= '''This page is under construction! ''' = \\\\\\ = 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 need to start either with {{{#}}}, {{{%}}}, {{{IC:}}}, {{{OC:}}}, {{{EC:}}}, {{{BD:}}}, or {{{BDT:}}}. Empty line are allowed too. * 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 $jobname has finished" | mailx username@email-address }}} * lines starting with {{{EC:}}} define unix commands that shall be executed in case that the PALM code or the {{{palmrun}}} script terminated because of any kind of error. You can restrict execution of error commands to specific kinds of error: {{{ EC:[[ ]] && error-command }}} * lines starting with {{{BD:}}} define directives that are required for batch jobs, i.e. if PALM shall be run in batch mode. Explanations for batch directives are given further below. * lines starting with {{{BDT:}}} define directives for an additional batch job that is required in case of running PALM in batch mode on a remote host. This additional job transfers the job protocol file of the main PALM job back to the local host. === environment variables and their meaning The [source:palm/trunk/SCRIPTS/.palm.config.default default template] contains settings for the minimum set of variables that always need to be defined, plus suggestions for other variables that you may need to uncomment, in case that you like/need to use them. The following table lists all relevant variables and their meaning. Default values are either those which are set in the scripts {{{palmrun}}} and {{{palmbuild}}} or which are suggested in the template file. ||='''Variable name''' =||='''meaning''' =||='''default value''' =|| |----------- ||base_directory ||Working directory from where {{{palmrun}}} or {{{palmbuild}}} is called. This folder must contain the configuration file {{{.palm.config....}}}. ||$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 [source:palm/trunk/SCRIPTS/.palm.iofiles .palm.iofiles], and the [wiki:doc/app/palm_iofiles 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 [wiki:doc/app/userint 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 || ||fast_io_catalog ||Path to a file system with fast discs (if available). This folder is used so store the temporary catalog generated by {{{palmrun}}} during each run. It should also be used to store large I/O files (e.g. restart data or 3D-output) in order to reduce I/O time. This variable is used in the default {{{.palm.iofiles}}} for the restart data files. The folder must be accessible from all compute nodes, i.e. it must reside in a global file system. WARNING: {{{/tmp}}} will only work on single node systems! In case of batch jobs on remote hosts, the variable refers to a folder on the remote host. The variable has no default value and must be set by the user. ||no default value || ||local_jobcatalog ||Folder on the local host to store the batch job protocols. In case of batch jobs running on remote hosts, the job protocol will be created on the {{{remote_jobcatalog}}} and then be transferred via scp to the {{{local_jobcatalog}}}. ||$HOME/job_queue || ||remote_jobcatalog ||In case of batch jobs running on remote hosts, the job protocol will be put in this folder, and then automatically transferred via scp to the {{{local_jobcatalog}}}. The transfer is done by a separate small batch job, which directives are defined by the {{{BDT:}}} lines. The variable has no default value and must be set by the user. Absolute paths need to be given. Using {{{$HOME}}} is not allowed / does not work. ||no default value || ||local_ip ||IP-address of your local computer / the computer on which you call the {{{palmrun}}}/{{{palmbuild}}} command. You may use {{{127.0.0.0}}} if you are running PALM in interactive mode or in batch mode on your local computer. The address is only used to identify where to send the output data in case of batch jobs on a remote host. ||no default value || ||local_username ||Your username on the local computer / the computer on which you call the {{{palmrun}}}/{{{palmbuild}}} command. The local username is required for running batch jobs on a remote host in order to allow the batch job to access your local system (e.g. for sending back output data or for automatically starting restart runs). ||no default value || ||remote_ip ||IP-address of the remote system where the batch job shall be started. On large cluster systems this will usually be the address of a login node. Setting this variable in the configuration file will cause {{{palmrun}}} to run in remote batch job mode, i.e. a batch job will be created and send to the remote system automatically without giving {{{palmrun}}}-option {{{-b}}}. ||no default value || ||remote_username ||Your username on the remote computer that is given by {{{remote_ip}}}. ||no default value || ||ssh_key ||Filename from which the identity (private key) for public key authentication is read. This file is assumed to be in folder {{{$HOME/.ssh}}}. ||no default value || ||remote_loginnode ||Name of the login node of the remote computer. Nodes on big compute clusters are separated into compute nodes and login nodes (and sometimes I/O nodes). Some computer centers only allow the login nodes to establish ssh/scp connections to addresses outside the computing center. In such cases, since {{{palmrun}}} is executed on the compute nodes, it first has to send the output data to the login node, from where it is then forwarded to your local computer. If the compute nodes on your remote host do not allow direct ssh/scp connections to your local computer, you need to provide the name of the login node of the remote host. Typically, this is a mnemonic name like ''loginnode1'' and not an IP-address (like ''111.111.11.11''). Several login nodes often exist. You just have to give one of them. If you do not provide a name, you probably will not receive data on your local host from the PALM run. ||no default value || ||defaultqueue ||Batch job queue to be used if no queue is explicitly given with {{{palmrun}}} option {{{-q}}}. ||no default value || ||submit_command ||Full path to the command that has to be used to submit batch jobs on your system (either on the local, or on the remote host), including required option. See documentation of your batch system / computing center to find out which command has to be used. An example for a {{{moab}}} batch system could be {{{/opt/moab/default/bin/msub -E}}}. If you only know the command name (e.g. ''msub''), entering {{{which msub}}} on the local/remote host will give you the full path. ||no default value || ||compiler_name ||Name of the FORTRAN compiler to be used to create the PALM executable. Typically, this is the name of a wrapper script like ''mpif90'' or e.g. ''ftn'' on Cray machines, which automatically invokes the required MPI library and MPI include file. If you don't have a wrapper script, you may need to explicitly give compiler options (see {{{compiler_options}}}) to provide paths to the library / include file. If you like to run PALM without MPI (serial mode, or OpenMP parallelization), you should not use a wrapper script and give the original compiler name instead. ||no default value || ||compiler_name_ser ||FORTRAN compiler name to create non-MPI executables. This name is required, because {{{palmbuild}}} generates several helper programs for pre-/post-processing, which run in serial mode on just one code. Here you give the original compiler name, like ''ifort'', ''pgfortran'', ''gfortran'', or ''xlf95''. ||no default value || ||cpp_options ||Preprocessor directives to be used for compiling the PALM code. They allow for conditional compilation using the {{{-D}}} compiler option. Compiling PALM with MPI support requires options {{{-D__parallel -DMPI_REAL=MPI_DOUBLE_PRECISION -DMPI_2REAL=MPI_2DOUBLE_PRECISION}}}. Many compilers require to set an additional option to run the FORTRAN preprocessor on source files before compilation (e.g. ''-fpp'' for the Intel compiler). This option has to be given here too. Alternatively, you can provide it as part of the {{{compiler_options}}}. See [wiki:doc/app/cpp_options cpp_options] for a complete list of preprocessor define strings that are used in the PALM code. ||no default value || ||make_options ||Options for the UNIX {{{make}}}-command, which is used by {{{palmbuild}}} to compile the PALM code. In order to speed up compilation, you may use the {{{-j}}} option, which specifies the number of jobs to run simultaneously. If you have e.g. 4 cores on your local computer system, then {{{-j 4}}} starts 4 instances of the FORTRAN compiler, i.e. 4 FORTRAN-files are compiled simultaneously (if the dependencies allow for that). Do not try to start more instances than the number of available cores, because this will decrease the compiler performance significantly. ||no default value || ||compiler_options ||Options to be used by the compiler that has been specified by {{{compiler_name}}} / {{{compiler_name_ser}}} in order to compile the PALM and utilities source code. Please see [wiki:doc/app/recommended_compiler_options] for recommended compiler options for specific compilers. Library paths do not have to be given here (although you can do that), but paths to INCLUDE files may need to be specified. ||no default value || ||linker_options ||Compiler options to be used to link the PALM executable. Typically, these are paths to libraries used by PALM, e.g. NetCDF, FFTW, MPI, etc. You may repeat the options that you have given with {{{compiler_options}}} here. See your local system documentation / software manuals for required path settings. Requirements differ from system to system and also depend on the respective libraries that you are using. See [wiki:doc/app/recommended_compiler_options] for specific path settings that we, the PALM group, are using on our computers. Be aware, that these settings probably will not work on your computer system. ||no default value || ||'''hostfile''' ||'''Name of the hostfile that is used by MPI to determine the nodes on which the MPI processes are started.'''\\\\ {{{palmrun}}} automatically generates the hostfile if you set {{{auto}}}. All MPI processes will then be started on the node on which {{{palmrun}}} is executed. The real name of the hostfile will then be set to {{{hostfile}}} (instead of {{{auto}}}) and, depending on your local MPI implementation, you may have to give this name in the {{{execute_command}}}. MPI implementations on large computer centers often do not require to explicitly specify a hostfile (in such a case you can remove this line from the configuration file), or the batch systems provides a hostfile which name you may access via environment variables (e.g. {{{$PBS_NODEFILE}}}) and which needs to be given in the {{{execute_command}}}. Please see your local system / batch system documentation about the hostfile policy on your system. ||no default value || ||execute_command ||MPI command to start the PALM executable. \\ Please see your local MPI documentation about which command needs to be used on your system. The name of the PALM executable, usually the last argument of the execute command, must be {{{palm}}}. Typically, the command requires to give several further options like the number of MPI processes to be started, or the number of compute nodes to be used. Values of these options may change from run to run. Don't give specific values here and use variables instead which will be automatically replaced by {{{palmrun}}} with values that you have specified with respective {{{palmrun}}} options. As an example {{{aprun -n {{mpi_tasks}} -N {{tasks_per_node}} palm}}} will be interpreted as {{{aprun -n 240 -N 24 palm}}} if you call {{{palmrun ... -X240 -T24 ...}}}. ||no default value || # 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 === batch job directives === === UNIX commands ===