Changes between Version 33 and Version 34 of doc/app/palmrun
- Timestamp:
- Aug 29, 2018 9:38:45 AM (6 years ago)
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doc/app/palmrun
v33 v34 4 4 5 5 == Introduction == 6 {{{palmrun}}} is the main script to execute PALM in interactive mode (running PALM in a terminal) or in batch mode. This chapter describes the actions / operations carried out by {{{palmrun}}} and gives a complete list and description of its available options. At the end of this chapter you will find detailed information sfor experienced PALM-users who migrate from the old {{{mrun / mbuild}}} scripts to the new scripts {{{palmrun / palmbuild}}}.6 {{{palmrun}}} is the main script to execute PALM in interactive mode (running PALM in a terminal) or in batch mode. This chapter describes the actions / operations carried out by {{{palmrun}}} and gives a complete list and description of its available options. At the end of this chapter you will find detailed information for experienced PALM-users who migrate from the old {{{mrun / mbuild}}} scripts to the new scripts {{{palmrun / palmbuild}}}. 7 7 8 8 9 9 == Mode of operation == 10 Explanations will follow about the order of actions carried out by {{{palmrun}}} in case of interactive runs, batch runs, and batch runs on remote machines 10 11 ... 11 12 13 12 14 == {{{palmrun}}} options == 13 There are two groups of options, one that you can specify yourself, and another group for {{{palmrun}}} internal usage, that you normally should not touch. The second internal group is used and set by {{{palmrun}}} itself for automatically generated {{{palmrun}}} calls used within batch jobs and for the automatic start of restart jobs.15 There are two groups of options, one are the '''user options''' that you can specify yourself when manually calling {{{palmrun}}} from the terminal, and another group of '''internal options''' that are used for automatically created internal calls of {{{palmrun}}}. Internal calls of {{{palmrun}}} are those that are part of the batch job, and those used for automatically starting restart jobs. Normally, you should never use the internal options. User options from a manual call are automatically added to the internal calls of {{{palmrun}}}. 14 16 15 17 The following gives complete lists of {{{palmrun}}} user and internal options. A {{{---}}} in the second column means that the respective option has no argument. … … 32 34 ||-O ||1 ||OpenMP threads to be started per MPI task. Environment variable {{{OMP_NUM_THREADS}}} will be set to this value || 33 35 ||-q ||none ||name of the job queue to which batch jobs will be submitted || 34 35 36 ||-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. || 37 ||-t ||" " ||cpu time request for batch jobs in seconds || 38 ||-T ||" " ||MPI tasks per node request for batch jobs || 39 ||-v ||--- ||Suppresses parts of {{{palmrun}}}'s terminal output and prevents {{{palmrun}}} queries || 40 ||-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. || 41 ||-w ||as -X||Number of parallel I/O streams to be opened by PALM. In the default case, all MPI processes write at the same time. This may cause file system problems in case of a very large number of cores. || 42 ||-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. || 43 ||-x ||--- ||Causes {{{palmrun}}} to output excessive debug information for both interactive sessions as well as batch jobs. || 44 ||-X ||1 ||Total number of cores to be used for the run. || 45 ||-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. || 46 ||-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. || 47 ||-Z ||--- ||Do not call {{{combine_plot_fields}}} after PALM has finished. In that case, data output of 2d-cross section or 3d-volumes that has been done be each core into a separate file will not be collected into one file. In order to later process these files, option {{{-B}}} should 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. || 48 ||? ||--- ||Print a short list of available user options on the terminal. || 36 49 37 50 … … 42 55 ||-C ||--- ||Tells that it is a {{{palmrun}}} call for a restart job that has been automatically created || 43 56 ||-G ||" " ||Global revision number of the PALM code in {{{trunk/SOURCES}}} || 57 ||-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. || 44 58 ||-j ||--- ||Tells that {{{palmrun}}} is running within a batch job || 45 || || ||Five digit random number that gives a run-id and that is used as part of the batch job name as well as the temporary working directory and other files 59 ||-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. || 60 ||-u ||" " ||Username on the remote host as given in the configuration file by variable {{{remote_username}}} || 61 ||-U ||" " ||Username on the local host as given in the configuration file by variable {{{local_username}}} || 62 63 46 64 47 65
