[gmx-developers] Workload for parallel run

Mikhail Plotnikov m_plot at mail.ru
Thu Apr 26 13:00:11 CEST 2007

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,

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