[gmx-users] run gromacs on a single machine with mutiple CPUs
lindahl at cbr.su.se
Thu Dec 21 07:41:23 CET 2006
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.
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