| 1 | #$Id: .palm.config.idefix 2554 2017-10-18 08:06:07Z basit $ |
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| 2 | #This configuration file is for running jobs locally (interactive or batch mode) |
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| 3 | #on host idefix. |
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| 4 | #------------------------------------------------------------------------------- |
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| 5 | #column 1 column 2 |
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| 6 | #name of variable value of variable (~ must not be used) |
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| 7 | #------------------------------------------------------------------------------- |
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| 8 | %base_data ~/palm/current_version/JOBS |
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| 9 | %base_directory $HOME/palm/current_version |
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| 10 | %fast_io_catalog /work/<replace_by_your_IDEFIX_username> |
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| 11 | %local_jobcatalog $HOME/job_queue |
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| 12 | %output_path /work/<replace_by_your_IDEFIX_username>/JOBS/$fname |
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| 13 | %remote_jobcatalog $HOME/job_queue |
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| 14 | %source_path $HOME/palm/current_version/trunk/SOURCE |
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| 15 | %user_source_path $base_directory/JOBS/$fname/USER_CODE |
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| 16 | # |
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| 17 | %local_ip 130.75.105.239 |
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| 18 | %local_username <replace_by_your_IDEFIX_username> |
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| 19 | %defaultqueue workq |
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| 20 | %submit_command /opt/pbspro/default/bin/qsub |
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| 21 | # |
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| 22 | %compiler_name mpif90 |
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| 23 | %compiler_name_ser ifort |
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| 24 | %cpp_options -cpp -D__parallel -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__netcdf -D__netcdf4 -D__netcdf4_parallel -D__fftw -D__intel_compiler |
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| 25 | %make_options -j 4 |
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| 26 | %compiler_options -fpe0 -O3 -cpp -fp-model source -ftz -fno-alias -no-prec-div -no-prec-sqrt -ip -nbs -diag-disable 8290,8291 -I /opt/netcdf4_hdf5parallel/4411c_443f/intel/include -L/opt/netcdf4_hdf5parallel/4411c_443f/intel/lib -L/opt/hdf5-parallel/1.10.0-patch1/intel/lib -lnetcdf -lnetcdff -I /opt/fftw/3.3.6-pl1/mvapich2-intel/include -L/opt/fftw/3.3.6-pl1/mvapich2-intel/lib -lfftw3 |
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| 27 | %linker_options -fpe0 -O3 -cpp -fp-model source -ftz -fno-alias -no-prec-div -no-prec-sqrt -ip -nbs -diag-disable 8290,829 -I /opt/netcdf4_hdf5parallel/4411c_443f/intel/include -L/opt/netcdf4_hdf5parallel/4411c_443f/intel/lib -L/opt/hdf5-parallel/1.10.0-patch1/intel/lib -lnetcdf -lnetcdff -I /opt/fftw/3.3.6-pl1/mvapich2-intel/include -L/opt/fftw/3.3.6-pl1/mvapich2-intel/lib -lfftw3 |
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| 28 | %hostfile auto |
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| 29 | %module_commands module load intel-compiler/2017.1.132 mvapich2/2.2/intel fftw/3.3.6-pl1/mvapich2-intel hdf5-parallel/1.10.0-patch1/intel netcdf4_hdf5parallel/4411c_443f/intel |
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| 30 | # |
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| 31 | %execute_command mpirun -machinefile hostfile -n {{MPI_TASKS}} palm |
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| 32 | # |
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| 33 | # |
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| 34 | # BATCH-directives to be used for batch jobs. |
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| 35 | BD:#!/bin/bash |
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| 36 | BD:#PBS -N{{JOB_ID}} |
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| 37 | BD:#PBS -l walltime={{CPU_HOURS}}:{{CPU_MINUTES}}:{{CPU_SECONDS}} |
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| 38 | BD:#PBS -l ncpus={{CORES}} |
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| 39 | BD:#PBS -o{{JOBFILE}} |
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| 40 | BD:#PBS -j oe |
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| 41 | BD:#PBS -q{{QUEUE}} |
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| 42 | # |
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| 43 | # BATCH-directives for batch jobs used to send back the jobfile from a remote to a local host |
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| 44 | BDT:#!/bin/bash |
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| 45 | BDT:#PBS -N job_protocol_transfer |
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| 46 | BDT:#PBS -l walltime=00:30:00 |
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| 47 | BDT:#PBS -l ncpus=1 |
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| 48 | BDT:#PBS -o{{JOB_TRANSFER_PROTOCOL_FILE}} |
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| 49 | BDT:#PBS -j oe |
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| 50 | BDT:#PBS -q workq |
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| 51 | # |
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| 52 | # |
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| 53 | #---------------------------------------------------------------------------- |
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| 54 | # INPUT-commands, executed before running PALM - lines must start with "IC:" |
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| 55 | #---------------------------------------------------------------------------- |
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| 56 | IC:export MV2_ENABLE_AFFINITY=0 |
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| 57 | IC:export MV2_SHOW_CPU_BINDING=1 |
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| 58 | IC:export MV2_CPU_BINDING_POLICY=scatter |
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| 59 | IC:ulimit -s unlimited |
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| 60 | # |
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| 61 | #---------------------------------------------------------------------------- |
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| 62 | # ERROR-commands - executed when program terminates abnormally |
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| 63 | #---------------------------------------------------------------------------- |
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| 64 | EC:[[ \$locat = execution ]] && cat RUN_CONTROL |
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| 65 | EC:[[ \$locat = execution ]] && cat PARTICLE_INFOS/* |
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| 66 | # |
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| 67 | #---------------------------------------------------------------------------- |
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| 68 | # OUTPUT-commands - executed when program terminates normally |
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| 69 | #---------------------------------------------------------------------------- |
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| 70 | # |
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| 71 | # Combine 1D- and 3D-profile output (these files are not usable for plotting) |
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| 72 | OC:[[ -f LIST_PROFIL_1D ]] && cat LIST_PROFIL_1D >> LIST_PROFILE |
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| 73 | OC:[[ -f LIST_PROFIL ]] && cat LIST_PROFIL >> LIST_PROFILE |
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| 74 | # |
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| 75 | # Combine all particle information files |
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| 76 | OC:[[ -f PARTICLE_INFOS/_0000 ]] && cat PARTICLE_INFOS/* >> PARTICLE_INFO |
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