Cluster functions for Univa Grid Engine / Oracle Grid Engine / Sun Grid Engine (http://www.univa.com/).
Job files are created based on the brew template template. This
file is processed with brew and then submitted to the queue using the
qsub command. Jobs are killed using the qdel command and the
list of running jobs is retrieved using qselect. 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 resources passed to submitJobs
as well as all variables stored in the JobCollection.
It is the template file's job to choose a queue for the job and handle the desired resource
allocations.
makeClusterFunctionsSGE(template = "sge", scheduler.latency = 1,
fs.latency = 65)[character(1)]
Either a path to a brew template file (with extension “tmpl”), or a short descriptive name enabling the following heuristic for the file lookup:
“batchtools.[template].tmpl” in the current working directory.
“[template].tmpl” in the user config directory (see user_config_dir); on linux this is usually “~/.config/batchtools/[template].tmpl”.
“.batchtools.[template].tmpl” in the home directory.
“[template].tmpl” in the package installation directory in the subfolder “templates”.
Here, the default for template is “sge”.
Alternatively, the template itself can be provided as a single string (including at least one newline “\n”).
[numeric(1)]
Time to sleep after important interactions with the scheduler to ensure a sane state.
Currently only triggered after calling submitJobs.
[numeric(1)]
Expected maximum latency of the file system, in seconds.
Set to a positive number for network file systems like NFS which enables more robust (but also more expensive) mechanisms to
access files and directories.
Usually safe to set to NA which disables the expensive heuristic if you are working on a local file system.
Other ClusterFunctions: makeClusterFunctionsDocker,
makeClusterFunctionsInteractive,
makeClusterFunctionsLSF,
makeClusterFunctionsMulticore,
makeClusterFunctionsOpenLava,
makeClusterFunctionsSSH,
makeClusterFunctionsSlurm,
makeClusterFunctionsSocket,
makeClusterFunctionsTORQUE,
makeClusterFunctions