batchtools: getJobTable – R documentation

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getJobTable

Query Job Information

Description

getJobStatus returns the internal table which stores information about the computational status of jobs, getJobPars a table with the job parameters, getJobResources a table with the resources which were set to submit the jobs, and getJobTags the tags of the jobs (see Tags).

getJobTable returns all these tables joined.

Usage

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

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

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

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

getJobTags(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 the following columns (not necessarily in this order):

job.id: Unique Job ID as integer.
submitted: Time the job was submitted to the batch system as POSIXct.
started: Time the job was started on the batch system as POSIXct.
done: Time the job terminated (successfully or with an error) as POSIXct.
error: Either NA if the job terminated successfully or the error message.
mem.used: Estimate of the memory usage.
batch.id: Batch ID as reported by the scheduler.
log.file: Log file. If missing, defaults to [job.hash].log.
job.hash: Unique string identifying the job or chunk.
time.queued: Time in seconds (as difftime) the job was queued.
time.running: Time in seconds (as difftime) the job was running.
pars: List of parameters/arguments for this job.
resources: List of computational resources set for this job.
tags: Tags as joined string, delimited by “,”.
problem: Only for ExperimentRegistry: the problem identifier.
algorithm: Only for ExperimentRegistry: the algorithm identifier.

Examples

tmp = makeRegistry(file.dir = NA, make.default = FALSE)
f = function(x) if (x < 0) stop("x must be > 0") else sqrt(x)
batchMap(f, x = c(-1, 0, 1), reg = tmp)
submitJobs(reg = tmp)
waitForJobs(reg = tmp)
addJobTags(1:2, "tag1", reg = tmp)
addJobTags(2, "tag2", reg = tmp)

# Complete table:
getJobTable(reg = tmp)

# Job parameters:
getJobPars(reg = tmp)

# Set and retrieve tags:
getJobTags(reg = tmp)

# Job parameters with tags right-joined:
rjoin(getJobPars(reg = tmp), getJobTags(reg = tmp))

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