[gmx-users] Launching MPI/OpenMP hybrid run
alex.bjorling at gmail.com
Tue Mar 4 13:44:00 CET 2014
Carsten Kutzner wrote
> On 04 Mar 2014, at 13:08, Alexander Björling <
> > wrote:
>> Dear users,
>> I'm trying to run simulations on a cluster of nodes, each sporting two
>> Opteron 8-core CPU:s. I would like to have one MPI process on each CPU,
>> with OpenMP threads on the 8 cores of each. I've compiled gromacs 5.0
>> intel MPI and OpenMP enabled.
>> To get it running I'm just using two nodes, so 4 MPI processes. I've been
>> using various combinations of the type:
>> mpirun -np 4 -perhost 2 gmx_mpi mdrun -ntomp 8 ...,
>> but I never manage to get the MPI process spread out on the two nodes.
>> Rather, in the example above, 4 MPI processes with 4 OpenMP threads each
>> runs on the first node, and the second node does nothing.
> Did you provide a hostfile / machinefile containing the names of your
> nodes you want the MPI processes to be started on?
No, I just asked SLURM for two nodes, the way I would if I was running
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