Thanks for the guideline. I installed the lam/mpi 7.0.6 and compile the gromance with "--enable-mpi" option. When I run mdrun, I got message that lamboot is not start. Then I start the lamboot and try to run mdrun witn "-np 4 -v N 4" (gromacs user guide example). However, the gromacs still run on single CPU. It does not take the advantage of other three CPUs on the server. Do I miss anything? Or I misunderstand the parallel computing/MPI concept? Thanks.
Best, Ocean On 12/20/06, Erik Lindahl <[EMAIL PROTECTED]> wrote:
Hi, On Dec 21, 2006, at 3:12 AM, Seaclear Theory wrote: > Hi! All, > > I have a linux server with 4 CPUs. How can I run gromacs on all CPUs? > The gromacs manual has very limit information. And it does not works. > I installed Lam/mpi and compile gromacs with mpi. Thanks lot! > The problem is that there is no standard for how you start MPI programs - that is entirely up to the MPI implementation. Essentially, add "-np 4" to grompp to get a parallel input file, boot your "virtual" parallel computer with "lamboot <hostfile>", and then start a parallel run as "mpirun -np 4 mdrun <normal args>". Most MPI libraries use mpirun is some form, but they differ in how you specify the machines to run on. Cheers, Erik _______________________________________________ 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
_______________________________________________ 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
