[gmx-users] Paralellization limit?
and.carotti at farmchim.uniba.it
Wed Apr 19 13:36:08 CEST 2006
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 18.104.22.168 and fftw 2.1.5.
Thanks in advance
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