[gmx-users] Gromacs 4.5.4 on multi-node cluster

[Mark Abraham]

On 8/12/2011 1:26 AM, Nikos Papadimitriou wrote:
> Dear All,
>
> I had been running Gromacs 4.0.7 on a 12-node cluster (Intel i7-920 
> 4-cores) with OS Rocks 5.4.2. Recently, I have upgraded the cluster OS 
> to Rocks 5.4.3 and I have installed Gromacs 4.5.4 from the Bio Roll 
> repository. When running in parallel on the same node, everything 
> works fine. However, when I am trying to run on more than one nodes 
> the run stalls immediately with the following message:
>
> [gromacs at tornado Test]$ /home/gromacs/.Installed/openmpi/bin/mpirun 
> -np 2 -machinefile machines 
> /home/gromacs/.Installed/gromacs/bin/mdrun_mpi -s md_run.tpr -o 
> md_traj.trr -c md_confs.gro -e md.edr -g md.log -v
> NNODES=2, MYRANK=0, HOSTNAME=compute-1-1.local
> NNODES=2, MYRANK=1, HOSTNAME=compute-1-2.local
> NODEID=0 argc=12
> NODEID=1 argc=12
>
> The mdrun_mpi thread seems to start in both nodes but the run does not 
> go on and no file is produced. It seems that the nodes are waiting for 
> some kind of communication between them. The problem occurs even for 
> the simplest case (i.e. NVT simulation of 1000 Argon atoms without 
> Coulombic interactions). Openmpi and networking between the nodes seem 
> to work fine since there are not any problems with other software that 
> run with MPI.

Can you run 2-processor MPI test program with that machine file?

Mark

>
> In an attempt to find a solution, I have manually compiled and 
> installed Gromacs 4.5.5 (with --enable-mpi) after having installed the 
> latest version of openmpi and fftw3 and no error occurred during the 
> installation. However, when trying to run on two different nodes 
> exactly the same problem appears.
>
> Have you any idea what might cause this situation?
> Thank you in advance!
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111208/f9c3f4f5/attachment.html>