| 1 | #$Id: .palm.config.aurora 4370 2020-01-10 14:00:44Z moh.hefny $ |
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| 2 | #column 1 column 2 |
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| 3 | #name of variable value of variable (~ must not be used) |
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| 4 | #---------------------------------------------------------------------------- |
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| 5 | %base_data ~/palm/current_version/JOBS |
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| 6 | %base_directory $HOME/palm/current_version |
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| 7 | %fast_io_catalog /scratch/<replace by LUIS username> |
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| 8 | %source_path $HOME/palm/current_version/trunk/SOURCE |
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| 9 | %user_source_path $base_directory/JOBS/$run_identifier/USER_CODE |
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| 10 | %local_jobcatalog $HOME/job_queue |
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| 11 | # |
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| 12 | %local_ip 130.75.7.130 |
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| 13 | %local_username <replace by LUIS username> |
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| 14 | %compiler_name mpinfort |
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| 15 | %compiler_name_ser mpinfort |
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| 16 | %cpp_options -fpp -D__parallel -D__nec -D__netcdf -D__netcdf4 -D__netcdf4_parallel -D__fftw -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION |
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| 17 | %make_options -j 4 |
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| 18 | %compiler_options -O3 -traceback -finline-functions -g -report-all -Werror -I /home/nhbkklau/opt/NetCDF_parallel_nec/include -I /home/nhbkklau/opt/fftw3_nec/include |
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| 19 | %linker_options -L/home/nhbkklau/opt/NetCDF_parallel_nec/lib -lnetcdff -lnetcdf -Wl,-rpath=/home/nhbkklau/opt/NetCDF_parallel_nec/lib -L/home/nhbkklau/opt/hdf5_parallel_nec/lib -lhdf5 -lhdf5_hl -Wl,-rpath=/home/nhbkklau/opt/hdf5_parallel_nec/lib -L/home/nhbkklau/opt/fftw3_nec/lib -lfftw3 -lmpi |
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| 20 | #%hostfile auto |
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| 21 | %defaultqueue all |
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| 22 | %submit_command /usr/bin/qsub |
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| 23 | %memory 2000 |
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| 24 | %login_init_cmd source /opt/nec/ve/mpi/2.2.0/bin/necmpivars.sh |
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| 25 | %execute_command mpirun -v -ve 0-3 -np {{mpi_tasks}} ./palm |
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| 26 | # |
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| 27 | #---------------------------------------------------------------------------- |
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| 28 | # INPUT-commands, executed before running PALM - lines must start with "IC:" |
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| 29 | #---------------------------------------------------------------------------- |
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| 30 | #IC:ulimit -s unlimited |
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| 31 | # |
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| 32 | #---------------------------------------------------------------------------- |
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| 33 | # ERROR-commands - executed when program terminates abnormally |
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| 34 | #---------------------------------------------------------------------------- |
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| 35 | EC:[[ \$locat = execution ]] && cat RUN_CONTROL |
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| 36 | EC:[[ \$locat = execution ]] && cat PARTICLE_INFOS/* |
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| 37 | # |
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| 38 | #---------------------------------------------------------------------------- |
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| 39 | # OUTPUT-commands - executed when program terminates normally |
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| 40 | #---------------------------------------------------------------------------- |
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| 41 | # |
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| 42 | # Combine 1D- and 3D-profile output (these files are not usable for plotting) |
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| 43 | OC:[[ -f LIST_PROFIL_1D ]] && cat LIST_PROFIL_1D >> LIST_PROFILE |
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| 44 | OC:[[ -f LIST_PROFIL ]] && cat LIST_PROFIL >> LIST_PROFILE |
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| 45 | # |
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| 46 | # Combine all particle information files |
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| 47 | OC:[[ -f PARTICLE_INFOS/_0000 ]] && cat PARTICLE_INFOS/* >> PARTICLE_INFO |
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| 48 | # |
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| 49 | # BATCH-directives to be used for batch jobs. |
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| 50 | # ATTENTION: The batch following batch directives still need to be adjusted for the |
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| 51 | # NEC Aurora system!!!!!!!!!!!!!! |
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| 52 | BD:#!/bin/bash |
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| 53 | BD:#PBS -N {{run_id}} |
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| 54 | BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}} |
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| 55 | BD:#PBS -l ncpus={{cores}} |
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| 56 | BD:#PBS -l nodes={{nodes}}:ppn={{tasks_per_node}} |
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| 57 | BD:#PBS -l mem={{memory}}mb |
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| 58 | BD:#PBS -W x=PARTITION:lena |
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| 59 | BD:#PBS -o {{job_protocol_file}} |
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| 60 | BD:#PBS -j oe |
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| 61 | BD:#PBS -q {{queue}} |
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