[gmx-users] using_gromacs_with_openmpi

[Justin Lemkul]

On 4/22/15 4:14 PM, Hossein H wrote:
> isn't gigabyte Ethernet adequate even for 2 nodes?
>

Well, what does your benchmarking show you?  Likely the performance degrades 
because the interconnect is simply too slow to benefit from additional CPU 
horsepower.

-Justin

> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================