availableWorkers: Get Set of Available Workers

In MINATILO/parallelly: Enhancing the 'parallel' Package

Description

Get Set of Available Workers

Usage

availableWorkers(
  methods = getOption2("parallelly.availableWorkers.methods", c("mc.cores",
    "BiocParallel", "_R_CHECK_LIMIT_CORES_", "PBS", "SGE", "Slurm", "LSF", "custom",
    "system", "fallback")),
  na.rm = TRUE,
  logical = getOption2("parallelly.availableCores.logical", TRUE),
  default = getOption2("parallelly.localhost.hostname", "localhost"),
  which = c("auto", "min", "max", "all")
)

Arguments

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 as-is to availableCores().
default	The default set of workers.
which	A character specifying which set / sets to return. If "auto" (default), the first non-empty set found. If "min", the minimum value is returned. If "max", the maximum value is returned (be careful!) If "all", all values are returned.

Details

The default set of workers for each method is rep("localhost", times = availableCores(methods = method, logical = logical)), which means that each will at least use as many parallel workers on the current machine that availableCores() allows for that method.

In addition, the following settings ("methods") are also acknowledged:

• "PBS" - Query TORQUE/PBS environment variable PBS_NODEFILE. If this is set and specifies an existing file, then the set of workers is read from that file, where one worker (node) is given per line. An example of a job submission that results in this is qsub -l nodes = 4:ppn = 2, which requests four nodes each with two cores.

• "SGE" - Query Sun/Oracle Grid Engine (SGE) environment variable PE_HOSTFILE. An example of a job submission that results in this is qsub -pe mpi 8 (or qsub -pe ompi 8), which requests eight cores on a any number of machines.

• "LSF" - Query LSF/OpenLava environment variable LSB_HOSTS.

• "Slurm" - Query Slurm environment variable SLURM_JOB_NODELIST (fallback to legacy SLURM_NODELIST) and parse set of nodes. Then query Slurm environment variable SLURM_JOB_CPUS_PER_NODE (fallback SLURM_TASKS_PER_NODE) to infer how many CPU cores Slurm have alloted to each of the nodes. If SLURM_CPUS_PER_TASK is set, which is always a scalar, then that is respected too, i.e. if it is smaller, then that is used for all nodes. For example, if SLURM_NODELIST="n1,n[03-05]" (expands to c("n1", "n03", "n04", "n05")) and SLURM_JOB_CPUS_PER_NODE="2(x2),3,2" (expands to c(2, 2, 3, 2, 2)), then c("n1", "n1", "n03", "n03", "n04", "n04", "n04", "n05", "n05") is returned. If in addition, SLURM_CPUS_PER_TASK=1, which can happen depending on hyperthreading configurations on the Slurm cluster, then c("n1", "n03", "n04", "n05") is returned.

• "custom" - If option parallelly.availableWorkers.custom is set and a function, then this function will be called (without arguments) and it's value will be coerced to a character vector, which will be interpreted as hostnames of available workers.

Value

Return a character vector of workers, which typically consists of names of machines / compute nodes, but may also be IP numbers.

Known limitations

availableWorkers(methods = "Slurm") will expand SLURM_JOB_NODELIST using scontrol show hostnames "$SLURM_JOB_NODELIST", if available. If not available, then it attempts to parse the compressed nodelist based on a best-guess understanding on what the possible syntax may be. One known limitation is that "multi-dimensional" ranges are not supported, e.g. "a[1-2]b[3-4]" is expanded by scontrol to c("a1b3", "a1b4", "a2b3", "a2b4"). If scontrol is not available, then any components that failed to be parsed are dropped with an informative warning message. If no compents could be parsed, then the result of methods = "Slurm" will be empty.

See Also

To get the number of available workers on the current machine, see availableCores().

Examples

message(paste("Available workers:",
        paste(sQuote(availableWorkers()), collapse = ", ")))

## Not run: 
options(mc.cores = 2L)
message(paste("Available workers:",
        paste(sQuote(availableWorkers()), collapse = ", ")))

## End(Not run)

## Not run: 
## Always use two workers on host 'n1' and one on host 'n2'
options(parallelly.availableWorkers.custom = function() {
  c("n1", "n1", "n2")
})
message(paste("Available workers:",
        paste(sQuote(availableWorkers()), collapse = ", ")))

## End(Not run)

MINATILO/parallelly documentation built on Dec. 17, 2021, 2:11 a.m.