Minimal support for array jobs via <modellauncher> #3480
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infotroph
commented
Mar 11, 2025
| if (!is.null(qsub_extra)) { | ||
| qsub <- paste(qsub, qsub_extra) | ||
| } | ||
| qsub <- gsub("@NAME@", paste0("PEcAn-", run_id_string), qsub_string) | ||
| qsub <- gsub("@STDOUT@", file.path(host_outdir, run_id_string, stdout_log), qsub) | ||
| qsub <- gsub("@STDERR@", file.path(host_outdir, run_id_string, stderr_log), qsub) |
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Moving these down so that @NAME@ etc get replaced in qsub.extra too
infotroph
commented
Mar 11, 2025
| close(jobfile) | ||
| compt_run <- 0 | ||
| jobfile <- NULL | ||
| } |
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No change in logic here, just consolidating if blocks for readability
infotroph
commented
Mar 11, 2025
| } | ||
| # HACK: Code below gets 'run' from names(jobids) so need an entry for | ||
| # each run. But when using modellauncher all runs have the same jobid | ||
| jobids[run] <- sub(settings$host$qsub.jobid, "\\1", out[length(out)]) | ||
| } | ||
|
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| } else { | ||
| pb <- utils::txtProgressBar(min = 0, max = nruns, style = 3) | ||
| pbi <- 0 | ||
| for (run in job_modellauncher) { | ||
| out <- PEcAn.remote::start_serial( | ||
| run = run, |
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With the loop missing this run was set to the last run processed in one of the loops above, which is likely to be a directory WITHOUT a launcher.sh in it.
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Description
I wanted a quick way to submit array jobs to Slurm, and realized I could lightly abuse the modellauncher system by passing my own shell script as a binary. This patch mostly allows passing the number of jobs in the run into the qsub string as
@NJOBS@so that I could write<qsub.extra>-a 1-@NJOBS@</qsub.extra>, plus a couple small cleanups in the modellauncher logic ofstart_model_runs.Also: While I was thinking about it, deleted the long-defunct
start.model.runsfrom PEcAn.remote and decided to just roll it in here rather than make a separate PR.Motivation and Context
I'm currently using this as
with slurm_array_submit.sh being a thin wrapper that reads a path from line number $SLURM_ARRAY_TASK_ID of joblist.txt and calls the
job.shthat lives at that path.Review Time Estimate
Types of changes
Checklist: