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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>
<br>
<br>
<br>
<br>
<br>
On 12/08/2011 11:44 AM, Nikos Papadimitriou wrote:
<blockquote cite="mid:1323337476.3605.2.camel@Carnot" type="cite">
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addingions?</title>
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<blockquote type="CITE"> <br>
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<blockquote type="CITE"> -------- Forwarded Message --------<br>
<b>From</b>: Nikos Papadimitriou <<a moz-do-not-send="true"
href="mailto:Nikos%20Papadimitriou%20%3cnikpap@ipta.demokritos.gr%3e">nikpap@ipta.demokritos.gr</a>><br>
<b>To</b>: <a moz-do-not-send="true"
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>
</blockquote>
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<blockquote type="CITE"> -------- Forwarded Message --------<br>
<b>From</b>: Mark Abraham <<a moz-do-not-send="true"
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"
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
<b>To</b>: Discussion list for GROMACS users <<a
moz-do-not-send="true"
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>
<br>
</blockquote>
</blockquote>
</blockquote>
<br>
<br>
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