[gmx-users] Signal 11 error with parallel runs

[David van der Spoel]

On Tue, 2003-11-04 at 15:11, sophie.vilarem at laposte.net wrote:
> Hi everybody,
> 
> I am trying to run the d.poly-ch2 benchmark, on a dual xeon
> cluster.
> I have installed the latest LAM version of MPI, and the latest
> version of Gromacs.
> It works all right on 1 CPU, but it fails on 2 CPUs (or
> more...) with the following error :
> 
> ...
> MPI_Send: process in local group is dead (rank 1, MPI_COMM_WORLD)
> Rank (1, MPI_COMM_WORLD): Call stack within LAM:
> Rank (1, MPI_COMM_WORLD):  - MPI_Send()
> Rank (1, MPI_COMM_WORLD):  - MPI_Sendrecv()
> Rank (1, MPI_COMM_WORLD):  - main()
> -----------------------------------------------------------------------------
> One of the processes started by mpirun has exited with a
> nonzero exit
> code.  This typically indicates that the process finished in
> error.
> If your process did not finish in error, be sure to include a
> "return
> 0" or "exit(0)" in your C code before exiting the application.
>  
> PID 8399 failed on node n0 (10.10.100.5) due to signal 11.
> 
> 
> Can anybody help me please? I'm stuck!
> Thank you very much...

I have fixed this in the latest CVS code. You will also have to change
an option in the mdp file:
pbc = full


> 
> Sophie Vilarem
> 
> Accédez au courrier électronique de La Poste : www.laposte.net ; 
> 3615 LAPOSTENET (0,34/mn) ; tél : 08 92 68 13 50 (0,34/mn)
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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