---
title: "Introduction to *BiocParallel*"
author:
- name: "Valerie Obenchain"
- name: "Vincent Carey"
- name: "Michael Lawrence"
- name: "Phylis Atieno"
  affiliation: "Vignette translation from Sweave to Rmarkdown / HTML"
- name: "Martin Morgan"
  email: "Martin.Morgan@RoswellPark.org"
date: "Edited: October, 2022; Compiled: `r format(Sys.time(), '%B %d, %Y')`"
package: BiocParallel
vignette: >
  %\VignetteIndexEntry{Introduction to BiocParallel}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
output:
  BiocStyle::html_document
---

# Introduction

Numerous approaches are available for parallel computing in R. The
CRAN Task View for high performance and parallel computing provides
useful high-level summaries and [package
categorization](https://cran.r-project.org/web/views/HighPerformanceComputing.html).
Most Task View packages cite or identify one or more of
[*snow*](https://cran.r-project.org/package=snow) ,
[*Rmpi*](https://cran.r-project.org/package=Rmpi),
[*multicore*](https://cran.r-project.org/package=multicore) or
[*foreach*](https://cran.r-project.org/package=foreach) as relevant
parallelization infrastructure. Direct support in *R* for *parallel*
computing started with release 2.14.0 with inclusion of the
[parallel](https://cran.r-project.org/package=parallel) package which
contains modified versions of
[*multicore*](https://cran.r-project.org/package=multicore) and
[*snow*](https://cran.r-project.org/package=snow).

A basic objective of [*BiocParallel*][] is to reduce the complexity
faced when developing and using software that performs parallel
computations. With the introduction of the `BiocParallelParam` object,
[*BiocParallel*][] aims to provide a unified interface to existing
parallel infrastructure where code can be easily executed in different
environments. The `BiocParallelParam` specifies the environment of
choice as well as computing resources and is invoked by 'registration'
or passed as an argument to the [*BiocParallel*][] functions.

[*BiocParallel*][] offers the following conveniences over the 'roll
your own' approach to parallel programming.

- unified interface: `BiocParallelParam` instances define the method
  of parallel evaluation (multi-core, snow cluster, etc.) and
  computing resources (number of workers, error handling, cleanup,
  etc.).

- parallel iteration over lists, files and vectorized operations:
  `bplapply`, `bpmapply` and `bpvec` provide parallel list iteration
  and vectorized operations. `bpiterate` iterates through files
  distributing chunks to parallel workers.

- cluster scheduling: When the parallel environment is managed by a
  cluster scheduler through
  [*batchtools](https://cran.r-project.org/package=batchtools), job
  management and result retrieval are considerably simplified.

- support of `foreach` : The
  [*foreach*](https://cran.r-project.org/package=foreach) and
  [*iterators*](https://cran.r-project.org/package=iterators) packages
  are fully supported. Registration of the parallel back end uses
  `BiocParallelParam` instances.

# Quick start


The [*BiocParallel*][] package is available at bioconductor.org and
can be downloaded via `BiocManager`:

```
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("BiocParallel")
```

Load [*BiocParallel*][]

```{r}
library(BiocParallel)
```

The test function simply returns the square root of "x".

```{r quick_start FUN}
FUN <- function(x) { round(sqrt(x), 4) }
```

Functions in [*BiocParallel*][] use the registered back-ends for
parallel evaluation. The default is the top entry of the registry
list.

```{r quick_start registry}
registered()
```

Configure your R session to always use a particular back-end configure
by setting options named after the back ends in an `.RProfile` file,
e.g.,

```{r configure_registry, eval=FALSE}
options(MulticoreParam=MulticoreParam(workers=4))
```

When a [*BiocParallel*][] function is invoked with no `BPPARAM`
argument the default back-end is used.

```{r quickstart_bplapply_default, eval=FALSE}
bplapply(1:4, FUN)
```

Environment specific back-ends can be defined for any of the registry
entries. This example uses a 2-worker SOCK cluster.

```{r quickstart_snow}
param <- SnowParam(workers = 2, type = "SOCK")
bplapply(1:4, FUN, BPPARAM = param)
```

# The *BiocParallel* Interface

## Classes

### `BiocParallelParam`

`BiocParallelParam` instances configure different parallel evaluation
environments. Creating or `register()` ing a '`Param`' allows the same
code to be used in different parallel environments without a code
re-write. Params listed are supported on all of Unix, Mac and Windows
except `MulticoreParam` which is Unix and Mac only.

- `SerialParam`:

  Supported on all platforms.

  Evaluate [*BiocParallel*][]-enabled code with parallel evaluation
  disabled. This approach is useful when writing new scripts and
  trying to debug code.

- `MulticoreParam`:

  Supported on Unix and Mac. On Windows, `MulticoreParam` dispatches
  to `SerialParam`.

  Evaluate [*BiocParallel*][]-enabled code using multiple cores on a
  single computer.  When available, this is the most efficient and
  least troublesome way to parallelize code. Windows does not
  support multi-core evaluation (the `MulticoreParam` object can be
  used, but evaluation is serial). On other operating systems, the
  default number of workers equals the value of the global option
  `mc.cores` (e.g.,`getOption("mc.cores")` ) or, if that is not set,
  the number of cores returned by `arallel::detectCores() - 2` ;
  when number of cores cannot be determined, the default is 1.

  `MulticoreParam` uses 'forked' processes with 'copy-on-change'
  semantics -- memory is only copied when it is changed. This makes
  it very efficient to invoke compared to other back-ends.

  There are several important caveats to using
  `MulticoreParam`. Forked processes are not available on
  Windows. Some environments, e.g., *RStudio*, do not work well with
  forked processes, assuming that code evaluation is
  single-threaded. Some external resources, e.g., access to files or
  data bases, maintain state in a way that assumes the resource is
  accessed only by a single thread. A subtle cost is that *R*'s
  garbage collector runs periodically, and 'marks' memory as in
  use. This effectively triggers a copy of the marked memory. *R*'s
  generational garbage collector is triggered at
  difficult-to-predict times; the effect in a long-running forked
  process is that the memory is eventually copied. See [this
  post](https://support.bioconductor.org/p/70196/#70509) for
  additional details.

  `MulticoreParam` is based on facilities originally implemented in
  the [*multicore*](https://cran.r-project.org/package=multicore)
  package and subsequently the
  [*parallel*](https://cran.r-project.org/package=parallel) package
  in base.

- `SnowParam`:

  Supported on all platforms.

  Evaluate [*BiocParallel*][]-enabled code across several distinct
  instances, on one or several computers. This is a straightforward
  approach for executing parallel code on one or several computers,
  and is based on facilities originally implemented in the
  [*snow*](https://cran.r-project.org/package=snow)
  package. Different types of
  [*snow*](https://cran.r-project.org/package=snow) 'back-ends' are
  supported, including socket and MPI clusters.

- `BatchtoolsParam`:

  Applicable to clusters with formal schedulers.

  Evaluate [*BiocParallel*][]-enabled code by submitting to a
  cluster scheduler like SGE.

- `DoparParam`:

  Supported on all platforms.

  Register a parallel back-end supported by the
  [*foreach*](https://cran.r-project.org/package=foreach) package
  for use with [*BiocParallel*][].

The simplest illustration of creating `BiocParallelParam` is

```{r BiocParallelParam_SerialParam}
serialParam <- SerialParam()
serialParam
```

Most parameters have additional arguments influencing behavior, e.g.,
specifying the number of 'cores' to use when creating a
`MulticoreParam` instance

```{r BiocParallelParam_MulticoreParam}
multicoreParam <- MulticoreParam(workers = 8)
multicoreParam
```

Arguments are described on the corresponding help page, e.g.,
`?MulticoreParam.`.

### `register()`ing `BiocParallelParam` instances

The list of registered `BiocParallelParam` instances represents the
user's preferences for different types of back-ends. Individual
algorithms may specify a preferred back-end, and different back-ends
maybe chosen when parallel evaluation is nested.

The registry behaves like a 'stack' in that the last entry registered
is added to the top of the list and becomes the "next used" (i.e., the
default).

`registered` invoked with no arguments lists all back-ends.

```{r register_registered}
registered()
```

`bpparam` returns the default from the top of the list.

```{r register_bpparam}
bpparam()
```

Add a specialized instance with `register`. When `default` is TRUE,
the new instance becomes the default.

```{r register_BatchtoolsParam}
default <- registered()
register(BatchtoolsParam(workers = 10), default = TRUE)
```

`BatchtoolsParam` has been moved to the top of the list and is now the
default.

```{r register_BatchtoolsParam2}
names(registered())
bpparam()
```

Restore the original registry

```{r register_restore}
for (param in rev(default))
    register(param)
```

## Functions


### Parallel looping, vectorized and aggregate operations

These are used in common functions, implemented as much as possible for
all back-ends. The functions (see the help pages, e.g., `?bplapply` for a full
definition) include

`bplapply(X, FUN, ...)`:

Apply in parallel a function `FUN` to each element of `X`. `bplapply`
invokes `FUN length(X)` times, each time with a single element of `X`.

`bpmapply(FUN, ...)`:

Apply in parallel a function to the first, second, etc., elements of
each argument in ....

`bpiterate(ITER, FUN, ...)`:

Apply in parallel a function to the output of function `ITER`. Data
chunks are returned by `ITER` and distributed to parallel workers
along with `FUN`. Intended for iteration though an undefined number of
data chunks (i.e., records in a file).

`bpvec(X, FUN, ...)`:

Apply in parallel a function `FUN` to subsets of `X`.`bpvec` invokes
function as many times as there are cores or cluster nodes, with
receiving a subset (typically more than 1 element, in contrast to
`bplapply`) of `X`.

`bpaggregate(x, data, FUN, ...)`:

Use the formula in `X` to aggregate `data` using `FUN`.

### Parallel evaluation environment

These functions query and control the state of the parallel evaluation
environment.

`bpisup(x)`: Query a `BiocParallelParam` back-end `X` for its status.

`bpworkers`; `bpnworkers`: Query a `BiocParallelParam` back-end for
the number of workers available for parallel evaluation.

`bptasks`: Divides a job (e.g., single call to \*lapply function) into
tasks.  Applicable to `MulticoreParam` only;`DoparParam` and
`BatchtoolsParam` have their own approach to dividing a job among
workers.

`bpstart(x)`: Start a parallel back end specified by
`BiocParallelParam x, `, if possible.

`bpstop(x)`: Stop a parallel back end specified by `BiocParallelParam x`.

### Error handling and logging

Logging and advanced error recovery is available in `BiocParallel`
1.1.25 and later.  For a more details see the vignette titled "Error
Handling and Logging":

```{r error-vignette, eval=FALSE}
browseVignettes("BiocParallel")
```

### Locks and counters

Inter-process (i.e., single machine) locks and counters are supported
using `ipclock()`, `ipcyield()`, and friends. Use these to synchronize
computation, e.g., allowing only a single process to write to a file
at a time.

# Use cases

Sample data are BAM files from a transcription profiling experiment
available in the *RNAseqData.HNRNPC.bam.chr14* package.

```{r use_cases_data}
library(RNAseqData.HNRNPC.bam.chr14)
fls <- RNAseqData.HNRNPC.bam.chr14_BAMFILES
```

## Single machine

Common approaches on a single machine are to use multiple cores in
forked processes, or to use clusters of independent processes.

For purely -based computations on non-Windows computers, there are
substantial benefits, such as shared memory, to be had using forked
processes. However, this approach is not portable across platforms,
and fails when code uses functionality, e.g., file or data base
access, that assumes only a single thread is accessing the
resource. While use of forked processes with `MulticoreParam` is an
attractive solution for scripts using pure functionality, robust and
complex code often requires use of independent processes and
`SnowParam`.

### Forked processes with `MulticoreParam`

This example counts overlaps between BAM files and a defined set of
ranges. First create a GRanges with regions of interest (in practice
this could be large).

```{r forking_gr, message=FALSE}
library(GenomicAlignments) ## for GenomicRanges and readGAlignments()
gr <- GRanges("chr14", IRanges((1000:3999)*5000, width=1000))
```

A `ScanBamParam` defines regions to extract from the files.

```{r forking_param}
param <- ScanBamParam(which=range(gr))
```

`FUN` counts overlaps between the ranges in 'gr' and the files.

```{r forking_FUN}
FUN <- function(fl, param) {
    gal <- readGAlignments(fl, param = param)
    sum(countOverlaps(gr, gal))
}
```

All parameters necessary for running a job in a multi-core environment
are specified in the `MulticoreParam` instance.

```{r forking_default_multicore}
MulticoreParam()
```

The [*BiocParallel*][] functions, such as `bplapply`, use information
in the `MulticoreParam` to set up the appropriate back-end and pass
relevant arguments to low-level functions.

```{verbatim}
> bplapply(fls[1:3], FUN, BPPARAM = MulticoreParam(), param = param)
$ERR127306
[1] 1185

$ERR127307
[1] 1123

$ERR127308
[1] 1241
```

Shared memory environments eliminate the need to pass large data
between workers or load common packages. Note that in this code the
GRanges data was not passed to all workers in `bplapply` and FUN did
not need to load
[*GenomicAlignments*[](http://bioconductor.org/packages/GenomicAlignments)for
access to the `readGAlign ments` function.

Problems with forked processes occur when code implementating
functionality used by the workers is not written in anticipation of use
by forked processes. One example is the database connection underlying
Bioconductor's `org.*` packages. This pseudo-code

```{r db_problems, eval = FALSE}
library(org.Hs.eg.db)
FUN <- function(x, ...) {
...
mapIds(org.Hs.eg.db, ...)
...
}
bplapply(X, FUN, ..., BPPARAM = MulticoreParam())
```

is likely to fail, because `library(org.Hs.eg.db)` opens a database
connection that is accessed by multiple processes. A solution is to
ensure that the database is opened independently in each process

```
FUN <- function(x, ...) {
library(org.Hs.eg.db)
...
mapIds(org.Hs.eg.db, ...)
...
}
bplapply(X, FUN, ..., BPPARAM = MulticoreParam())
```

### Clusters of independent processes with `SnowParam`

Both Windows and non-Windows machines can use the cluster approach to
spawn processes. [*BiocParallel*][] back-end choices for clusters on a
single machine are *SnowParam* for configuring a Snow cluster or the
*DoparParam* for use with the *foreach* package.

To re-run the counting example, FUN needs to modified such that 'gr'
is passed as a formal argument and required libraries are loaded on
each worker. (In general, this is not necessary for functions defined
in a package name space, see [Section 6](#sec:developers).)

```{r cluster_FUN}
FUN <- function(fl, param, gr) {
    suppressPackageStartupMessages({
        library(GenomicAlignments)
    })
    gal <- readGAlignments(fl, param = param)
    sum(countOverlaps(gr, gal))
}
```

Define a 2-worker SOCK Snow cluster.

```{r cluster_snow_param}
snow <- SnowParam(workers = 2, type = "SOCK")
```

A call to `bplapply` with the *SnowParam* creates the cluster and
distributes the work.

```{r cluster_bplapply}
bplapply(fls[1:3], FUN, BPPARAM = snow, param = param, gr = gr)
```

The FUN written for the cluster adds some overhead due to the passing
of the GRanges and the loading of
[*GenomicAlignments*](http://bioconductor.org/packages/GenomicAlignments)
on each worker. This approach, however, has the advantage that it
works on most platforms and does not require a coding change when
switching between windows and non-windows machines.

If several `bplapply()` statements are likely to require the same
resource, it often makes sense to create a cluster once using
`bpstart()`. The workers are re-used by each call to `bplapply()`, so
they do not have to re-load packages, etc.

```{r db_solution_2, eval = FALSE}
register(SnowParam()) # default evaluation
bpstart() # start the cluster
...
bplapply(X, FUN1, ...)
...
bplapply(X, FUN2, ...) # re-use workers
...
bpstop()
```

## *Ad hoc* cluster of multiple machines

We use the term *ad hoc* cluster to define a group of machines that can
communicate with each other and to which the user has password-less
log-in access. This example uses a group of compute machines (\"the
rhinos\") on the FHCRC network.

### *Ad hoc* Sockets

On Linux and Mac OS X, a socket cluster is created across machines by
supplying machine names as the`workers``argument to a
*BiocParallelParam* instance instead of a number. Each name represents
an *R* process; repeat names indicate multiple workers on the same
machine.

Create a with *SnowParam* 2 cpus from 'rhino01' and 1 from 'rhino02'.

```
hosts <- c("rhino01", "rhino01", "rhino02")
param <- SnowParam(workers = hosts, type = "SOCK")
```

Execute FUN 4 times across the workers.

```{verbatim}
> FUN <- function(i) system("hostname", intern=TRUE)
> bplapply(1:4, FUN, BPPARAM = param)
[[1]]
[1] "rhino01"

[[2]]
[1] "rhino01"

[[3]]
[1] "rhino02"

[[4]]
[1] "rhino01"
```

When creating a cluster across Windows machines must be IP addresses
(e.g., \"140.107.218.57\") instead of machine names.

 ### MPI

An MPI cluster across machines is created with *mpirun* or *mpiexec*
from the command line or a script. A list of machine names provided as
the -hostfile argument defines the mpi universe.

The hostfile requests 2 processors on 3 different machines.

```{verbatim}
rhino01 slots=2
rhino02 slots=2
rhino03 slots=2
```

From the command line, start a single interactive process on the current
machine.

```{verbatim}
mpiexec --np 1 --hostfile hostfile R --vanilla
```

Load [*BiocParallel*][] and create an MPI Snow cluster. The number
`workers` of in should match the number of slots requested in the
hostfile. Using a smaller number of workers uses a subset of the
slots.

```{verbatim}
> library(BiocParallel)
> param <- SnowParam(workers = 6, type = "MPI")
```

Execute FUN 6 times across the workers.

```{verbatim}
> FUN <- function(i) system("hostname", intern=TRUE)
> bplapply(1:6, FUN, BPPARAM = param)
bplapply(1:6, FUN, BPPARAM = param)
        6 slaves are spawned successfully. 0 failed.
[[1]]
[1] "rhino01"

[[2]]
[1] "rhino02"

[[3]]
[1] "rhino02"

[[4]]
[1] "rhino03"

[[5]]
[1] "rhino03"

[[6]]
[1] "rhino01"
```

Batch jobs can be launched with mpiexec and R CMD BATCH. Code to be
executed is in 'Rcode.R'.

```{verbatim}
mpiexec --hostfile hostfile R CMD BATCH Rcode.R
```

## Clusters with schedulers

Computer clusters are far from standardized, so the following may
require significant adaptation; it is written from experience here at
FHCRC, where we have a large cluster managed via SLURM. Nodes on the
cluster have shared disks and common system images, minimizing
complexity about making data resources available to individual nodes.
There are two simple models for use of the cluster, Cluster-centric and
R-centric.

### Cluster-centric

The idea is to use cluster management software to allocate resources,
and then arrange for an script to be evaluated in the context of
allocated resources. NOTE: Depending on your cluster configuration it
may be necessary to add a line to the template file instructing workers
to use the version of R on the master / head node. Otherwise the default
R on the worker nodes will be used.

For SLURM, we might request space for 4 tasks (with `salloc` or
`sbatch`), arrange to start the MPI environment (with `orterun`) and on
a single node in that universe run an script `BiocParallel-MPI.R`. The
command is

```{verbatim}
$ salloc -N 4 orterun -n 1 R -f BiocParallel-MPI.R
```

The *R* script might do the following, using MPI for parallel evaluation.
Start by loading necessary packages and defining `FUN` work to be done

```{r cluster-MPI-work, eval=FALSE}
library(BiocParallel)
library(Rmpi)
FUN <- function(i) system("hostname", intern=TRUE)
```

Create a *SnowParam* instance with the number of nodes equal to the
size of the MPI universe minus 1 (let one node dispatch jobs to
workers), and register this instance as the default

```{r cluster-MPI, eval=FALSE}
param <- SnowParam(mpi.universe.size() - 1, "MPI")
register(param)
```

Evaluate the work in parallel, process the results, clean up, and quit

```{r cluster-MPI-do, eval=FALSE}
xx <- bplapply(1:100, FUN)
table(unlist(xx))
mpi.quit()
```

The entire session is as follows:

```{verbatim}
$ salloc -N 4 orterun -n 1 R --vanilla -f BiocParallel-MPI.R
salloc: Job is in held state, pending scheduler release
salloc: Pending job allocation 6762292
salloc: job 6762292 queued and waiting for resources
salloc: job 6762292 has been allocated resources
salloc: Granted job allocation 6762292
## ...
> FUN <- function(i) system("hostname", intern=TRUE)
>
> library(BiocParallel)
> library(Rmpi)
> param <- SnowParam(mpi.universe.size() - 1, "MPI")
> register(param)
> xx <- bplapply(1:100, FUN)
4 slaves are spawned successfully. 0 failed.
> table(unlist(xx))
gizmof13 gizmof71 gizmof86 gizmof88
25 25 25 25
>
> mpi.quit()
salloc: Relinquishing job allocation 6762292
salloc: Job allocation 6762292 has been revoked.
```

One advantage of this approach is that the responsibility for managing
the cluster lies firmly with the cluster management software -- if one
wants more nodes, or needs special resources, then adjust parameters
to `salloc` (or `sbatch`).

Notice that workers are spawned within the `bplapply` function; it
might often make sense to more explicitly manage workers with
`bpstart` and `bpstop`, e.g.,

```{r cluster-MPI-bpstart, eval=FALSE}
param <- bpstart(SnowParam(mpi.universe.size() - 1, "MPI"))
register(param)
xx <- bplapply(1:100, FUN)
bpstop(param)
mpi.quit()
```

### R-centric

A more *R*-centric approach might start an *R* script on the head
node, and use *batchtools* to submit jobs from within *R* the
session. One way of doing this is to create a file containing a
template for the job submission step, e.g., for SLURM; a starting
point might be found at

```{r slurm}
tmpl <- system.file(package="batchtools", "templates", "slurm-simple.tmpl")
noquote(readLines(tmpl))
```

The *R* script, run interactively or from the command line, might then
look like

```{r cluster-batchtools, eval=FALSE}
## define work to be done
FUN <- function(i) system("hostname", intern=TRUE)
library(BiocParallel)

## register SLURM cluster instructions from the template file
param <- BatchtoolsParam(workers=5, cluster="slurm", template=tmpl)
register(param)

## do work
xx <- bplapply(1:100, FUN)
table(unlist(xx))
```

The code runs on the head node until `bplapply` , where the script
interacts with the SLURM scheduler to request a SLURM allocation, run
jobs, and retrieve results.  The argument `4` to `BatchtoolsParam`
specifies the number of workers to request from the scheduler;
`bplapply` divides the 100 jobs among the 4 workers. If
`BatchtoolsParam` had been created without specifying any workers,
then 100 jobs implied by the argument to `bplapply` would be
associated with 100 tasks submitted to the scheduler.

Because cluster tasks are running in independent `R` instances, and
often on physically separate machines, a convenient 'best practice' is
to write `FUN` in a 'functional programming' manner, such that all
data required for the function is passed in as arguments or (for large
data) loaded implicitly or explicitly (e.g., via an *R* library) from
disk.

# Analyzing genomic data in *Bioconductor*


General strategies exist for handling large genomic data that are well
suited to *R* programs. A manuscript titled *Scalable Genomics with R
and BioConductor* (<http://arxiv.org/abs/1409.2864>) by Michael
Lawrence and Martin Morgan, reviews several of these approaches and
demonstrate implementation with *Bioconductor * packages. Problem
areas include scalable processing, summarization and
visualization. The techniques presented include restricting queries,
compressing data, iterating, and parallel computing.

Ideas are presented in an approachable fashion within a framework of
common use cases. This is a benificial read for anyone anyone tackling
genomics problems in *R*.

# For developers {#sec:developers}


Developers wishing to use [*BiocParallel*][] in their own packages
should include [*BiocParallel*][] in the `DESCRIPTION` file

```{verbatim}
Imports: BiocParallel
```

and import the functions they wish to use in the `NAMESPACE` file,
e.g.,

```{verbatim}
importFrom(BiocParallel, bplapply)
```

Then invoke the desired function in the code, e.g.,

```{r devel-bplapply}
system.time(x <- bplapply(1:3, function(i) { Sys.sleep(i); i }))

unlist(x)
```

This will use the back-end returned by `bpparam()` , by default a
`MulticoreParam()` on Linux / macOS, on Windows, or the user's
preferred back-end if they have used `register()`.

The `MulticoreParam` back-end does not require any special
configuration or set-up and is therefore the safest option for
developers. Unfortunately, `MulticoreParam` provides only serial
evaluation on Windows.

Developers should document that their function uses [*BiocParallel*][]
functions on the main page, and should perhaps include in their
function signature an argument `BPPARAM=bpparam()`.  Developers should
NOT use 'register()' in package code -- this sets a preference that
influences use of 'bplapply()' and friends in all packages, not just
their package.

Developers wishing to invoke back-ends other than `MulticoreParam` ,
or to write code that works across Windows, macOS and Linux, no longer
need to take special care to ensure that required packages, data, and
functions are available and loaded on the remote nodes. By default,
will export global variables to the workers due to the
default. Nonetheless, a good practice during development is to use
independent processes (via ) rather than relying on forked (via )
processes. For instance, clusters include the costs of setting up the
computational environment (loading required packages, for instance)
that may discourage use of parallelization when parallelization
provides only marginal performance gains from the computation *per
se*. Likewise, may be more sensitive to inappropriate calls to shared
libraries, revealing errors that are only transient under.

In `bplapply()`, the environment of `FUN` (other than the global
environment) is serialized to the workers. A consequence is that, when
`FUN ` is inside a package name space, other functions available in
the name space are available to `FUN ` on the workers.

# For server administrators {#sec:administrators}

If the package is installed on a server used by multiple users, then the
default value of cores used can sometimes lead to many more tasks being
run than the server has cores if two or more users run a
parallel-enabled function simultaneously. A more conservative number of
cores than all of them minus 2 may be desirable, so that one user does
not take all of the cores unless they explicitly specify so. This can be
implemented with environment variables. Setting or for all system users
to the number of cores divided by the typical number of concurrent users
is a reasonable approach to avoiding this scenario.

# sessionInfo

```{r sessionInfo}
sessionInfo()
```

[*BiocParallel*]: https://bioconductor.org/packages/BiocParallel