[gmx-users] using_gromacs_with_openmpi

[Hossein H]

isn't gigabyte Ethernet adequate even for 2 nodes?

On Thu, Apr 23, 2015 at 12:36 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/22/15 3:59 PM, Hossein H wrote:
>
>> Dear GROMACS users and developers
>>
>> I've compiled GROMACS 4.5.5 with gcc and *enable-mpi* option for a small
>> cluster e.g 4 nodes on 1GbE network
>> The code was compiled without problem and i can use it in sequential and
>> parallel mode (using mpirun command), but the performance over the network
>> is very poor. indeed i can run the jobs on one nodes faster than 4 nodes.
>>
>> because each nodes has 4 cores, i run jobs over network using following
>> command:
>>
>>  mpirun -np 16 --host node01,node02,node03,node04 mdrun -deffnm input -v
>>>
>>
>>
>> Someone has any idea why the performance is so poor?
>>
>>
> Because you're using gigabit ethernet as your connection.  That's not
> adequate for parallelization across machines.
>
> -Justin
>
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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