1): In call to DEFINE_GEO_COORDINATES, an array temporary was created for argument #2 Image PC Routine Line Source palm 00000000044082DF Unknown Unknown Unknown palm 0000000002683D2D netcdf_interface_ 4151 netcdf_interface_mod.f90 palm 0000000000AA6FB4 check_open_ 672 check_open.f90 palm 0000000000E8F131 data_output_2d_ 257 data_output_2d.f90 palm 000000000286E5FA MAIN__ 340 palm.f90 palm 00000000004140A2 Unknown Unknown Unknown libc-2.31.so 000014E974DA5CCA __libc_start_main Unknown Unknown palm 0000000000413FAA Unknown Unknown Unknown forrtl: warning (406): fort: (1): In call to DEFINE_GEO_COORDINATES, an array temporary was created for argument #3 Image PC Routine Line Source palm 00000000044082DF Unknown Unknown Unknown palm 0000000002683FE6 netcdf_interface_ 4151 netcdf_interface_mod.f90 palm 0000000000AA6FB4 check_open_ 672 check_open.f90 palm 0000000000E8F131 data_output_2d_ 257 data_output_2d.f90 palm 000000000286E5FA MAIN__ 340 palm.f90 palm 00000000004140A2 Unknown Unknown Unknown libc-2.31.so 000014E974DA5CCA __libc_start_main Unknown Unknown palm 0000000000413FAA Unknown Unknown Unknown forrtl: warning (406): fort: (1): In call to DEFINE_GEO_COORDINATES, an array temporary was created for argument #2 Image PC Routine Line Source palm 00000000044082DF Unknown Unknown Unknown palm 000000000261EB9D netcdf_interface_ 1444 netcdf_interface_mod.f90 palm 0000000000AA81FA check_open_ 811 check_open.f90 palm 0000000000F2C4E2 data_output_3d_ 143 data_output_3d.f90 palm 000000000286E61B MAIN__ 346 palm.f90 palm 00000000004140A2 Unknown Unknown Unknown libc-2.31.so 000014E974DA5CCA __libc_start_main Unknown Unknown palm 0000000000413FAA Unknown Unknown Unknown forrtl: warning (406): fort: (1): In call to DEFINE_GEO_COORDINATES, an array temporary was created for argument #3 Image PC Routine Line Source palm 00000000044082DF Unknown Unknown Unknown palm 000000000261EE56 netcdf_interface_ 1444 netcdf_interface_mod.f90 palm 0000000000AA81FA check_open_ 811 check_open.f90 palm 0000000000F2C4E2 data_output_3d_ 143 data_output_3d.f90 palm 000000000286E61B MAIN__ 346 palm.f90 palm 00000000004140A2 Unknown Unknown Unknown libc-2.31.so 000014E974DA5CCA __libc_start_main Unknown Unknown palm 0000000000413FAA Unknown Unknown Unknown 16:24:35 -start---- time-stepping srun: Job step aborted: Waiting up to 32 seconds for job step to finish. slurmstepd: error: *** STEP 446161.0 ON ilk-129 CANCELLED AT 2022-08-02T16:25:50 ***