Hi, Berk:<br><br>the nodes I've been using each have two<br>
quad-core Xeon CPUs - Gromacs4 was compiled for use over an Infiniband<br>
network. Do you need more information? <br><br>Yes, I think this situation is so strange. Thanks. <br>-Xianghong Qi<br><br><div class="gmail_quote">On Wed, Nov 5, 2008 at 7:36 AM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>
Hi,<br><br>That is very strange.<br>If you did not set the -cpt option, mdrun should only write a checkpoint file<br>every 15 minutes, not every 5 seconds.<br><br>What kind of machine are you running on?<br><br>Berk<br><br>
<br><hr>Date: Wed, 5 Nov 2008 06:58:33 -0500<div class="Ih2E3d"><br>From: <a href="mailto:xianghong001@gmail.com" target="_blank">xianghong001@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
</div>Subject: Re: [gmx-users] Re: writing checkpoint<div><div></div><div class="Wj3C7c"><br><br><div>Thanks, Berk:</div>
<div> </div>
<div>My log file actually stop somewhere since its size didn't change for a long time. </div>
<div>Yes, looks like it keeps writing checkpoint info. </div>
<div>I should continue the simulation since the other file looks reasonable. </div>
<div> </div>
<div>I didn't use option -cpt. </div>
<div>Thanks. <br></div>
<div>-Xianghong Qi<br></div>
<div>On Wed, Nov 5, 2008 at 6:39 AM, Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span> wrote:<br>
<blockquote style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div>Hi,<br><br>Why do the log file seem to stop?<br>It keeps writing checkpoint info, right?<br>So I assume it is still running fine.<br><br>But it seems you have selected checkpointing at (nearly) every step.<br>Did you use -cpt 0?<br>
If you don't want checkpoints, you have to set -cpt -1.<br><br>Berk<br><br>
<hr>
Date: Wed, 5 Nov 2008 06:10:03 -0500<br>From: <a href="mailto:xianghong001@gmail.com" target="_blank">xianghong001@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Re: writing checkpoint
<div>
<div></div>
<div><br><br>
<div>Hello, all:</div>
<div> </div>
<div>I got a message when I run my simulation: </div>
<div> </div>
<div><font color="#3333ff">Writing checkpoint, step 100200 at Wed Nov 5 05:22:42 2008</font></div>
<div><font color="#3333ff">Writing checkpoint, step 100210 at Wed Nov 5 05:22:46 2008</font></div>
<div><font color="#3333ff">Writing checkpoint, step 100220 at Wed Nov 5 05:22:51 2008</font></div>
<div><font color="#3333ff">Writing checkpoint, step 100230 at Wed Nov 5 05:22:55 2008</font></div>
<div><font color="#3333ff">Writing checkpoint, step 100240 at Wed Nov 5 05:23:00 2008</font><br clear="all"></div>
<div>.log file seems stop, but simulation is still running, and I can see</div>
<div>.xtc , .edr file are growing. Does anyone has some idea about this</div>
<div>situation? Thanks in advance. </div>
<div> </div>
<div>-Xianghong Qi</div>
<div> </div>
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