Hi Andrea,
Andrea Carotti wrote:
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 1.2.5.2 and fftw 2.1.5.
I have encountered similar problems when using mpich 1.2.x on
Ethernet. Upgrading to mpich-2.x or using LAM solved the problems.
There is only a parallelisation limit in the sense that using more
CPUs does not always result in faster execution. 56 k atoms should
run happily on 8 CPUs.
Good luck,
Carsten
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