#$Id: .palm.config.default 4814 2020-12-09 13:08:08Z suehring $ #column 1 column 2 #name of variable value of variable (~ must not be used except for base_data) #----------------------------------------------------------------------------- # working directory from where palmrun or palmbuild are called %base_directory $HOME/palm/current_version # directory where PALM I/O is stored (used in .palm.iofiles) %base_data ~/palm/current_version/JOBS # path to PALM's FORTRAN sources (installation folder) %source_path $base_directory/trunk/SOURCE # path to user interface routines %user_source_path $base_data/$run_identifier/USER_CODE # path to temporary working directory. This folder contains the files # temporarily created by PALM during execution. # WARNING: # Large I/O files are generated during execution! It is recommended to direct # this path to a file system with fast discs (if available). This folder must # be accessible from all compute nodes, i.e. it must reside in a global file # system. %fast_io_catalog $base_directory/tmp # directory where PALM restart files are stored. It is recommended to set this # path to the same file system as the temporary directory (fast_io_catalog) to # allow internal linking of the restart files instead of copying (increases # post-processing performance of palmrun). %restart_data_path $fast_io_catalog # directory where PALM output files are stored (see also .palm.iofiles) %output_data_path $base_data # folder for job protocols %local_jobcatalog $base_data/$run_identifier/LOG_FILES # folder for job protocols to be used on the remote host #%remote_jobcatalog $local_jobcatalog # local ip of your computer. Use 127.0.0.0 if you are running PALM # in interactive mode on your local computer %local_ip # your local UNIX username %local_username # ip address of the remote host #%remote_ip # username on the remote host #%remote_username # ssh-key to be used for ssh/scp calls to the remote host #%ssh_key ~/.ssh/id_rsa # name of login-node on the remote machine #%remote_loginnode # default queue to be used if palmrun-option -q is omitted #%defaultqueue # default project account to be used if palmrun-option -A is omitted. For this # setting to be active, the batch directive must also be activated (see BD and # BDT settings below). #%project_account # command to submit batch jobs #%submit_command /opt/moab/default/bin/msub -E # compilername to generate MPI executables %compiler_name mpif90 # compilername to generate non-MPI executables running on one core %compiler_name_ser ifort # preprocessor directives to be used for compiling the PALM code %cpp_options -cpp -D__parallel -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__fftw -D__netcdf # used for parallel compilation %make_options -j 4 # options to be used to compile PALM %compiler_options -fpe0 -O3 -xHost -fp-model source -ftz -no-prec-div -no-prec-sqrt -ip -I /path/to/fftw/include -I /path/to/netcdf/include # options to be used to link the PALM executable %linker_options -L/path/to/fftw/lib -lfftw3 -L/path/to/netcdf/lib -lnetcdf -lnetcdff # name of hostfile to be used (see online documentation for more details) #%hostfile auto # command to start the PALM executable %execute_command mpirun -n {{mpi_tasks}} ./palm # memory request per core #%memory 2300 # module commands to load required libraries #%module_commands module switch env-ivybridge env-haswell && module load fftw netcdf # special commands to be carried out at login and start of batch jobs on the remote host #%login_init_cmd .execute_special_profile #------------------------------------------------------------------------------- # Directives to be used for batch jobs # Lines must start with "BD:". If $-characters are required, hide them with \ # Internal variables can be used as {{variable_name}}. Please see documentation. #------------------------------------------------------------------------------- # Example using PBS: BD:#!/bin/bash #BD:#PBS -A {{project_account}} BD:#PBS -N {{run_id}} BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}} BD:#PBS -l nodes={{nodes}}:ppn={{tasks_per_node}} BD:#PBS -o {{job_protocol_file}} BD:#PBS -j oe BD:#PBS -q {{queue}} # # Example using SLURM: #BD:#!/bin/bash ##BD:#SBATCH --dependency=afterany:{{previous_job}} #BD:#SBATCH -A {{project_account}} #BD:#SBATCH --job-name={{run_id}} #BD:#SBATCH --time={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}} #BD:#SBATCH --ntasks={{mpi_tasks}} #BD:#SBATCH --nodes={{nodes}} #BD:#SBATCH --ntasks-per-node={{tasks_per_node}} #BD:#SBATCH --partition={{queue}} #BD:#SBATCH --output={{job_protocol_file}} #BD:#SBATCH --error={{job_protocol_file}} #BD:#SBATCH --mail-type=ALL #BD:#SBATCH --mail-user=user@somewhere #------------------------------------------------------------------------------- # Directives for batch jobs used to send back the jobfiles from a remote to a local host # Lines must start with "BDT:". If $-characters are required, excape them with triple backslash # Internal variables can be used as {{variable_name}}. Please see documentation. #------------------------------------------------------------------------------- # Example using PBS: BDT:#!/bin/bash #BDT:#PBS -A {{project_account}} BDT:#PBS -N job_protocol_transfer BDT:#PBS -l walltime=00:30:00 BDT:#PBS -l nodes=1:ppn=1 BDT:#PBS -o {{job_transfer_protocol_file}} BDT:#PBS -j oe BDT:#PBS -q dataq # # Example using SLURM: #BDT:#!/bin/bash #BDT:#SBATCH -A {{project_account}} #BDT:#SBATCH --job-name=job_transfer #BDT:#SBATCH --time=00:30:00 #BDT:#SBATCH --ntasks=1 #BDT:#SBATCH --nodes=1 #BDT:#SBATCH --ntasks-per-node=1 #BDT:#SBATCH --partition={{queue}} #BDT:#SBATCH --output={{job_transfer_protocol_file}} #BDT:#SBATCH --error={{job_transfer_protocol_file}} #---------------------------------------------------------------------------- # INPUT-commands, executed before running PALM - lines must start with "IC:" #---------------------------------------------------------------------------- #IC:ulimit -s unlimited # #---------------------------------------------------------------------------- # ERROR-commands - executed when program terminates abnormally #---------------------------------------------------------------------------- #EC:[[ \$locat = execution ]] && cat RUN_CONTROL # #---------------------------------------------------------------------------- # OUTPUT-commands - executed when program terminates normally #---------------------------------------------------------------------------- #OC:echo \\\"PALM job finished\\\" | mailx user@somewhere