<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><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">----- Original Message ----<BR>From: liu xin <zgxjlx@gmail.com><BR>To: Discussion list for GROMACS users <gmx-users@gromacs.org><BR>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 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">Check the MPICH manuals for how to specify the nodes to run on. From memory, the option -machinefile lets you do this.
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<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">----- Original Message ----<BR>From: liu xin <<A href="mailto:zgxjlx@gmail.com" target=_blank rel=nofollow> zgxjlx@gmail.com</A>><BR>To: Discussion list for GROMACS users <<A 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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