[gmx-users] cluster problem

[David]

On Tue, 2004-10-19 at 18:46, gerph at correo.unam.mx wrote:
> Hi everybody,
> 
> we have a cluster beowulf with smp nodes running (almost well, but not
> totally) GROMACS but we can only run the demo s-peptide as just as 5
> task, no more than that.
> If we try to use both processors of the node it fails, even if we only
> create 2 tasks and try to run them in the same node. Apparently, one of
> the task hangs up (the master or task 0) and the process never ends.
> I know that 'cause I kill the job taking out from pbs scheduler.
> 
> We can run that demo with one process (P) for each node;
>        with P <= 5
> 
> We're using mpiexec and pbs.

try running the water box from the tutorial first. Do you mean it
doesn't work, or crashes, or does not become faster?
> 
> Test it with gromacs 3.1.1 & 3.2.1
> 
> 
> Next, we sumarize our cluster's configuration:
> 
> 
> %mpiexec -v
> 
>   Version 0.71, configure options: --with-pbs=/usr/local/pbs
> --with-default-comm=mpich-p4 --with-mpicc=/local/mpich/bin/mpicc
> 
> 
> mpich-1.2.4
> 
> 
> OpenPBS_2_3_16
> 
> 
> All nodes configuration:         2.4.18papikernel #2 SMP  RH 7.2
> 
> 
> 
> Gromac's version:                3.1  &  3.2.1
> 
> 
> 
> Hope you can help us.
> 
> 
> -------------------------------------------------
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> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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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