[gmx-users] only one cpu "works" in my linux cluster

liu xin zgxjlx at gmail.com
Tue Oct 9 14:38:50 CEST 2007

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
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 <anoddlad at yahoo.com> 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 < zgxjlx at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at 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 at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20071009/e7c38a30/attachment.html>

More information about the gromacs.org_gmx-users mailing list