[gmx-users] Paralellization limit?

Andrea Carotti and.carotti at farmchim.uniba.it
Wed Apr 19 13:36:08 CEST 2006

Hi all,
I'm trying to simulate a system with two identical proteins (42aa each one), 
solvent spc (18430 mols) and 6 ions NA+...for a total of  ~56100 atoms.
Now the "problem" is that if I run the MD on 4 nodes everything works fine, 
but when I try to use 6 or 8 cpus the process stops on the master and 
continue only on the last two slaves (4 cpus, the systems are dual xeon). 
The problem is that I can't find any error message on the log files.
 I've tried using the d.dppc benchmark files, and all goes fine with 2-4-6 
and 8 cpus.
So my question is: is there a limit of parallelization in gromacs depending 
on the simulated system?
I'm using gromacs 3.3.1, mpich and fftw 2.1.5.
Thanks in advance

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