[gmx-users] Biomolecule shuffling in parallel runs crash MD

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 19 17:30:04 CET 2002

On Thu, 2002-12-19 at 15:11, Marcin Wojciechowski wrote:
> Hi fellows,
> Problem is as follows:
> I have a system with one protein neutralized with ions and solvated in
> water box. I runned it for a total 1ns of MD on 16 cpu cluster. Recently i
> tried to start it on 32 cpus ('cos i have scali mpi and scaling on 32 is
> acceptable, approx. 60%). Unfortunatelly i always had an error regarding
> LINCS warnings and terminating the simulation. The facts I observed:
> 1. Division over CPUs is like 1 protein on 1 cpu and some waters, plus
> rest of the water on other cpus (shuffle and sort used): no problem,
> simulation goes fine.
> 2. Division over CPUSs is like 1 protein and 0 waters (when you use more
> cpus), plus rest of the water on other cpus (shuffle and sort used): MD
> crash after first step (LINCS warnangle warnings).

Your system probably has to be deshuffled using trjconv. Problem is that
you can not desort...

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://xray.bmc.uu.se/~spoel

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