[gmx-users] Long trajectory split

[Mark Abraham]

Normally an MPI-enabled mdrun would be named mdrun_mpi, and running a
non-MPI mdrun would produce symptoms like yours depending exactly how your
filesystem chooses to do things, so Justin and Vitaly's theory is sound.
Look at the top section of your .log file for what mdrun thinks about MPI!

Mark


On Sun, Feb 23, 2014 at 5:32 PM, Marcelo Depólo <marcelodepolo at gmail.com>wrote:

> Maybe I should explain it better.
>
> I am using "*mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o prt.trr*", pretty
> much a standard line. This job in a batch creates the outputs and, after
> some (random) time, a back up is done and new files are written, but the
> job itself do not finish.
>
>
> 2014-02-23 17:12 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > On 2/23/14, 11:00 AM, Marcelo Depólo wrote:
> >
> >> But it is not quite happening simultaneously, Justin.
> >>
> >> It is producing one after another and, consequently, backing up the
> files.
> >>
> >>
> > You'll have to provide the exact commands you're issuing.  Likely you're
> > leaving the output names to the default, which causes them to be backed
> up
> > rather than overwritten.
> >
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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>
> --
> Marcelo Depólo Polêto
> Uppsala Universitet - Sweden
> Science without Borders - CAPES
> Phone: +46 76 581 67 49
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