rQsub: Submit (qsub) R jobs.

In paodan/funcTools: some useful function tools in practice

Submit (qsub) R jobs.

Description

Submit R jobs in parallel (array).

Usage

rQsub(
  path = getwd(),
  rFile = "testQsub.R",
  jobName = "job",
  threaded = 1,
  memoryG = 10,
  rTimeHour = 2,
  logFile = "logfilename.log",
  email = NULL,
  when2Email = "aes",
  computeNode = "all.q@n00[0-9][0-9]*",
  moreQsubParams = "",
  preCMD = "echo \"module load R/3.3.0 && Rscript ",
  param1 = 1:10,
  ...
)

Arguments

path	file path.
rFile	the R script to run.
jobName	the job name(s).
threaded	integer or integer vector to specify the number of threads of each job.
memoryG	numeric or numeric vector to specify the memory (in Gb) of each job.
rTimeHour	numeric or numeric vector. Maximum running time (in hour) of each job.
logFile	the log file(s) for errors and warnings.
email	email to receive report from HPC. The default is NULL.
when2Email	when will the server send a email. This can be "b" (start) and/or "e" (end) and/or "a" (abortion) and/or "s" (suspension) of your job. The default is "aes". This parameter will not be used if email is NULL.
computeNode	which computing CPU node will be used? Support regular expression. The default is "all.q@n00[0-9][0-9]*"
moreQsubParams	more qsub parameters.
preCMD	the command to run R script, the default is 'echo "module load R/3.3.0 && Rscript '.
param1	the first parameter passed to R script.
...	other parameter passed to R script.

Value

A list of output of running rFile.

Examples

## Not run: 
# This function can only run on HPC.

## Section 1, the format of R script file (for example myfile.R) to submit:
args = commandArgs(TRUE)
if (FALSE){
 # Input the code to use rQsub, see section
 # And run the code manually in this if`{}` statement , for example:
 rQsub(path = getwd(), rFile = "myfile.R", param1 = 1:5)
}
arg1 = args[1]
# Then input R code to use the arg1 variable. for example:
cat("test code result:", arg1, "\n")

## Section 2, the code to use rQsub
# One parameter in R script
path = "/my/file/path"
rQsub(path = "/my/file/path",
      rFile = paste0(path, "/testQsub.R"),
      jobName = "job", threaded = 1,
      memoryG = 10, rTimeHour = 2,
      logFile = paste0(path, "/logfilename.log"),
      preCMD = 'echo "module load R/3.3.0 && Rscript ',
      param1 = 1:10)
# Multiple parameters in R script and using 2 threads
rQsub(path = "/my/file/path",
      rFile = paste0(path, "/testQsub.R"),
      jobName = "job", threaded = 2,
      param1 = 1:10, param2 = 2:11, param3 = 3:12)

# Specify job names, threads, memories and running time.
rQsub(path = "/my/file/path",
      rFile = paste0(path, "/testQsub.R"),
      jobName = paste0("job_", formatN(1:10, 2)),
      logFile = paste0(path, "/logfilename_", formatN(1:10, 2), ".log"),
      threaded = rep(c(1, 2), each = 5),
      memoryG = rep(c(10, 20), each = 5),
      rTimeHour = rep(c(24, 48), each = 5),
      param1 = 1:10)

## End(Not run)

paodan/funcTools documentation built on April 1, 2024, 12:01 a.m.