Thanks for your quick comment Alan :)<br><br>
<div><span class="gmail_quote">On 10/9/07, <b class="gmail_sendername">Alan Dodd</b> <<a href="mailto:anoddlad@yahoo.com">anoddlad@yahoo.com</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
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<div style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Yeah.</div>
<div style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Check the machinefile tells mpich what you think it does. It looks pretty certain to be an issue with mpich rather than gromacs. Unfortunately, I don't use mpich any more because I find LAM better. Standard procedure, turn up the verbosity on everything, check the outputs, re-read the relevant manuals.
<br> </div>
<div style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"><span class="q">----- Original Message ----<br>From: liu xin <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:zgxjlx@gmail.com" target="_blank">
zgxjlx@gmail.com</a>><br>To: Discussion list for GROMACS users <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br></span>
<div><span class="e" id="q_1158516e9b8d277a_2">Sent: Tuesday, October 9, 2007 1:38:50 PM<br>Subject: Re: [gmx-users] only one cpu "works" in my linux cluster<br><br>
<div>Thanks Alan</div>
<div>in fact I've already added the option -machinefile, here's the script:</div>
<div><br>cat $PBS_NODEFILE >/home/liuxin/mpd.hosts<br>/home/liuxin/mpich2/bin/mpdboot -n 6 -f mpd.hosts<br>/home/liuxin/mpich2/bin/mpiexec -machinefile $PBS_NODEFILE -np 12 /home/liuxin/<br>programs/gromacs33mpi/bin/mdrun -v -s
12np.tpr -o -c -e -g -np 12</div>
<div> </div>
<div>I am a little busy today, sorry for replying so late...<br> </div>
<div><span class="gmail_quote">On 10/8/07, <b class="gmail_sendername">Alan Dodd</b> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:anoddlad@yahoo.com" target="_blank" rel="nofollow">anoddlad@yahoo.com
</a>> wrote: </span>
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<div style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">
<div style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">Check the MPICH manuals for how to specify the nodes to run on. From memory, the option -machinefile lets you do this.
<div><span><br><br>
<div style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<br>From: liu xin <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:zgxjlx@gmail.com" target="_blank" rel="nofollow">
zgxjlx@gmail.com</a>><br>To: Discussion list for GROMACS users <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org" target="_blank" rel="nofollow">gmx-users@gromacs.org</a>
><br>Sent: Monday, October 8, 2007 1:51:12 PM <br>Subject: [gmx-users] only one cpu "works" in my linux cluster<br><br>
<div>Dear GMXers</div>
<div> </div>
<div>this is how I've done it so far:</div>
<div>grompp -f -c -p -o 12np.tpr -np 12</div>
<div>qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s 12np.tpr -np 12 )</div>
<div>then it seems my mdrun works fine, but when I ssh to each node to check the cpu efficiency with "top", I find that there's only one cpu works with 12 processes! The other nodes are completely idle.</div>
<div> </div>
<div>the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info:</div>
<div>Linux login 2.4.21-32.EL #1 SMP Fri Apr 15 21:02:58 EDT 2005 x86_64 x86_64 x86_64 GNU/Linux</div>
<div>our administrator have installed mpich1.2.7 in the default DIR (/usr/local), but I have some problems to do mpi-mdrun with mpich1.2.7, so I installed mpich2 in my personal dir.</div>
<div>I've searched the list, but cant get any solution. Does it have something to do with the kernel or there's some conflict between mpich1 and 2, or something else?</div>
<div> </div>
<div>This is the first time I build up a Linux Cluster on my own, ANY suggestions are appreciated !</div>
<div> </div>
<div>Xin Liu</div></div><br></span></div></div></div><span><br>
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