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palmrun

Timestamp:: Nov 20, 2018 2:35:48 PM (6 years ago)
Author:: scharf
Comment:: --

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doc/app/palmrun

-                      v42
+                      v43
 == [=#interactive Interactive mode] ==
 You can follow the progress of the simulation on the terminal where a lot of informative messages will be output. You can also stop the simulation at any time by typing {{{CTRL C}}}.
+You can follow the progress of the simulation on the terminal where a lot of informative messages will be output. You can also stop the simulation at any time by typing {{{Ctrl+C}}}.
 The following instructions assume, that the [wiki:doc/install/automatic automatic installer] has run without any problems. You should now be able to start the first PALM simulation yourself. Please enter
 …
    palmrun  -r example_cbl  -c default  -a "d3#"  -X4
 }}}
-{{{example_cbl}}} is the so-called ''run identifier'' and tells {{{palmrun}}} to use the NAMELIST file {{{example_cbl_p3d}}} from {{{JOBS/example_cbl/INPUT}}}. It also determines folders and names of output files generated by PALM using informations from the default file configuration file {{{..../trunk/SCRIPTS/.palm.iofiles}}}. Chapter [wiki:doc/app/palm_iofiles PALM iofiles] explains the format of this file and how you can modify or extend it. As a new user, you should not need to care about this file because the default settings should do the job for you.
-Option {{{-c}}} 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}}}. The configuration file contains all the computer (host) specific settings, e.g. which compiler and compiler options should be used, the pathnames of libraries (e.g. NetCDF or MPI), or the name of the execution command (e.g. {{{mpirun}}} or {{{mpiexec}}}), as well as many other important settings. If the automatic installer worked correctly, it created this file for you with settings based on your responses during the installation process. You may create additional configuration files with different settings for other computers (hosts), or for the same computer, e.g. if you like to compile and run PALM with debug compiler options (see chapter [wiki:doc/app/palm_config PALM configuration file]).
-Option {{{-a}}} is used for steering the handling of input and output files that are required / generated by PALM. Its argument is called the file activation string(s). The file configuration file {{{..../trunk/SCRIPTS/.palm.iofiles}}} contains a complete list of PALM's I/O files, one line per file. PALM expects its input files in a temporary working directory that is created by each call of {{{palmrun}}} and it outputs data to this temporary directory too. The file configuration file tells {{{palmrun}}} where to find your input files and where to copy the output files (because the temporary working directory is automatically deleted before {{{palmrun}}} has finished). The default setting is that all these files are in subdirectory {{{$HOME/palm/current_version/JOBS/<run_identifier>}}}, where {{{<run_identifier>}}} is the one given with option {{{-d}}}. The argument of option {{{-a}}} tells {{{palmrun}}} which of these files need to be copied. If the option is omitted, no I/O files will be copied at all. Argument {{{"d3#"}}} means that the parameter/NAMELIST file for steering PALM shall be provided as input file. This is the minimum setting for option {{{-a}}}, because PALM cannot run without this parameter file. Multiple activation strings can be given. See chapter [wiki:doc/app/palm_iofiles PALM iofiles] for handling PALM I/O files.
-Option {{{-X}}} specifies on how many cores the simulation shall run. The argument should not be larger than the maximum number of cores available on your computer (except in case of hyperthreading), because that would usually slow down the performance significantly.
 After entering the {{{palmrun}}} command, some general settings will be listed on the terminal and the user is prompted for confirmation:
 …
 ||='''option''' =||='''default value''' =||='''meaning''' =||
 |-----------
 ||-a   ||" "  ||activation string list  ||
+||-a   ||" "  ||For steering the handling of input and output files as defined in the [wiki:doc/app/palm_iofiles file configuration file] {{{..../trunk/SCRIPTS/.palm.iofiles}}}. Argument {{{"d3#"}}} means that the parameter/NAMELIST file for steering PALM shall be provided as input file. This is the minimum setting for option {{{-a}}}, because PALM cannot run without this parameter file. ||
 ||-A   ||" "  ||project account number  ||
 ||-b   ||---  ||create a batch job  ||
 ||-B   ||---  ||Do not delete the temporary working directory  ||
 ||-c   ||default ||configuration identifier  ||
+||-c   ||default ||Specifies the so-called configuration identifier. It tells {{{palmrun}}} which [wiki:doc/app/palm_config 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 a batch job file only, and do not submit it.  ||
 …
 ||-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  ||
 ||-r   ||test  ||Name of the run  ||
+||-r   ||test ||The name of the run 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 default file configuration file {{{..../trunk/SCRIPTS/.palm.iofiles}}}. Chapter [wiki:doc/app/palm_iofiles PALM iofiles] explains the format of this file and how you can modify or extend it. ||
 ||-s   ||" "  ||List of subroutines (Fortran file names) from the SVN repository (under {{{.../trunk/SOURCES}}}) 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 repository that have been modified by the used will be compiled.  ||
 ||-t   ||" "  ||cpu time request for batch jobs in seconds  ||
 …
 ||-W   ||" "  ||Name (id) of a previous job. Can be used as variable {{{ {{previous_job}} }}} 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 have been given 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 to be used for the run.  ||
+||-X   ||1    ||Total number of cores to be used for the run.  The argument should not be larger than the maximum number of cores available on your computer (except in case of hyperthreading), because that would usually slow down the performance significantly.||
 ||-y   ||---  ||Use file appendix {{{_O}}} for local PALM-I/O files in case of uncoupled ocean runs, e.g. if the run is a precursor run and files shall later be used for coupled atmosphere-ocean runs. ||
 ||-Y   ||" "  ||In case of a coupled atmosphere-ocean run, the parameter tells PALM how many cores shall be assigned to the atmosphere- and ocean-model, respectively. For example, in case of {{{-X 64  -Y "16 48""}}} 16 cores are assigned to the atmosphere model, and 48 cores to the ocean model.  ||