[gmx-users] Launching MPI/OpenMP hybrid run

[Carsten Kutzner]

On 04 Mar 2014, at 13:43, alex.bjorling <alex.bjorling at gmail.com> wrote:

> Carsten Kutzner wrote
>> On 04 Mar 2014, at 13:08, Alexander Björling &lt;
> 
>> alex.bjorling@
> 
>> &gt; wrote:
>> 
>>> Dear users,
>>> 
>>> I'm trying to run simulations on a cluster of nodes, each sporting two
>>> AMD
>>> 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
>>> with
>>> 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
> MPI-only jobs.
Then SLURM is not positioning your MPI processes correctly. 
This problem should be independent of Gromacs.

Carsten

> 
> 
> 
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