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The PALM configuration file
Running PALM with the palmrun script or compiling PALM with palmbuild requires a configuration file in the working directory from where the scripts are called. The configuration file contains information about
- the compiler and compiler options to be used
- paths to required libraries (e.g. MPI, netCDF, or fftw)
- preprocessor directives to switch on/off special features of PALM
- paths to be used for storing PALM's input and output files
- paths where user-interface routines and job protocol files can be found
- the execute command to be used for starting the PALM executable
- settings of other UNIX environment variable
- batch job directives
- unix commands to be executed before / after the PALM code is started, or that should be carried out in case of errors that appeared during the run
If PALM has been successfully installed by the automatic installer, the installer creates a configuration file named .palm.config.default in the working directory of the user (which by default is assumed to be $HOME/palm/current_version). This file should contain all relevant information to run PALM on the respective computer.
The installer may fail for various reasons, e.g. because of mismatches in the user's system configuration. Problems may appear if the user has installed more than one FORTRAN compiler, and/or if the netCDF libraries have been generated with a different compiler than is used for compiling PALM. Furthermore, the automatic installer cannot be used on many larger computer systems where software (compilers, libraries) is managed via the module environment, or if you like to run batch jobs an a remote host. In all these cases, the user has to setup the configuration file manually.
How to generate a configuration file manually
As a first step, copy the default template of the configuration file (which is part of the PALM download) to your working directory:
cd $HOME/palm/current_version cp trunk/SCRIPTS/.palm.config.default .
Configuration file format
The configuration file is an ASCII file which may be opened with any editor. The format of the file is simple:
- lines starting with a # in the first column are comment lines
# this is a comment line
- lines starting with a % in the first column are defining unix environment variables used in palmrun and palmbuild.
%var value of var
means that a variable named var with value value of var is created. There must be at least one blank between the variable name and its value. The value may contain an arbitrary number of blanks. The value can contain already defined variables:%default_folder /work/abcd %subfolder1 $default_folder/efgh
which means that subfolder1 has the value /work/abcd/efgh. You can also use any variables that are already defined within the palmrun/palmbuild scripts. The most important one is jobname, which value is given with palmrun option -d, and which defines the so-called jobname. This variable is mentioned here because it is used in the default configuration files for naming I/O files and to better sort I/O files from different PALM runs in an organized folder structure. Beside the value replacement using the UNIX shell syntax (i.e. $abcd gives the value of variable abcd), another way to insert values of environment variables is to write them in double curly brackets, i.e. {{abcd}} will be replaced by the value of abce. This way of variable replacement is required for some special variables and in the job directives.
- lines starting with IC: define any unix commands that are executed by palmrun just before the PALM code is started. A typical input command might be
IC:ulimit -s unlimited
to increase the system's stack size (if this is not unlimited by default), which is required for PALM runs with larger memory demands.
- lines starting with OC: define unix commands that are executed by palmrun just after the PALM code has stopped. For example, you may inform yourself about termination of the program by sending an email:
OC:echo "PALM simulation $jobname has finished" | mailx username@email-address
- lines starting with EC: define unix commands that shall be executed in case that the PALM code or the palmrun script terminated because of any kind of error. You can restrict execution of error commands to specific kinds of error:
EC:[[ ]] && error-command
- lines starting with BD: define directives that are required for batch jobs, i.e. if PALM shall be run in batch mode. Explanations for batch directives are given further below.
- lines starting with BDT: define directives for an additional batch job that is required in case of running PALM in batch mode on a remote host. This additional job transfers the job protocol file of the main PALM job back to the local host.
environment variables and their meaning
The default template contains settings for the minimum set of variables that always need to be defined, plus suggestions for other variables that you may need to uncomment, in case that you like/need to use them. The following table lists all relevant variables and their meaning. Default values are either those which are set in the scripts palmrun and palmbuild or which are suggested in the template file.
| Variable name | meaning | default value |
|---|---|---|
| base_directory | Working directory from where palmrun or palmbuild is called. This folder must contain the configuration file .palm.config..... | $HOME/palm/current_version |
| base_data | Directory where the PALM I/O-files are stored. This variable is used in the file configuration file (see .palm.iofiles, and the description of this file). Since this variable is also used to determine file locations on remote hosts, it must use the ~ instead of $HOME. | ~/palm/current_version/JOBS |
| source_path | Path to PALM's FORTRAN source files. This is the place where the automatic installer has put the download, or which has been defined in the user's svn checkout command. | $HOME/palm/current_version/trunk/SOURCE |
| user_source_path | Path to the user interface routines. The variable jobname that is used in the default path is replaced by the argument given with palmrun-option -d. | $base_directory/JOBS/$jobname/USER_CODE |
# path to file system with fast discs (if available). This folder # is used for temporary catalogs generated by palmrun and to store large # I/O files (used in .palm.iofiles). This folder must be accessible from # all compute nodes, i.e. it must reside in a global file system %fast_io_catalog <replace by a folder name which allows for fast I/O>
# folder for job protocols #%local_jobcatalog $HOME/job_queue
# folder for job protocols to be used on the remote host #%remote_jobcatalog <path/to/directory on remote host>
# local ip of your computer. Use 127.0.0.0 if you are running PALM # in interactive mode on your local computer %local_ip <replace by your computers IP address>
# your local UNIX username %local_username <replace by your unix username>
# ip address of the remote host #%remote_ip <ip>
# username on the remote host #%remote_username <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 <loginnode>
# default queue to be used if palmrun-option -q is omitted #%defaultqueue <queue>
# 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 -Dparallel -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION -Dfftw -Dnetcdf
# used for parallel compilation %make_options -j 4
# options to be used to compile PALM %compiler_options -openmp -fpe0 -O3 -xHost -fp-model source -ftz -fno-alias -no-prec-div -no-prec-sqrt -ip -nbs -I /muksoft/packages/fftw/3.3.4/include -L/muksoft/packages/fftw/3.3.4/lib64 -lfftw3 -I /muksoft/packages/netcdf/4_intel/include -L/muksoft/packages/netcdf/4_intel/lib -lnetcdf -lnetcdff
# options to be used to link the PALM executable %linker_options -openmp -fpe0 -O3 -xHost -fp-model source -ftz -fno-alias -no-prec-div -no-prec-sqrt -ip -nbs -I /muksoft/packages/fftw/3.3.4/include -L/muksoft/packages/fftw/3.3.4/lib64 -lfftw3 -I /muksoft/packages/netcdf/4_intel/include -L/muksoft/packages/netcdf/4_intel/lib -lnetcdf -lnetcdff
# name of hostfile to be used %hostfile auto
# command to start the PALM executable %execute_command mpiexec -machinefile hostfile -n {{mpi_tasks}} palm
# memory request per core #%memory 2300
# module commands to load required libraries #%module_commands module load fftw cray-hdf5-parallel cray-netcdf-hdf5parallel
# special commands to be carried out at login and start of batch jobs on the remote host #%login_init_cmd module switch craype-ivybridge craype-haswell
