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

[David van der Spoel]

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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