From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Jul 16 2015 - 16:06:37 CDT
You might want to try different ways. You can try with
ibrun $BINDIR/namd2 config.namd
and see whether that is faster or slower than the method I first
indicated. I would first try on a single node.
Gianluca
On Thu, 16 Jul 2015, Maxime Boissonneault wrote:
> Hi,
> Yes, the goal is to see how that user can scale its NAMD computation on
> multiple GPU nodes. He already gets a good scaling on a single node. Each of
> our nodes have 8 x K20s.
>
> Thanks,
>
> Maxime
>
> Le 2015-07-16 16:56, Gianluca Interlandi a écrit :
>> Exactly, mpiexec is just a launcher. You will be using ibverbs and not MPI.
>> This is at least my understanding. I tried out different ways of running
>> NAMD with ibverbs and found that the method from Jim Philipps (one of the
>> NAMD developers) is fastest.
>>
>> Are you running on multiple nodes?
>>
>> Gianluca
>>
>> On Thu, 16 Jul 2015, Maxime Boissonneault wrote:
>>
>>> Hi Gianluca,
>>>
>>> So, the NAMD ibverbs package requires MPI ? I thought the whole point of
>>> doing an ibverbs was to get rid of MPI and run directly through the
>>> Infiniband verbs.
>>>
>>> Or is mpiexec only used as a launcher (and could be done through pdsh or
>>> something like that ?)
>>>
>>> Thanks,
>>>
>>> Maxime
>>>
>>> Le 2015-07-16 16:31, Gianluca Interlandi a écrit :
>>>> Hi Maxime,
>>>>
>>>> I usually use the option "++mpiexec" to run NAMD with ibverbs (the
>>>> following is a single line):
>>>>
>>>> $BINDIR/charmrun +p${NPROCS} ++mpiexec ++remote-shell mpiexec_wrapper
>>>> $BINDIR/namd2 config.namd
>>>>
>>>> $BINDIR is the path to your NAMD executable.
>>>>
>>>> "mpiexec_wrapper" is a script that I got a while ago from Jim Philipps.
>>>> You can copy the following lines to a file called "mpiexec_wrapper" and
>>>> make it executable:
>>>>
>>>> #!/bin/csh
>>>>
>>>> exec mpiexec -machinefile $PBS_NODEFILE $*
>>>>
>>>>
>>>> If you run on GPU as well, you should be able to simply add to the line
>>>> above:
>>>>
>>>> +devices 0,1,2 +idlepoll
>>>>
>>>> However, I need to say that if you are running on a single node and you
>>>> do not need to use the network, the multicore version might be slightly
>>>> faster than ibverbs. This is because you will not have the overhead of
>>>> the network libraries. I usually use ibverbs only if running on more than
>>>> one node.
>>>>
>>>> Gianluca
>>>>
>>>> On Thu, 16 Jul 2015, Maxime Boissonneault wrote:
>>>>
>>>>> Hi,
>>>>> One of our user would like to use namd 2.10 ibverbs with GPU on our GPU
>>>>> cluster. I cannot find documentation on how to use it. Is there such
>>>>> documentation ? We're used to either use the multicore-cuda version or
>>>>> the Cuda+MPI version, but since you now provide an ibverbs+GPU binaries,
>>>>> we downloaded them and wanted to try them.
>>>>>
>>>>> Thanks,
>>>>>
>>>>>
>>>>> --
>>>>> ---------------------------------
>>>>> Maxime Boissonneault
>>>>> Analyste de calcul - Calcul Québec, Université Laval
>>>>> Président - Comité de coordination du soutien à la recherche de Calcul
>>>>> Québec
>>>>> Ph. D. en physique
>>>>>
>>>>>
>>>>
>>>> -----------------------------------------------------
>>>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>>>> +1 (206) 685 4435
>>>> http://artemide.bioeng.washington.edu/
>>>>
>>>> Research Assistant Professor at the Department of Bioengineering
>>>> at the University of Washington, Seattle WA U.S.A.
>>>> -----------------------------------------------------
>>>
>>>
>>> --
>>> ---------------------------------
>>> Maxime Boissonneault
>>> Analyste de calcul - Calcul Québec, Université Laval
>>> Président - Comité de coordination du soutien à la recherche de Calcul
>>> Québec
>>> Ph. D. en physique
>>>
>>>
>>
>> -----------------------------------------------------
>> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
>> +1 (206) 685 4435
>> http://artemide.bioeng.washington.edu/
>>
>> Research Assistant Professor at the Department of Bioengineering
>> at the University of Washington, Seattle WA U.S.A.
>> -----------------------------------------------------
>
>
> --
> ---------------------------------
> Maxime Boissonneault
> Analyste de calcul - Calcul Québec, Université Laval
> Président - Comité de coordination du soutien à la recherche de Calcul Québec
> Ph. D. en physique
>
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------
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