[maker-devel] /tmp full

[Benjamin Rubin]

OK, thanks for the tips. Knowing the particulars of how SLURM might be
causing this is extremely helpful. I'll try to just empty /tmp before
running MAKER on each node, as you suggest. I suspect that will work but
will work on getting MPI running as well.

Thanks!
Ben

On Sat, Jan 7, 2017 at 6:29 PM, Carson Holt <carsonhh at gmail.com> wrote:

> If you use the MPI settings, then all processes will share a single
> temporary directory, otherwise they each will have a separate one since
> they can’t intercommunicate.
>
> MAKER tries to cleanup its files on finish or failure, but if you or the
> system kill it with certain signals, then it is reaped immediately by the
> system and not allowed to finish cleaning up. Signals 9 and 19 for example
> will do that. If a failure is related to the drive being full or a memory
> issue, then your system may be hitting it with one of these uncatchable
> signals. For example SLURM may use signal 9 or 19 if a process fails to
> respond to signal 15 in a timely manner (i.e. MAKER may be removing files,
> but SLURM gets impatient and kills it more aggressively because it thinks
> the process is not responding). You can always try and empty /tmp as the
> first step in your batch script, and it will remove files belonging to you
> before launching MAKER.
>
> —Carson
>
>
>
>
> > On Jan 6, 2017, at 6:22 PM, Benjamin Rubin <brubin at fieldmuseum.org>
> wrote:
> >
> > Hi all,
> >
> > Maker keeps filling up the /tmp directories on the cluster I am using.
> It appears that most of the space is taken with many versions of various
> blast databases. I suspect that this issue is partly due to my not using
> MPI and instead launching multiple instances of maker (typically 16) in the
> same working directory. However, it appears that maker is also leaving some
> of these databases in /tmp even after it has died or been killed and they
> are piling up.
> >
> > I am submitting my jobs to the cluster via SLURM but have installed
> maker locally rather than system-wide. My system administrator is going to
> try creating a larger locally mounted directory on some of the nodes for me
> but I wanted to check to see if you have any other suggestions to solve the
> issue or make sure that maker cleans up /tmp as aggressively as possible.
> >
> > I am using maker3-beta.
> >
> > Thanks for any help,
> > Ben
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>


-- 
_____________________________________________________
Benjamin ER Rubin, PhD
Committee on Evolutionary Biology
University of Chicago
benrubin.org

Division of Insects
Zoology Department
Field Museum of Natural History
1400 South Lake Shore Drive
Chicago, IL 60605
USA
Office: (312) 665-7776
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