#$Id: .palm.config.idefix 4814 2020-12-09 13:08:08Z banzhafs $ #This configuration file is for running jobs locally (interactive or batch mode) #on host idefix. #------------------------------------------------------------------------------- #column 1 column 2 #name of variable value of variable (~ must not be used) #------------------------------------------------------------------------------- %base_directory $HOME/palm/current_version %base_data ~/palm/current_version/JOBS %source_path $HOME/palm/current_version/trunk/SOURCE %user_source_path $base_directory/JOBS/$run_identifier/USER_CODE %fast_io_catalog /work/ %restart_data_path $fast_io_catalog %output_data_path /work//JOBS/ %local_jobcatalog $base_data/$run_identifier/LOG_FILES %remote_jobcatalog $base_data/$run_identifier/LOG_FILES %local_ip 130.75.105.239 %local_username %defaultqueue workq %submit_command /opt/pbspro/default/bin/qsub %compiler_name mpif90 %compiler_name_ser ifort %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 %make_options -j 4 %compiler_options -fpe0 -O3 -cpp -fp-model source -ftz -no-prec-div -no-prec-sqrt -ip -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 %linker_options -fpe0 -O3 -cpp -fp-model source -ftz -no-prec-div -no-prec-sqrt -ip -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 %hostfile auto %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 %execute_command mpirun -machinefile hostfile -n {{mpi_tasks}} palm # BATCH-directives to be used for batch jobs. BD:#!/bin/bash BD:#PBS -N{{run_id}} BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}} BD:#PBS -l ncpus={{cores}} BD:#PBS -o{{job_protocol_file}} BD:#PBS -j oe BD:#PBS -q{{queue}} # BATCH-directives for batch jobs used to send back the jobfile from a remote to a local host BDT:#!/bin/bash BDT:#PBS -N job_protocol_transfer BDT:#PBS -l walltime=00:30:00 BDT:#PBS -l ncpus=1 BDT:#PBS -o{{job_transfer_protocol_file}} BDT:#PBS -j oe BDT:#PBS -q workq #---------------------------------------------------------------------------- # INPUT-commands, executed before running PALM - lines must start with "IC:" #---------------------------------------------------------------------------- IC:export MV2_ENABLE_AFFINITY=0 IC:export MV2_SHOW_CPU_BINDING=1 IC:export MV2_CPU_BINDING_POLICY=scatter IC:ulimit -s unlimited #---------------------------------------------------------------------------- # ERROR-commands - executed when program terminates abnormally #---------------------------------------------------------------------------- EC:[[ \$locat = execution ]] && cat RUN_CONTROL EC:[[ \$locat = execution ]] && cat PARTICLE_INFOS/* #---------------------------------------------------------------------------- # OUTPUT-commands - executed when program terminates normally #---------------------------------------------------------------------------- # Combine 1D- and 3D-profile output (these files are not usable for plotting) OC:[[ -f LIST_PROFIL_1D ]] && cat LIST_PROFIL_1D >> LIST_PROFILE OC:[[ -f LIST_PROFIL ]] && cat LIST_PROFIL >> LIST_PROFILE # Combine all particle information files OC:[[ -f PARTICLE_INFOS/_0000 ]] && cat PARTICLE_INFOS/* >> PARTICLE_INFO