well I installed the mpi enabled mdrun and execute it with option -np 8, but still I see only core is being used at 100% instead of 8.<br><br>Is there additional settings to be done to correct this.?<br><br>thanks<br>sikandar<br>
<br><div class="gmail_quote">On Tue, Jun 1, 2010 at 4:18 PM, Mark Abraham <span dir="ltr"><<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5"><br><br>----- Original Message -----<br>From: Sikandar Mashayak <<a href="mailto:symashayak@gmail.com" target="_blank">symashayak@gmail.com</a>><br>Date: Wednesday, June 2, 2010 7:17<br>
Subject: [gmx-users] Running gromacs in parallel on multicore machine<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hi<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I am wondering whether its possible to run gromacs in parallel on single processor machine with multiple cores?<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have 8 core processor, when I run mdrun in serial I see only one of those is used at 100%. I am thinking, if possible, to use all cores approximately equally by running mdrun in parallel and hoping to get results faster.<br>
<font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Any suggestions?<br>
<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"></font></div></div>Compiling with MPI and running in parallel is your only current option. See GROMACS webpage.<br>
<font color="#888888"><br>Mark
</font><br>--<br>
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