mlr-org / mlr-org/batchtools

clusterFunctionsSlurm.R returns incorrect "batch.id"

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R
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Description

On a cluster that I'm using, sbatch prints multiple outputs. So, e.g., reg$status$batch.id always returns incorrect batch.id which further causes some difficulties (e.g., cannot distinguish running jobs and expired jobs).

To illustrate my issue, please see below my simple syntax taken from clusterFunctionsSlurm.R.

res = runOSCommand("sbatch", "~/test.slurm")
# > res
# $sys.cmd
# [1] "sbatch"

# $sys.args
# [1] "~/test.slurm"

# $exit.code
# [1] 0

# $output
# [1] "sbatch: This job will be charged to the account \"liu\". Base Allocation:500,000.00 hours, Current Balance:497,218.77 hours (99% remaining)"
# [2] "Submitted batch job 1556425"

output = stri_flatten(stri_trim_both(res$output), "\n")
# > output
# [1] "sbatch: This job will be charged to the account \"liu\". Base Allocation:500,000.00 hours, Current Balance:497,218.77 hours (99% remaining)\nSubmitted batch job 1556425"

id = stri_split_fixed(output[1L], " ")[[1L]][4L]
# > id
# [1] "will"

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Research direction

Inspect clusterFunctionsSlurm.R and reproduce the reported sbatch output with multiple lines. Check how res$output is flattened and parsed; the fix is done when batch.id extracts 1556425 from the submission line instead of "will", allowing running and expired jobs to be distinguished.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
hpc
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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