[gmx-users] using_gromacs_with_openmpi

[Hossein H]

the performance degrades even when I only use two nodes!!! and the mdrun
process uses almost 100% of CPU on each node

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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