parallelly (version 1.32.1)

availableCores: Get Number of Available Cores on The Current Machine

Description

The current/main R session counts as one, meaning the minimum number of cores available is always at least one.

Usage

availableCores(
  constraints = NULL,
  methods = getOption2("parallelly.availableCores.methods", c("system", "cgroups.cpuset",
    "cgroups.cpuquota", "nproc", "mc.cores", "BiocParallel", "_R_CHECK_LIMIT_CORES_",
    "LSF", "PJM", "PBS", "SGE", "Slurm", "fallback", "custom")),
  na.rm = TRUE,
  logical = getOption2("parallelly.availableCores.logical", TRUE),
  default = c(current = 1L),
  which = c("min", "max", "all"),
  omit = getOption2("parallelly.availableCores.omit", 0L)
)

Value

Return a positive (>= 1) integer. If which = "all", then more than one value may be returned. Together with na.rm = FALSE missing values may also be returned.

Arguments

constraints

An optional character specifying under what constraints ("purposes") we are requesting the values. For instance, on systems where multicore processing is not supported (i.e. Windows), using constrains = "multicore" will force a single core to be reported.

methods

A character vector specifying how to infer the number of available cores.

na.rm

If TRUE, only non-missing settings are considered/returned.

logical

Passed to detectCores(logical = logical), which, if supported, returns the number of logical CPUs (TRUE) or physical CPUs/cores (FALSE). This argument is only if argument methods includes "system".

default

The default number of cores to return if no non-missing settings are available.

which

A character specifying which settings to return. If "min" (default), the minimum value is returned. If "max", the maximum value is returned (be careful!) If "all", all values are returned.

omit

(integer; non-negative) Number of cores to not include.

Avoid ending up with zero cores

Note that some machines might have a limited number of cores, or the R process runs in a container or a cgroup that only provides a small number of cores. In such cases:

ncores <- availableCores() - 1

may return zero, which is often not intended and is likely to give an error downstream. Instead, use:

ncores <- availableCores(omit = 1)

to put aside one of the cores from being used. Regardless how many cores you put aside, this function is guaranteed to return at least one core.

Advanced usage

It is possible to override the maximum number of cores on the machine as reported by availableCores(methods = "system"). This can be done by first specifying options(parallelly.availableCores.methods = "mc.cores") and then the number of cores to use, e.g. options(mc.cores = 8).

Details

The following settings ("methods") for inferring the number of cores are supported:

• "system" - Query detectCores(logical = logical).

• "cgroups.cpuset" - On Unix, query control group (cgroup) value cpuset.set.

• "cgroups.cpuquota" - On Unix, query control group (cgroup) value cpu.cfs_quota_us / cpu.cfs_period_us.

• "nproc" - On Unix, query system command nproc.

• "mc.cores" - If available, returns the value of option mc.cores. Note that mc.cores is defined as the number of additional R processes that can be used in addition to the main R process. This means that with mc.cores = 0 all calculations should be done in the main R process, i.e. we have exactly one core available for our calculations. The mc.cores option defaults to environment variable MC_CORES (and is set accordingly when the parallel package is loaded). The mc.cores option is used by for instance mclapply() of the parallel package.

• "BiocParallel" - Query environment variables BIOCPARALLEL_WORKER_NUMBER (integer), which is defined and used by BiocParallel (>= 1.27.2), and BBS_HOME (logical) used by the Bioconductor Build System. If the former is set, this is the number of cores considered. If the latter is set, then a maximum of 4 cores is considered.

• "LSF" - Query Platform Load Sharing Facility (LSF) environment variable LSB_DJOB_NUMPROC. Jobs with multiple (CPU) slots can be submitted on LSF using bsub -n 2 -R "span[hosts=1]" < hello.sh.

• "PJM" - Query Fujitsu Technical Computing Suite (that we choose to shorten as "PJM") environment variables PJM_VNODE_CORE and PJM_PROC_BY_NODE. The first is set when submitted with pjsub -L vnode-core=8 hello.sh.

• "PBS" - Query TORQUE/PBS environment variables PBS_NUM_PPN and NCPUS. Depending on PBS system configuration, these resource parameters may or may not default to one. An example of a job submission that results in this is qsub -l nodes=1:ppn=2, which requests one node with two cores.

• "SGE" - Query Sun Grid Engine/Oracle Grid Engine/Son of Grid Engine (SGE) environment variable NSLOTS. An example of a job submission that results in this is qsub -pe smp 2 (or qsub -pe by_node 2), which requests two cores on a single machine.

• "Slurm" - Query Simple Linux Utility for Resource Management (Slurm) environment variable SLURM_CPUS_PER_TASK. This may or may not be set. It can be set when submitting a job, e.g. sbatch --cpus-per-task=2 hello.sh or by adding #SBATCH --cpus-per-task=2 to the hello.sh script. If SLURM_CPUS_PER_TASK is not set, then it will fall back to use SLURM_CPUS_ON_NODE if the job is a single-node job (SLURM_JOB_NUM_NODES is 1), e.g. sbatch --ntasks=2 hello.sh.

• "custom" - If option parallelly.availableCores.custom is set and a function, then this function will be called (without arguments) and it's value will be coerced to an integer, which will be interpreted as a number of available cores. If the value is NA, then it will be ignored. It is safe for this custom function to call availableCores(); if done, the custom function will not be recursively called.

For any other value of a methods element, the R option with the same name is queried. If that is not set, the system environment variable is queried. If neither is set, a missing value is returned.

See Also

To get the set of available workers regardless of machine, see availableWorkers().

Examples

message(paste("Number of cores available:", availableCores()))

if (FALSE) {
options(mc.cores = 2L)
message(paste("Number of cores available:", availableCores()))
}

if (FALSE) {
## IMPORTANT: availableCores() may return 1L
options(mc.cores = 1L)
ncores <- availableCores() - 1      ## ncores = 0
ncores <- availableCores(omit = 1)  ## ncores = 1
message(paste("Number of cores to use:", ncores))
}

if (FALSE) {
## Use 75% of the cores on the system but never more than four
options(parallelly.availableCores.custom = function() {
  ncores <- max(parallel::detectCores(), 1L, na.rm = TRUE)
  ncores <- min(as.integer(0.75 * ncores), 4L)
  max(1L, ncores)
})
message(paste("Number of cores available:", availableCores()))

## Use 50% of the cores according to availableCores(), e.g.
## allocated by a job scheduler or cgroups.
## Note that it is safe to call availableCores() here.
options(parallelly.availableCores.custom = function() {
  0.50 * parallelly::availableCores()
})
message(paste("Number of cores available:", availableCores()))
}