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<BLOCKQUOTE TYPE=CITE>
<BLOCKQUOTE TYPE=CITE>
-------- Forwarded Message --------<BR>
<B>From</B>: Nikos Papadimitriou <<A HREF="mailto:Nikos%20Papadimitriou%20%3cnikpap@ipta.demokritos.gr%3e">nikpap@ipta.demokritos.gr</A>><BR>
<B>To</B>: <A HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>
<B>Subject</B>: [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster<BR>
<B>Date</B>: Thu, 8 Dec 2011 11:44:36 +0200<BR>
<BLOCKQUOTE TYPE=CITE>
<BLOCKQUOTE TYPE=CITE>
-------- Forwarded Message --------<BR>
<B>From</B>: Nikos Papadimitriou <<A HREF="mailto:Nikos%20Papadimitriou%20%3cnikpap@ipta.demokritos.gr%3e">nikpap@ipta.demokritos.gr</A>><BR>
<B>To</B>: <A HREF="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>
<B>Subject</B>: [gmx-users] Gromacs 4.5.4 on multi-node cluster<BR>
<B>Date</B>: Wed, 7 Dec 2011 16:26:46 +0200<BR>
<BR>
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>
<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>
-------- Forwarded Message --------<BR>
<B>From</B>: Mark Abraham <<A HREF="mailto:Mark%20Abraham%20%3cMark.Abraham@anu.edu.au%3e">Mark.Abraham@anu.edu.au</A>><BR>
<B>Reply-to</B>: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>
<B>To</B>: Discussion list for GROMACS users <<A HREF="mailto:Discussion%20list%20for%20GROMACS%20users%20%3cgmx-users@gromacs.org%3e">gmx-users@gromacs.org</A>><BR>
<B>Subject</B>: [gmx-users] Gromacs 4.5.4 on multi-node cluster<BR>
<B>Date</B>: Wed, 7 Dec 2011 16:53:49 +0200<BR>
<BR>
On 8/12/2011 1:26 AM, Nikos Papadimitriou wrote: <BR>
<BLOCKQUOTE TYPE=CITE>
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>
</BLOCKQUOTE>
<BR>
Can you run 2-processor MPI test program with that machine file?<BR>
<BR>
Mark<BR>
<BR>
</BLOCKQUOTE>
</BLOCKQUOTE>
"Unfortunately", other MPI programs run fine on 2 or more nodes. There seems to be no problem with MPI.<BR>
<BLOCKQUOTE TYPE=CITE>
<BLOCKQUOTE TYPE=CITE>
<BLOCKQUOTE 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>
</BLOCKQUOTE>
</BLOCKQUOTE>
</BLOCKQUOTE>
-------- Forwarded Message --------<BR>
<B>From</B>: Dimitris Dellis <<A HREF="mailto:Dimitris%20Dellis%20%3cntelll@gmail.com%3e">ntelll@gmail.com</A>><BR>
<B>Reply-to</B>: "Discussion list for GROMACS users" <gmx-users@gromacs.org><BR>
<B>To</B>: Nikos Papadimitriou <<A HREF="mailto:Nikos%20Papadimitriou%20%3cnikpap@ipta.demokritos.gr%3e">nikpap@ipta.demokritos.gr</A>>, Discussion list for GROMACS users <<A HREF="mailto:Discussion%20list%20for%20GROMACS%20users%20%3cgmx-users@gromacs.org%3e">gmx-users@gromacs.org</A>><BR>
<B>Subject</B>: [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster<BR>
<B>Date</B>: Thu, 8 Dec 2011 12:06:10 +0200<BR>
<BR>
Hi.<BR>
This is openmpi related.<BR>
<BR>
Probably you have active the virbr0 interface with IP 192.168.122.1 on nodes.<BR>
Stop and disable the libvirtd (and probably libvirt-guests) service if you don't need it.<BR>
<BR>
Alternatively, <BR>
1. add --mca btl_tcp_if_exclude lo,virbr0 in mpirun flags <BR>
or<BR>
2. add in /home/gromacs/.Installed/openmpi/etc/openmpi-mca-params.conf the following line :<BR>
btl_tcp_if_exclude = lo,virbr0<BR>
to exclude virbr0 from the interfaces list that openmpi can use for communication.<BR>
<BR>
(if virtbr1 etc. are present, add also in exclude list)<BR>
<BR>
<BR>
</BLOCKQUOTE>
</BLOCKQUOTE>
Thank you very much! It works
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