<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 4/18/2011 4:39 PM, delara aghaie wrote:
<blockquote cite="mid:847688.81757.qm@web130123.mail.mud.yahoo.com"
type="cite">
<table border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="font: inherit;" valign="top">
<div><br>
<br>
Dear Gromacs users</div>
<div>I run DPPC monolayer on Tip4p2005 water layer system
with gromacs 3.3</div>
<div>I had no problem before but when I run the system
with command</div>
<div>grompp_mpi -c .gro -f .mdp -n .ndx -p .top -o .tpr
-np 8</div>
<div>and then qsub .ll</div>
<div> </div>
<div>the run starts but it has break down several times,
each ime after for ex 987654 steps or more steps or
less.</div>
</td>
</tr>
</tbody>
</table>
</blockquote>
<br>
If you've changed nothing, and it used to work, and now doesn't,
then something about your computer has changed. We can't really help
there - and there must be better people to ask.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:847688.81757.qm@web130123.mail.mud.yahoo.com"
type="cite">
<table border="0" cellpadding="0" cellspacing="0">
<tbody>
<tr>
<td style="font: inherit;" valign="top">
<div> </div>
<div>I get in .o.ii file this message:</div>
<div> </div>
<div>----</div>
<div><font color="#00007f">PBS has allocated the following
nodes:<br>
cx1-25-8-4<br>
cx1-25-8-4<br>
cx1-25-8-4<br>
cx1-25-8-4<br>
cx1-25-8-4<br>
cx1-25-8-4<br>
cx1-25-8-4<br>
cx1-25-8-4<br>
---<br>
mpiexec.intel -genv I_MPI_DEVICE ssm -genv I_MPI_DEBUG
0 -genv I_MPI_PIN yes -genv I_MPI_PIN_MODE lib -genv
I_MPI_FALLBACK_DEVICE disable -genv
DAPL_MAX_CM_RETRIES 500 -genv
DAPL_MAX_CM_RESPONSE_TIME 300 -genv
I_MPI_DAPL_CONNECTION_TIMEOUT 300 -machinefile
/tmp/pbs.5455562.cx1/tmp.VRhkM11825 -n 8 -wdir
/tmp/pbs.5455562.cx1 mdrun_mpi -v -s topol.tpr -np 8</font></div>
<div><font color="#00007f">Job output begins below<br>
-----------------------<br>
mpdallexit: cannot connect to local mpd
(/tmp/pbs.5455562.cx1/mpd2.console_dmohamma_110411.074928);
possible causes:<br>
1. no mpd is running on this host<br>
2. an mpd is running but was started without a
"console" (-n option)<br>
</font>---</div>
<div>what can be the solvation of the possible problem?</div>
<div> </div>
<div>Thanks</div>
<div>D. Aghaie</div>
<div> </div>
</td>
</tr>
</tbody>
</table>
</blockquote>
<br>
</body>
</html>