[gmx-developers] Workload for parallel run

[David van der Spoel]

Mikhail Plotnikov wrote:
> Hi all,
> 
> I have 2 questions.
> 1. I got the following error while trying to create input file for running Lys/Cut test (downloaded from www.gromacs.org) on more than 16 nodes (for 8 nodes and less it is ok):
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: splitter.c, line: 121
> 
> Fatal error:
> Shake block crossing node boundaries
> constraint between atoms (1447,1454)
> -------------------------------------------------------
> 
> The following command line was used:
> 
> ./grompp -shuffle -sort -np 16 -f cutoff.mdp -p topol.top -c conf.gro -o lzmcutoff.tpr -po lzmcutoffmdout.mdp
> 
> Is there any way to overcome this error and run the test on >16 nodes?
> 
> 2. As I see, parallelization with multi-threading is not implemented in GROMACS-3.3.1 version. Is it going to be implemented in the nearest release? 
> 
> Best regards,
> Mikhail
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Have you checked this (closed) bugzilla?

http://bugzilla.gromacs.org/show_bug.cgi?id=110

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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