I never used mprun -np 2, and I had not problem. Before I didn't use "mprun -np 2", now I don't use "mprun -np 2" but simulation time now is twice. It has changed from a day to the other.<br>However I've just tried, like you suggested, to use " -np 2" (in grompp and in mdrun) but I obtain an error:
<br>-------------------------------------------<br>"Program mdrun_d, VERSION 3.3.1<br>Source code file: init.c, line: 69<br><br>Fatal error:<br>run input file DNA8_mdEq.tpr was made for 2 nodes,<br> while mdrun_d expected it to be for 1 nodes.
<br>"<br>-------------------------------------------<br>In fact I've only one node.<br><br>Laptop should be running in top speed, I never modified the configuration of energy profile.<br>Beniamino<br><br><br><div><span class="gmail_quote">
2006/6/3, Yang Ye <<a href="mailto:leafyoung81-group@yahoo.com">leafyoung81-group@yahoo.com</a>>:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
First, make sure that you used mdrun -np 2.<br>Second, check your energy profile. Is your laptop running in top speed?<br>or does it have sleep time?<br><br>Yang Ye<br><br>Beniamino Sciacca wrote:<br>> I don't understand what you talking about...
<br>> I didn't write any hostfile.... I'm not in a cluster. I only use my<br>> notebook with the two cores.<br>> In fact I type "lamboot" without -v.......<br>><br>> Beniamino<br>><br>> Mark Abraham ha scritto:
<br>>> Did your default LAM hostfile configuration (or whatever it is)<br>>> change from 2 processors to one?<br>>><br>>> Mark<br>>> _______________________________________________<br>>> gmx-users mailing list
<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please don't post (un)subscribe requests to the list. Use the www
<br>>> interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php
</a><br>>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the www<br>> interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br>--<br>/Regards,/<br>Yang Ye<br>/Computational Biology Lab<br>School of Biological Sciences
<br>Nanyang Technological University<br>Singapore<br>Tel: 6316-2884<br>/<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>