From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Jul 16 2015 - 15:56:14 CDT
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.
-----------------------------------------------------
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