make.pbs: Make Westgrid PBS files

Description Usage Arguments Value Author(s) References

View source: R/WestGridFunctions.R

Description

Take an individual Nemo .ini file and make a Westgrid PBS file for either orcinus, bugaboo, or grex servers.

Usage

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make.pbs(filename, input.directory = NULL, nemo.directory = NULL, RAM,
  walltime = NULL, westgrid.server = NULL)

Arguments

filename

The full name of the .ini file for which the PBS file is being created.

input.directory

The directory on the Westgrid server which holds the nemo .ini file. Defaults are set for each server.

nemo.directory

The directory on the Westgrid server from which the nemo executable is called. Defaults are set for each server.

RAM

The amount of RAM the run will be allowed to use, there is no default, and must include gb, mb, or kb in specification, e.g. "6gb".

walltime

Default is set at max for specified server (except bugaboo, which is set to default at 500 hours), but other lengths can be specified here in units "100:00:00" hours:minutes:seconds.

westgrid.server

Which westgrid server the PBS file is meant for. Options are "grex", "orcinus" or "bugaboo" currently.

Value

Creates PBS files from a .ini file for running Nemo on Westgrid's Orcinus, Bugaboo, or Grex servers. *IMPORTANT NOTE* Must have files "MiddleLine.txt", "GrexLine.txt", and "LastLine.txt" in the same directory for make.pbs to work properly, as it concatenates text from those files into the final PBS file.

Author(s)

Kimberly J Gilbert

References

Nemo is created and maintained by Fred Guillaume. The manual and source files are available online.


kjgilbert/aNEMOne documentation built on May 20, 2019, 10:25 a.m.