Generates a remote configuration for launching daemons using an HPC cluster resource manager such as Slurm sbatch, SGE and Torque/PBS qsub or LSF bsub.
Arguments
- command
[default "sbatch"] for Slurm. Replace with "qsub" for SGE / Torque / PBS, or "bsub" for LSF. See examples below.
- options
[default ""] options as would be supplied inside a script file passed to
command, e.g. "#SBATCH –mem=10G", each separated by a new line. See examples below.
Other shell commands e.g. to change working directory may also be included.
For certain setups, "module load R" as a final line is required, or for example "module load R/4.5.0" for a specific R version.
For the avoidance of doubt, the initial shebang line such as "#!/bin/bash" is not required.- rscript
[default "Rscript"] assumes the R executable is on the search path. Replace with the full path of the Rscript executable on the remote machine if necessary. If launching on Windows,
"Rscript"should be replaced with"Rscript.exe".
Value
A list in the required format to be supplied to the remote argument
of daemons() or launch_remote().
See also
ssh_config() for SSH launch configurations, or remote_config()
for generic configurations.
Examples
# Slurm Config:
cluster_config(
command = "sbatch",
options = "#SBATCH --job-name=mirai
#SBATCH --mem=10G
#SBATCH --output=job.out
module load R/4.5.0",
rscript = file.path(R.home("bin"), "Rscript")
)
#> $command
#> [1] "/bin/sh"
#>
#> $args
#> [1] "sbatch<<'EOF'\n#!/bin/sh\n#SBATCH --job-name=mirai\n#SBATCH --mem=10G\n#SBATCH --output=job.out\nmodule load R/4.5.0\n"
#> [2] "."
#> [3] "\nEOF"
#>
#> $rscript
#> [1] "/opt/R/4.5.1/lib/R/bin/Rscript"
#>
#> $quote
#> NULL
#>
# SGE Config:
cluster_config(
command = "qsub",
options = "#$ -N mirai
#$ -l mem_free=10G
#$ -o job.out
module load R/4.5.0",
rscript = file.path(R.home("bin"), "Rscript")
)
#> $command
#> [1] "/bin/sh"
#>
#> $args
#> [1] "qsub<<'EOF'\n#!/bin/sh\n#$ -N mirai\n#$ -l mem_free=10G\n#$ -o job.out\nmodule load R/4.5.0\n"
#> [2] "."
#> [3] "\nEOF"
#>
#> $rscript
#> [1] "/opt/R/4.5.1/lib/R/bin/Rscript"
#>
#> $quote
#> NULL
#>
# Torque/PBS Config:
cluster_config(
command = "qsub",
options = "#PBS -N mirai
#PBS -l mem=10gb
#PBS -o job.out
module load R/4.5.0",
rscript = file.path(R.home("bin"), "Rscript")
)
#> $command
#> [1] "/bin/sh"
#>
#> $args
#> [1] "qsub<<'EOF'\n#!/bin/sh\n#PBS -N mirai\n#PBS -l mem=10gb\n#PBS -o job.out\nmodule load R/4.5.0\n"
#> [2] "."
#> [3] "\nEOF"
#>
#> $rscript
#> [1] "/opt/R/4.5.1/lib/R/bin/Rscript"
#>
#> $quote
#> NULL
#>
# LSF Config:
cluster_config(
command = "bsub",
options = "#BSUB -J mirai
#BSUB -M 10000
#BSUB -o job.out
module load R/4.5.0",
rscript = file.path(R.home("bin"), "Rscript")
)
#> $command
#> [1] "/bin/sh"
#>
#> $args
#> [1] "bsub<<'EOF'\n#!/bin/sh\n#BSUB -J mirai\n#BSUB -M 10000\n#BSUB -o job.out\nmodule load R/4.5.0\n"
#> [2] "."
#> [3] "\nEOF"
#>
#> $rscript
#> [1] "/opt/R/4.5.1/lib/R/bin/Rscript"
#>
#> $quote
#> NULL
#>
if (FALSE) { # \dontrun{
# Launch 2 daemons using the Slurm sbatch defaults:
daemons(n = 2, url = host_url(), remote = cluster_config())
} # }