hi, On Tuesday 25 July 2006 14:34, David van der Spoel wrote: > Mr. M.N. Manoj wrote: > > Dear Sir/Madam > > > > We have been using gromacs 3.3 on our workstation succesfully > > Now we have purchased a Rocks 4.2 based cluster (dual xeon processor > > with 5 nodes) > > We have been able to compile Gromacs 3.3 with fftw 2.1.5 and MPI-LAM > > 7.1.2 on front node, its working there. Update to gmx 3.3.1 and fftw 3.1.1
> > Then we have copied the installation folder /usr/local/gromacs to each > > node easist is to use nfs for all nodes so no copy action is needed. You should mount nfs on all nodes. > > > > But when we run it, the performance is not better than one single node > > (master) in terms of ps/day > > Also from the ganglia it can be seen that hardly anything is happening > > on compute nodes, though it says its running mdrun_mpi > > > > Now we have few questions: > > > > 1. What is the exact procedure for installing gromacs on the the FULL > > CLUSTER ? > > 2. Do we have to install it (gmx and fftw2) on each node? > > 3. Any other way ? see above > > your installation is probably fine. > you have to tell mpirun to use more than one node, try "man mpirun" > Next step is to get a queing system like pbs/maui for your cluster, which puts all jobs on the nodes. > > please ask further questions on the mailing list. Greetings, Florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
