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
_______________________________________________ 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
