[gmx-users] MPI issue

David van der Spoel spoel at xray.bmc.uu.se
Thu Jan 17 08:45:51 CET 2008

Paul Whitford wrote:
> I am running gromacs on a machine with altivec support.  My 
> understanding is I have to use MVAPICH on this machine.
There is no coupling between altivec and MPI varirant.

> I occasionally have runs crash and I receive the following error
> n559(0): Loaded with Money
> n536(14): 14 - MPI_ALLREDUCE : Null communicator
> n536(14): [14] [] Aborting Program!
> n559(0): 0 - MPI_ALLREDUCE : Null communicator
> n559(0): [0] [] Aborting Program!
> Cleaning up all processes ...Cleaning up all processes ...done.
> Does this indicate a problem with the machine, mvapich, or gromacs?  
> Again, this doesn't always happen, just sometimes (which makes me 
> suspect it is a machine issue).  Any advice on where the problem might 
> be would be helpful.  thanks in advance.

If it is reproducible it could be MPI or GROMACS. I use openmpi, and 
sometimes when I abort a job the next one will not start, but the one 
after, due to some leftovers somewhere on the system.

Unless this is reproducible it is impossible to debug, otherwise it 
could even be flaky hardware.

> -Paul
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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