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On 8/12/2011 1:26 AM, Nikos Papadimitriou wrote:
<blockquote cite="mid:1323268006.2872.89.camel@Carnot" type="cite">
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Dear All,<br>
<br>
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:<br>
<br>
[gromacs@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<br>
NNODES=2, MYRANK=0, HOSTNAME=compute-1-1.local<br>
NNODES=2, MYRANK=1, HOSTNAME=compute-1-2.local<br>
NODEID=0 argc=12<br>
NODEID=1 argc=12<br>
<br>
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.<br>
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<br>
Can you run 2-processor MPI test program with that machine file?<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:1323268006.2872.89.camel@Carnot" type="cite">
<br>
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.<br>
<br>
Have you any idea what might cause this situation?<br>
Thank you in advance!
<br>
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