[gmx-users] using_gromacs_with_openmpi

[Hossein H]

But I wonder if the the performance degrade due to network latency why
mdrun process uses 100% CPU on each node!!!

On Thu, Apr 23, 2015 at 1:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>
>>> ==================================================
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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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