[gmx-developers] Workload for parallel run

[Yang Ye]

On 4/26/2007 7:00 PM, 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?
>   
I don't think that you can overcome this.
> 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? 
>   
Check the mail archive please.
> Best regards,
> Mikhail
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