Job files are created based on the brew template
template.file. This file is processed with brew and then
submitted to the queue using the bsub command. Jobs are
killed using the bkill command and the list of running jobs
is retrieved using bjobs -u $USER -w. The user must have the
appropriate privileges to submit, delete and list jobs on the
cluster (this is usually the case).
The template file can access all arguments passed to the
submitJob function, see here ClusterFunctions.
It is the template file's job to choose a queue for the job
and handle the desired resource allocations.
Examples can be found on
https://github.com/tudo-r/BatchJobs/tree/master/examples/cfOpenLava.
makeClusterFunctionsOpenLava(
template.file,
list.jobs.cmd = c("bjobs", "-u $USER", "-w")
)[character(1)]
Path to a brew template file that is used for the PBS job file.
[character]
Change default system command / options to list jobs.
The first entry is the command, the following the options.
See system3.
Other clusterFunctions:
makeClusterFunctionsInteractive(),
makeClusterFunctionsLSF(),
makeClusterFunctionsLocal(),
makeClusterFunctionsMulticore(),
makeClusterFunctionsSGE(),
makeClusterFunctionsSLURM(),
makeClusterFunctionsSSH(),
makeClusterFunctionsTorque(),
makeClusterFunctions()