Thanks for your quick comment Alan :)
On 10/9/07, Alan Dodd <[EMAIL PROTECTED]> wrote: > > Yeah. > 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. > > ----- Original Message ---- > From: liu xin <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Sent: Tuesday, October 9, 2007 1:38:50 PM > Subject: Re: [gmx-users] only one cpu "works" in my linux cluster > > Thanks Alan > in fact I've already added the option -machinefile, here's the script: > > cat $PBS_NODEFILE >/home/liuxin/mpd.hosts > /home/liuxin/mpich2/bin/mpdboot -n 6 -f mpd.hosts > /home/liuxin/mpich2/bin/mpiexec -machinefile $PBS_NODEFILE -np 12 > /home/liuxin/ > programs/gromacs33mpi/bin/mdrun -v -s 12np.tpr -o -c -e -g -np 12 > > I am a little busy today, sorry for replying so late... > > On 10/8/07, Alan Dodd <[EMAIL PROTECTED]> wrote: > > > > Check the MPICH manuals for how to specify the nodes to run on. From > > memory, the option -machinefile lets you do this. > > > > ----- Original Message ---- > > From: liu xin < [EMAIL PROTECTED]> > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Sent: Monday, October 8, 2007 1:51:12 PM > > Subject: [gmx-users] only one cpu "works" in my linux cluster > > > > Dear GMXers > > > > this is how I've done it so far: > > grompp -f -c -p -o 12np.tpr -np 12 > > qsub -l node=6 12np.sh (/home/me/mpich2/bin/mpirun -np 12 mdrun -s > > 12np.tpr -np 12 ) > > 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. > > > > the cluster have 56 Intel Xeon duo 3.0G CPUs, below is my system info: > > 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 > > 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. > > 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? > > > > This is the first time I build up a Linux Cluster on my own, ANY > > suggestions are appreciated ! > > > > Xin Liu > > > > > > ------------------------------ > > Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user > > panel<http://us.rd.yahoo.com/evt=48516/*http://surveylink.yahoo.com/gmrs/yahoo_panel_invite.asp?a=7+>and > > lay it on us. > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > ------------------------------ > Pinpoint customers > <http://us.rd.yahoo.com/evt=48250/*http://searchmarketing.yahoo.com/arp/sponsoredsearch_v9.php?o=US2226&cmp=Yahoo&ctv=AprNI&s=Y&s2=EM&b=50>who > are looking for what you sell. > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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