[gmx-developers] Seg fault in mdrun with AltiVec and LZM/PME

[Josh Hursey]

We have tryed running LZM/PME with the 3.2.0 beta version of gromacs, and
have had limited success. In our benchmarking we compile data from three
successive runs of the molecule. We run this though LAM-MPI using
2,4,6,and 8 node configurations.

We have been able to complete the three iterations of the run on 2,6,and 8
node configurations. However when running on only 4 nodes LZM/PME will
stall and never come back. It has completed the first iteration in two of
the tests, but then stalls upon the next iteration.

To help characterize this problem here are some pointers to the
directories where it runs:
http://cluster.earlham.edu/project/b-and-t-gromacs/results/cairo/raw-data/pme-Gromacs-Optimal-Configuration-3.2.0-4on4-4/
http://cluster.earlham.edu/project/b-and-t-gromacs/results/cairo/raw-data/pme-Gromacs-Optimal-Configuration-3.2.0-4on4-4-Run-1/
http://cluster.earlham.edu/project/b-and-t-gromacs/results/cairo/raw-data/pme-Gromacs-Optimal-Configuration-3.2.0-4on4-4-Run-2/
http://cluster.earlham.edu/project/b-and-t-gromacs/results/cairo/raw-data/pme-Gromacs-Optimal-Configuration-3.2.0-4on4-4-Run-3/
http://cluster.earlham.edu/project/b-and-t-gromacs/results/cairo/raw-data/pme-Gromacs-Optimal-Configuration-3.2.0-4on4-4-Run-4/

In each directory you will find all of the standard Gromacs files that are
used and generated. In addition you will find:
* pme.stderr  -- STDERR messages output by Gromacs (grompp and mdrun)
* pme.stdout  -- STDOUT messages output by Gromacs (grompp and mdrun)
* pme.pl      -- The script that we use to run the entire test

The configuration used is copied from the Benchmark distribution that we
have untar'ed here:
http://cluster.earlham.edu/project/b-and-t-gromacs/tests/etc/orignal-molecules/pme/

Thanks for your help,

Josh Hursey
Earlham College Cluster Computing Lab
http://cluster.earlham.edu/


> Subject: Re: [gmx-developers] Seg fault in mdrun with AltiVec and LZM/PME
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: gmx-developers at gromacs.org
> Date: Tue, 13 Jan 2004 13:11:27 +0100
> Reply-To: gmx-developers at gromacs.org
>
> On Tue, 2004-01-13 at 12:30, Charlie Peck wrote:
> > >On Tue, 2004-01-13 at 11:25, Charlie Peck wrote:
> > >>  We're trying to run the LZM molecule (with the PME configuration)
> > ...
> > >>  similar results.
> > >Could you try it with the 3.2.0 beta version?
> >
> > Sure, I just checked gromacs.org and didn't find it, could you send me
> > a pointer to it?
> ftp.gromacs.org/pub/beta
>
> >
> > charlie
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++