[gmx-users] parallel run crashes only when shuffled
Lynne E. Bilston
l.bilston at unsw.edu.au
Thu Oct 3 01:05:37 CEST 2002
>From: Mikko Huhtala <mhuhtala at abo.fi>
>Date: Tue, 1 Oct 2002 16:43:50 +0300
>To: gmx-users at gromacs.org
>Subject: [gmx-users] parallel run crashes only when shuffled
>Reply-To: gmx-users at gromacs.org
>I tried to use grompp with '-shuffle' to setup up a simulation for 4
>processors. The system is a protein dimer, one small-molecule ligand
>in each monomer, water and some ions. The suffled simulation crashes
>after 15 steps and some LINCS warnings with a fatal pressure scaling
>error (= system explodes). The exact same starting conformation runs
>on 4 processors just fine when it is set up without the suffle.
>I know that shuffle probably does not improve things much for a system
>like this, so I am happily running the unshuffled configuration. I was
>simply wondering if I missed something obvious or is this a bug in
>Gromacs? I am running version gromacs-3.1.4-1 (rpm) with
>lam-6.5.4-usysv.1 (rpm) on Pentium 4 Xeons.
I had the same problem on my dual athlons, and have discontinued using
shuffle/sort. Erik promised that there would be a new method of
shuffling/sorting soon, so I haven't tried to track down the bug using debug.
David - Can you elucidate your "shuffle manually" comment? Do you mean
re-order the input coordinate file as you suggest?
Lynne E. Bilston, PhD
Senior Scientist, Prince of Wales Medical Research Institute, and
Conjoint Associate Professor, Faculty of Medicine, University of New South
POWMRI, Barker St, Randwick, NSW 2031 Australia
Tel: +61-2-9382-7924 Fax: +61-2-9382-2643
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