Palmrun Options#
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There are two groups of options. One group defines the user options that are specified when manually calling palmrun from the terminal. Another group defines internal options that are used for automatically created internal calls of palmrun. Internal calls of palmrun are those in a batch job (that has been automatically generated by palmrun), and those used for automatically started restart jobs. Generally, internal options should never be used. User options from a manual call are automatically added to the internal calls of palmrun.
The following lists give a complete overview of palmrun user and internal options. A --- in the second column means that the respective option has no argument (and therefore no default value).
Palmrun user options#
| Option | Default Value | Meaning |
|---|---|---|
| -a | " " | For activating the copy of input and output files as defined in the file connection file .palm.iofiles. An argument "d3#" e.g. means that the parameter/NAMELIST file for steering the model shall be provided as input file. This is the minimum setting for option -a, because the model cannot without this parameter. |
| -A | " " | Project account number. |
| -b | --- | Create a batch job. |
| -B | --- | Do not delete the temporary working directory. |
| -c | default | Specifies the so-called configuration identifier. It tells palmrun which configuration file should be used. -c default means to use the configuration file .palm.config.default. |
| -C | --- | Tells that it is a palmrun call for a restart job that has been automatically created. This is an internal option but it can be used for manually generated restart runs, if the user likes to re-use the contents of the SOURCES_FOR_RUN... folder. |
| -F | --- | Create batch job file only, and do not submit it. |
| -k | --- | If set, input files that have the lnor lnpe attribute and that have been generated by a previous run within a job chain will NOT be automatically deleted at the end of the run. |
| -m | " " | Memory in MByte per MPI task to be requested in batch jobs. |
| -M | " " | Makefile to compile the PALM code and utility programs. By default, the name of the makefile is Makefile, and it is expected to be in the folder defined in the configuration file via variable source_path. |
| -O | 1 | OpenMP threads to be started per MPI task. Environment variable OMP_NUM_THREADS will be set to this value. |
| -q | none | Name of the job queue to which batch jobs will be submitted. See your batch system documentation about available queues and keep in mind that usually each queue has special limits for requested resources. If this option is not given, and variable defaultqueue has been defined in the configuration file, that one is used as job queue name. |
| -r | test | The name of the run (run-identifier) given by -r tells palmrun to use the NAMELIST file <run_identifier>_p3d from JOBS/<run_identifier>/INPUT. It also determines folders and names of output files generated by PALM using informations from the configuration file and the file connection file. See file connection file for the format of this file and how to modify or extend it. |
| -s | " " | List of subroutines (Fortran file names) from the local repository (under .../packages/palm/model/src) that shall be compiled for this run. Compiled files will be exclusively used for the run and not be put in the MAKE_DEPOSITORY. In case of -s LM, all files in the local repository folder that have been modified will be compiled. |
| -t | " " | Maximum CPU time (wall clock time) in seconds requested by the batch job. This option is ignored in interactive runs. |
| -T | " " | Number of MPI tasks to be started per node. Typically, <MPI tasks per node> is chosen as the total number of CPU cores available on a node, e.g. if a node has two CPUs with 64 cores each, then <MPI tasks per node> = 128. |
| -v | --- | Suppresses parts of palmrun's terminal output and prevents any palmrun queries. |
| -V | --- | Use existing SOURCES_FOR_RUN_... folder. Prevents palmrun from creating a new SOURCES_FOR_RUN_... folder. Use this option if you do not want the user interface files to be compiled again for each call of palmrun. |
| -w | as -X | Number of parallel I/O streams to be opened by the model. In the default case, all MPI tasks write at the same time. This may cause file system problems in case of a very large number of cores. |
| -W | " " | Name (id) of a previous job. Can be used as variable `` as part of job directives in the configuration file, in order to prevent the job to start before the specified previous job has been finished. The job name must be the one that has been assigned by the batch system. |
| -x | --- | Causes palmrun to output excessive debug information for both interactive sessions as well as batch jobs. |
| -X | 1 | Total number of cores (not CPUs!) to be used for the run. The argument should not be larger than the maximum number of cores available on the machine, because that would usually slow down the performance significantly. |
| -Z | --- | Do not call combine_plot_fields after the model has finished. In that case, data output of 2d-cross section or 3d-volumes done by each core into a separate file will not be collected into one file. In order to later process these files, option -Bshould be set too. -Z might be required for very large jobs in order to reduce computational demands, because combine_plot_fields is running on one core only, so that all other cores will run idle. This is a deprecated feature and not required if parallel netCDF I/O is available. |
| ? | --- | Print a short list of available user options on the terminal. |
Palmrun internal options#
| Option | Default Value | Meaning |
|---|---|---|
| -C | --- | Means that it is a palmrun call for a restart job that has been automatically generated. |
| -G | " " | PALM version string. This is automatically determined by the installed release, or it is the git SHA-1 hashtag of the active code branch if a clone of the gitlab repository is used (for developers only). |
| -i | Five digit random number that gives a run-id and that is used as part of the batch job name as well as the name of the temporary working directory and other files. A new random number is created for each call of palmrun (either a manual call by the user or an automatic call for generating a restart job), and is passed to the batch job internal call of palmrun via this option. |
|
| -j | --- | Tells that palmrun is running within a batch job. |
| -R | " " | Return address. Tells the remote batch job to which IP-address the PALM output and the job protocol file has to be send, and from which machine automatic restarts have to be generated. |
| -u | " " | Username on the remote host as given in the configuration file via variable remote_username. |
| -U | " " | Username on the local host as given in the configuration file via variable local_username. |