[gmx-users] parallel run crashes only when shuffled

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 2 16:02:21 CEST 2002

On Tue, 2002-10-01 at 15:43, Mikko Huhtala wrote:
> 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.
Could be a bug. You could improve your performance a bit by shuffling
protein 1
sol 10000
ions 999
protein 1
sol 10000

> Mikko
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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