[gmx-users] using_gromacs_with_openmpi

[Justin Lemkul]

On 4/22/15 4:24 PM, Hossein H wrote:
> the performance degrades even when I only use two nodes!!! and the mdrun
> process uses almost 100% of CPU on each node
>

Like I said, any benefit you might theoretically get from multiple CPU is being 
undermined by latency in the gigabit ethernet connection.  It's generally not 
adequate for high-performance MD simulations.

-Justin

> On Thu, Apr 23, 2015 at 12:47 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
>>
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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

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