getStatus: Summarize the Computational Status

In mllg/batchtools: Tools for Computation on Batch Systems

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)

mllg/batchtools documentation built on April 21, 2023, 11:49 a.m.