findJobs: Find and Filter Jobs
In mllg/batchtools: Tools for Computation on Batch Systems

findJobs

R Documentation

Find and Filter Jobs

Description

These functions are used to find and filter jobs, depending on either their parameters (findJobs and findExperiments), their tags (findTagged), or their computational status (all other functions, see getStatus for an overview).

Note that findQueued, findRunning, findOnSystem and findExpired are somewhat heuristic and may report misleading results, depending on the state of the system and the ClusterFunctions implementation.

See JoinTables for convenient set operations (unions, intersects, differences) on tables with job ids.

Usage

findJobs(expr, ids = NULL, reg = getDefaultRegistry())

findExperiments(
  ids = NULL,
  prob.name = NA_character_,
  prob.pattern = NA_character_,
  algo.name = NA_character_,
  algo.pattern = NA_character_,
  prob.pars,
  algo.pars,
  repls = NULL,
  reg = getDefaultRegistry()
)

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

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

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

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

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

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

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

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

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

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

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

findTagged(tags = character(0L), ids = NULL, reg = getDefaultRegistry())

Arguments

`expr`	[`expression`] Predicate expression evaluated in the job parameters. Jobs for which `expr` evaluates to `TRUE` are returned.
`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`).
`prob.name`	[`character`] Exact name of the problem (no substring matching). If not provided, all problems are matched.
`prob.pattern`	[`character`] Regular expression pattern to match problem names. If not provided, all problems are matched.
`algo.name`	[`character`] Exact name of the problem (no substring matching). If not provided, all algorithms are matched.
`algo.pattern`	[`character`] Regular expression pattern to match algorithm names. If not provided, all algorithms are matched.
`prob.pars`	[`expression`] Predicate expression evaluated in the problem parameters.
`algo.pars`	[`expression`] Predicate expression evaluated in the algorithm parameters.
`repls`	[`integer`] Whitelist of replication numbers. If not provided, all replications are matched.
`tags`	[`character`] Return jobs which are tagged with any of the tags provided.

Value

[data.table] with column “job.id” containing matched jobs.

Examples


tmp = makeRegistry(file.dir = NA, make.default = FALSE)
batchMap(identity, i = 1:3, reg = tmp)
ids = findNotSubmitted(reg = tmp)

# get all jobs:
findJobs(reg = tmp)

# filter for jobs with parameter i >= 2
findJobs(i >= 2, reg = tmp)

# filter on the computational status
findSubmitted(reg = tmp)
findNotDone(reg = tmp)

# filter on tags
addJobTags(2:3, "my_tag", reg = tmp)
findTagged(tags = "my_tag", reg = tmp)

# combine filter functions using joins
# -> jobs which are not done and not tagged (using an anti-join):
ajoin(findNotDone(reg = tmp), findTagged("my_tag", reg = tmp))

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