Use SLURM dependencies to wait for jobs before getting output #2
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msmorul
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Mar 6, 2017
R/slurm_utils.R
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| # Submit a dummy job with dependency to block R script | ||
| wait_for_job <- function(slr_job) { | ||
| srun <- sprintf( | ||
| 'srun -n1 -t0:1 -o/dev/null -Q -dafterany:%d /bin/hostname', |
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This will work, however may want to use --dependency= as there is a discrepency between the llnl docs say (-P) https://computing.llnl.gov/tutorials/linux_clusters/man/srun.txt and what srun on our cluster accepts (-d).
added 2 commits
March 7, 2017 13:37
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@msmorul After you mentioned today that
srunblocks until the job is done, I realized this provides a mechanism to block the R process too viasystem('srun ...'). Just had to make a slurm_job's output collection function execute a dummy job with srun that has the parent job as a dependency. I don’t believe it locks up a cluster node, but let me know what you think of this solution.