Built-in templates: Add support for running 'Rscript' in a Linux container, etc.

[HenrikBengtsson]

Wish

Add support for launching Rscript via a Linux container, e.g.

## Call batchtools inside container
module load apptainer/latest
export APPTAINER_BINDPATH="/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH"

apptainer exec /modules/admin-resources/ood-dev/unity-r_4.4.0.sif Rscript --no-restore --quiet --no-save -e 'batchtools::doJobCollection("<%= uri %>")'

Source: mlr-org/batchtools#314 (comment)

Idea

• Add support for specifying how Rscript is launched, e.g.

plan(batchtools_slurm, resources = list(rscript = c("/modules/admin-resources/ood-dev/unity-r_4.4.0.sif", '--bind="/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH"', "Rscript", "--no-restore", "--quiet", "--no-save"))

This would then become the following in the rendered job script:

/modules/admin-resources/ood-dev/unity-r_4.4.0.sif --bind="/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH" Rscript -e 'batchtools::doJobCollection("<%= uri %>")'

• Add support for specifying Rscript options when launching the batchtools job (inspired by https://parallelly.futureverse.org/reference/makeClusterPSOCK.html), e.g.

plan(batchtools_slurm, resources = list(rscript_args = c("--no-restore", "--quiet", "--no-save"))

This would then become the following in the rendered job script:

Rscript --no-restore --quiet --no-save -e 'batchtools::doJobCollection("<%= uri %>")'

• Add support for setting environment variables, e.g.

plan(batchtools_slurm, resources = list(rscript = c("/modules/admin-resources/ood-dev/unity-r_4.4.0.sif", "Rscript"), envs = c(APPTAINER_BINDPATH = "/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH"))

export APPTAINER_BINDPATH="/run/munge,/var/run/munge,/etc/slurm,/var/spool/slurm/slurmd/conf-cache/slurm.conf,$APPTAINER_BINDPATH"

/modules/admin-resources/ood-dev/unity-r_4.4.0.sif Rscript -e 'batchtools::doJobCollection("<%= uri %>")'

[HenrikBengtsson]

Implemented, e.g. https://future.batchtools.futureverse.org/reference/batchtools_slurm.html#ref-examples