################################################################################ # This is a configuration file for PALM. It must be named: .palm.config. # in order to use it, call palmbuild and palmrun with the option: -h # Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/jobcontrol ################################################################################ # #------------------------------------------------------------------------------- # General compiler and host configuration section. # Variable declaration lines must start with a percent character # Internal variables can be used as {{VARIABLE_NAME}}. Please see documentation. #------------------------------------------------------------------------------- # working directory from where palmrun or palmbuild are called %base_directory /glade/work/sreenath/palm/current_version # directory where PALM I/O is stored (used in .palm.iofiles) %base_data /glade/work/sreenath/palm/current_version/JOBS # path to PALM's FORTRAN sources (installation folder) %source_path /glade/work/sreenath/palm/current_version/palm_model_system/packages/palm/model/src # path to user interface routines %user_source_path /glade/work/sreenath/palm/current_version/JOBS/$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 /glade/scratch/sreenath/palm/current_version/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 /glade/scratch/sreenath/palm/current_version/JOBS # folder for job protocols %local_jobcatalog /glade/work/sreenath/palm/current_version/job_logfiles # folder for job protocols to be used on the remote host #%remote_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 127.0.0.1 %local_hostname $HOST # your local UNIX username %local_username $USER # ip address of the remote host #%remote_ip #%remote_hostname # name of login-node on the remote machine #%remote_loginnode # 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 # default queue to be used if palmrun-option -q is omitted %defaultqueue regular # command to submit batch jobs %submit_command /opt/pbs/bin/qsub # 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 # # compilername to generate MPI executables %compiler_name mpif90 #/glade/u/apps/ch/opt/mpt/2.23/bin/mpif90 # compilername to generate non-MPI executables running on one core %compiler_name_ser mpif90 #/glade/u/apps/ch/opt/ncarcompilers/0.5.0/intel/18.0.5/mpi/mpif90 # preprocessor directives to be used for compiling the PALM code %cpp_options -cpp -D__intel_compiler -D__parallel -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -D__netcdf -D__fftw -D__rrtmg -D__netcdf4 -D__netcdf4_parallel # used for parallel compilation %make_options -j 4 # options to be used to compile PALM %compiler_options -O3 -fp-model source -fno-alias -fpe0 -ftz -no-prec-div -fPIC -no-prec-sqrt -ip -nbs -diag-disable 8290,8291 -I/glade/u/apps/ch/opt/mpt/2.21/include -I/glade/u/apps/ch/opt/netcdf-mpi/4.7.3/mpt/2.21/intel/18.0.5/include -I/glade/u/apps/ch/opt/fftw-mpi/3.3.8/mpt/2.21/intel/18.0.5/include -I/glade/work/sreenath/palm/current_version/rrtmg/include # options to be used to link the PALM executable %linker_options -O3 -fp-model source -fno-alias -fpe0 -ftz -no-prec-div -fPIC -no-prec-sqrt -ip -nbs -diag-disable 8290,8291 -L/glade/u/apps/ch/opt/mpt/2.21/lib -L/glade/u/apps/ch/opt/netcdf-mpi/4.7.3/mpt/2.21/intel/18.0.5/lib -L/glade/u/apps/ch/opt/fftw-mpi/3.3.8/mpt/2.21/intel/18.0.5/lib /glade/work/sreenath/palm/current_version/rrtmg/lib/librrtmg.so -lnetcdf -lnetcdff -lfftw3 -lsz -lhdf5_hl -lhdf5 -lm -lz # name of hostfile to be used (see online documentation for more details) %hostfile auto # command to start the PALM executable %execute_command mpiexec_mpt -n {{mpi_tasks}} ./palm #%execute_command_for_combine mpiexec_mpt -n 1 ./combine_plot_fields.x # memory request per core %memory 2300 # module commands to load required libraries %module_commands module purge; module load ncarenv/1.3 intel/18.0.5 mpt/2.21 ncarcompilers/0.5.0 netcdf-mpi/4.7.3 fftw-mpi/3.3.8 # 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. #------------------------------------------------------------------------------- BD:#!/bin/bash BD:#PBS -N {{job_id}} BD:#PBS -A UWIS0030 BD:#PBS -l walltime={{cpu_hours}}:{{cpu_minutes}}:{{cpu_seconds}} BD:#PBS -l select={{nodes}}:ncpus={{tasks_per_node}}:mpiprocs={{tasks_per_node}} BD:#PBS -o {{job_protocol_file}} BD:#PBS -m abe BD:#PBS -M paleri@wisc.edu BD:#PBS -j oe BD:#PBS -q {{queue}} BD:source /etc/profile.d/modules.sh # #------------------------------------------------------------------------------- # 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. #------------------------------------------------------------------------------- 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 # #------------------------------------------------------------------------------- # INPUT-commands. These commands are executed before running PALM # Lines must start with "IC:" #------------------------------------------------------------------------------- IC:ulimit -s unlimited IC:export MPI_TYPE_DEPTH=16 IC:mkdir -p BINOUT IC:mkdir -p BINOUT_N02 # #------------------------------------------------------------------------------- # ERROR-commands. These commands are executed when PALM terminates abnormally # Lines must start with "EC:" #------------------------------------------------------------------------------- EC:[[ $locat = execution ]] && cat RUN_CONTROL # #------------------------------------------------------------------------------- # OUTPUT-commands. These commands are executed when PALM terminates normally # Lines must start with "OC:" #------------------------------------------------------------------------------- # # 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