[slurm-users] R jobs crashing when run in parallel
pgoetz at math.utexas.edu
Mon Mar 29 16:34:14 UTC 2021
Could this be a function of the R script you're trying to run, or are
you saying you get this error running the same script which works at
On 3/29/21 7:47 AM, Simon Andrews wrote:
> I've got a weird problem on our slurm cluster. If I submit lots of R
> jobs to the queue then as soon as I've got more than about 7 of them
> running at the same time I start to get failures, saying:
> /bi/apps/R/4.0.4/lib64/R/bin/exec/R: error while loading shared
> libraries: libpcre2-8.so.0: cannot open shared object file: No such file
> or directory
> ..which makes no sense because that library is definitely there, and
> other jobs on the same nodes worked both before and after the failed
> jobs. I recently ran 500 identical jobs and 152 of them failed in this way.
> There are no errors in the log files on the compute nodes where this
> failed and it happens across multiple nodes so it's not a single one
> being strange. The R binary is on an isilon network share, but the
> libpcre2 library is on the local disk for the node.
> Anyone come across anything like this before? Any suggestions for fixes?
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