getStatus {batchtools}

Summarize the Computational Status

Description

This function gives an encompassing overview over the computational status on your system. The status can be one or many of the following:

• “defined”: Jobs which are defined via batchMap or addExperiments, but are not yet submitted.

• “submitted”: Jobs which are submitted to the batch system via submitJobs, scheduled for execution.

• “started”: Jobs which have been started.

• “done”: Jobs which terminated successfully.

• “error”: Jobs which terminated with an exception.

• “running”: Jobs which are listed by the cluster functions to be running on the live system. Not supported for all cluster functions.

• “queued”: Jobs which are listed by the cluster functions to be queued on the live system. Not supported for all cluster functions.

• “system”: Jobs which are listed by the cluster functions to be queued or running. Not supported for all cluster functions.

• “expired”: Jobs which have been submitted, but vanished from the live system. Note that this is determined heuristically and may include some false positives.

Here, a job which terminated successfully counts towards the jobs which are submitted, started and done. To retrieve the corresponding job ids, see findJobs.

Usage

getStatus(ids = NULL, reg = getDefaultRegistry())

Arguments

ids

[data.frame or integer]
A data.frame (or data.table) with a column named “job.id”. Alternatively, you may also pass a vector of integerish job ids. If not set, defaults to all jobs. Invalid ids are ignored.

reg

[Registry]
Registry. If not explicitly passed, uses the default registry (see setDefaultRegistry).

Value

[data.table] (with class “Status” for printing).

See Also

findJobs

Other debug: getErrorMessages(), grepLogs(), killJobs(), resetJobs(), showLog(), testJob()

Examples

tmp = makeRegistry(file.dir = NA, make.default = FALSE)
fun = function(i) if (i == 3) stop(i) else i
ids = batchMap(fun, i = 1:5, reg = tmp)
submitJobs(ids = 1:4, reg = tmp)
waitForJobs(reg = tmp)

tab = getStatus(reg = tmp)
print(tab)
str(tab)