BiocParallelParam objects
The BiocParallelParam virtual class stores configuration parameters
for parallel execution. Concrete subclasses include SnowParam,
MulticoreParam, BatchtoolsParam, and DoparParam
and SerialParam.
BiocParallelParam is the virtual base class on which other
parameter objects build. There are 5 concrete subclasses:
SnowParam: distributed memory computing
MulticoreParam: shared memory computing
BatchtoolsParam: scheduled cluster computing
DoparParam: foreach computing
SerialParam: non-parallel execution
The parameter objects hold configuration parameters related to the method of parallel execution such as shared memory, independent memory or computing with a cluster scheduler.
The BiocParallelParam class is virtual and has no constructor.
Instances of the subclasses can be created with the following:
SnowParam()
MulticoreParam()
BatchtoolsParam()
DoparParam()
SerialParam()
In the code below BPPARAM is a BiocParallelParam object.
bpworkers(x), bpworkers(x, ...):
integer(1) or character(). Gets the number or names of
the back-end workers. The setter is supported for SnowParam and
MulticoreParam only.
bpnworkers(x):
integer(1). Gets the number of the back-end workers.
bptasks(x), bptasks(x) <- value:
integer(1). Get or set the number of tasks for a
job. value must be a scalar integer >= 0L. This argument
applies to SnowParam and MulticoreParam only;
DoparParam and BatchtoolsParam have their own
approach to dividing a job among workers.
We define a job as a single call to a function such as bplapply,
bpmapply etc. A task is the division of the
X argument into chunks. When tasks == 0 (default),
X is divided by the number of workers. This approach distributes
X in (approximately) equal chunks.
A tasks value of > 0 dictates the total number of tasks. Values
can range from 1 (all of X to a single worker) to the length of
X (each element of X to a different worker).
When the length of X is less than the number of workers each
element of X is sent to a worker and tasks is ignored.
Another case where the tasks value is ignored is when using the
bpiterate function; the number of tasks are defined by the number
of data chunks returned by the ITER function.
bpstart(x):
logical(1). Starts the back-end, if necessary.
bpstop(x):
logical(1). Stops the back-end, if necessary and possible.
bpisup(x):
logical(1). Tests whether the back-end is available for
processing, returning a scalar logical value. bp*
functions such as bplapply automatically start the
back-end if necessary.
bpbackend(x), bpbackend(x) <- value:
Gets or sets the parallel bpbackend. Not all back-ends can
be retrieved; see methods("bpbackend").
bplog(x), bplog(x) <- value:
Get or enable logging, if available. value must be a
logical(1).
bpthreshold(x), bpthreshold(x) <- value: Get or
set the logging threshold. value must be a
character(1) string of one of the levels defined in the
futile.logger package: “TRACE”, “DEBUG”,
“INFO”, “WARN”, “ERROR”, or “FATAL”.
bplogdir(x), bplogdir(x) <- value: Get or set an
optional directory for saving log files. The directory must
already exist with read / write ability.
bpresultdir(x), bpresultdir(x) <- value: Get or
set an optional directory for saving results as 'rda' files. The
directory must already exist with read / write ability.
bptimeout(x), bptimeout(x) <- value:
numeric(1) Time (in seconds) allowed for worker to
complete a task. This value is passed to base::setTimeLimit()
as both the cpu and elapsed arguments. If the
computation exceeds timeout an error is thrown with
message 'reached elapsed time limit'.
bpexportglobals(x), bpexportglobals(x) <- value:
logical(1) Export base::options() from manager to
workers? Default TRUE.
bpprogressbar(x), bpprogressbar(x) <- value:
Get or set the value to enable text progress bar.
value must be a logical(1).
bpRNGseed(x), bpRNGseed(x) <- value:
Get or set the seed for random number generaton. value must be a
numeric(1) or NULL.
bpjobname(x), bpjobname(x) <- value:
Get or set the job name.
In the code below BPPARAM is a BiocParallelParam object.
bpstopOnError(x), bpstopOnError(x) <- value:
logical(). Controls if the job stops when an error is hit.
stop.on.error controls whether the job stops after an
error is thrown. When TRUE, the output contains all
successfully completed results up to and including the error.
When stop.on.error == TRUE all computations stop once the
error is hit. When FALSE, the job runs to completion
and successful results are returned along with any error messages.
In the code below BPPARAM is a BiocParallelParam object.
Full documentation for these functions are on separate man pages: see
?bpmapply, ?bplapply, ?bpvec, ?bpiterate and
?bpaggregate.
bpmapply(FUN, ..., MoreArgs=NULL, SIMPLIFY=TRUE, USE.NAMES=TRUE,
BPPARAM=bpparam())
bplapply(X, FUN, ...,
BPPARAM=bpparam())
bpvec(X, FUN, ..., AGGREGATE=c, BPPARAM=bpparam())
bpiterate(ITER, FUN, ..., BPPARAM=bpparam())
bpaggregate(x, data, FUN, ..., BPPARAM=bpparam())
In the code below BPPARAM is a BiocParallelParam object.
show(x)
Martin Morgan and Valerie Obenchain.
SnowParam for computing in distributed memory
MulticoreParam for computing in shared memory
BatchtoolsParam for computing with cluster schedulers
DoparParam for computing with foreach
SerialParam for non-parallel execution
getClass("BiocParallelParam")
## For examples see ?SnowParam, ?MulticoreParam, ?BatchtoolsParam
## and ?SerialParam.Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.