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BiocParallel does not keep logs during job failure

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#103 2 commenti 0 reazioni 1 assegnatario Vedi su GitHub

@nturaga ci sta già lavorando.

Dal 6/9/2019.

Valutazione

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Descrizione

Hello,

I am currently running a parallel jobs (with bplapply) on an LSF cluster using BatchToolsParam and I found an issue where there are no logs produced in runs that have a few jobs failing.

Here is the error log from the failed run:

Quitting from lines 86-88 (demultiplex.Rmd) 
Error in .reduceResultsList(ids, fun, ..., missing.val = missing.val,  : 
  All jobs must be have been successfully computed
Calls: <Anonymous> ... bplapply -> bplapply -> <Anonymous> -> .reduceResultsList
Execution halted

When I tried to check the logs from the batchtools jobs, I noticed that there was no logs being produced at all which made figuring out the reason for the job failures difficult. I eventually managed to capture the logs manually by copying the temporary registry directory before the bplapply job finishes, where I found that the cause of the job failure is due to a missing executable in a few of the cluster nodes, resulting in the job exiting before R was even executed.

It would be really useful to actually be able to get the logs from the batchtools jobs even if some of the jobs failed to execute R, especially in LSF cluster as the logs contain the job execution information.

Lingua principale
R
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