| 1 | #$Id: .palm.config.idefix 2834 2018-02-23 14:04:07Z scharf $ |
|---|
| 2 | #This configuration file is for running jobs locally (interactive or batch mode) |
|---|
| 3 | #on host idefix. |
|---|
| 4 | #------------------------------------------------------------------------------- |
|---|
| 5 | #column 1 column 2 |
|---|
| 6 | #name of variable value of variable (~ must not be used) |
|---|
| 7 | #------------------------------------------------------------------------------- |
|---|
| 8 | %base_data ~/palm/current_version/JOBS |
|---|
| 9 | %base_directory $HOME/palm/current_version |
|---|
| 10 | %fast_io_catalog /work/<replace_by_your_IDEFIX_username> |
|---|
| 11 | %local_jobcatalog $HOME/job_queue |
|---|
| 12 | %output_path /work/<replace_by_your_IDEFIX_username>/JOBS/$jobname |
|---|
| 13 | %remote_jobcatalog $HOME/job_queue |
|---|
| 14 | %source_path $HOME/palm/current_version/trunk/SOURCE |
|---|
| 15 | %user_source_path $base_directory/JOBS/$jobname/USER_CODE |
|---|
| 16 | # |
|---|
| 17 | %local_ip 130.75.105.239 |
|---|
| 18 | %local_username <replace_by_your_IDEFIX_username> |
|---|
| 19 | %defaultqueue workq |
|---|
| 20 | %submit_command /opt/pbspro/default/bin/qsub |
|---|
| 21 | # |
|---|
| 22 | %compiler_name mpif90 |
|---|
| 23 | %compiler_name_ser ifort |
|---|
| 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 |
|---|
| 25 | %make_options -j 4 |
|---|
| 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 |
|---|
| 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 |
|---|
| 28 | %hostfile auto |
|---|
| 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 |
|---|
| 30 | # |
|---|
| 31 | %execute_command mpirun -machinefile hostfile -n {{mpi_tasks}} palm |
|---|
| 32 | # |
|---|
| 33 | # |
|---|
| 34 | # BATCH-directives to be used for batch jobs. |
|---|
| 35 | BD:#!/bin/bash |
|---|
| 36 | BD:#PBS -N{{job_id}} |
|---|
| 37 | BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}} |
|---|
| 38 | BD:#PBS -l ncpus={{cores}} |
|---|
| 39 | BD:#PBS -o{{job_protocol_file}} |
|---|
| 40 | BD:#PBS -j oe |
|---|
| 41 | BD:#PBS -q{{queue}} |
|---|
| 42 | # |
|---|
| 43 | # BATCH-directives for batch jobs used to send back the jobfile from a remote to a local host |
|---|
| 44 | BDT:#!/bin/bash |
|---|
| 45 | BDT:#PBS -N job_protocol_transfer |
|---|
| 46 | BDT:#PBS -l walltime=00:30:00 |
|---|
| 47 | BDT:#PBS -l ncpus=1 |
|---|
| 48 | BDT:#PBS -o{{job_transfer_protocol_file}} |
|---|
| 49 | BDT:#PBS -j oe |
|---|
| 50 | BDT:#PBS -q workq |
|---|
| 51 | # |
|---|
| 52 | # |
|---|
| 53 | #---------------------------------------------------------------------------- |
|---|
| 54 | # INPUT-commands, executed before running PALM - lines must start with "IC:" |
|---|
| 55 | #---------------------------------------------------------------------------- |
|---|
| 56 | IC:export MV2_ENABLE_AFFINITY=0 |
|---|
| 57 | IC:export MV2_SHOW_CPU_BINDING=1 |
|---|
| 58 | IC:export MV2_CPU_BINDING_POLICY=scatter |
|---|
| 59 | IC:ulimit -s unlimited |
|---|
| 60 | # |
|---|
| 61 | #---------------------------------------------------------------------------- |
|---|
| 62 | # ERROR-commands - executed when program terminates abnormally |
|---|
| 63 | #---------------------------------------------------------------------------- |
|---|
| 64 | EC:[[ \$locat = execution ]] && cat RUN_CONTROL |
|---|
| 65 | EC:[[ \$locat = execution ]] && cat PARTICLE_INFOS/* |
|---|
| 66 | # |
|---|
| 67 | #---------------------------------------------------------------------------- |
|---|
| 68 | # OUTPUT-commands - executed when program terminates normally |
|---|
| 69 | #---------------------------------------------------------------------------- |
|---|
| 70 | # |
|---|
| 71 | # Combine 1D- and 3D-profile output (these files are not usable for plotting) |
|---|
| 72 | OC:[[ -f LIST_PROFIL_1D ]] && cat LIST_PROFIL_1D >> LIST_PROFILE |
|---|
| 73 | OC:[[ -f LIST_PROFIL ]] && cat LIST_PROFIL >> LIST_PROFILE |
|---|
| 74 | # |
|---|
| 75 | # Combine all particle information files |
|---|
| 76 | OC:[[ -f PARTICLE_INFOS/_0000 ]] && cat PARTICLE_INFOS/* >> PARTICLE_INFO |
|---|
