batchtools: getStatus – R documentation

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getStatus

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).

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)

batchtools

Tools for Computation on Batch Systems

v0.9.15

LGPL-3

Authors

Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), Bernd Bischl [aut], Dirk Surmann [ctb] (<https://orcid.org/0000-0003-0873-137X>)

Initial release