Re: Which namd to use

From: Maxime Boissonneault (maxime.boissonneault_at_calculquebec.ca)
Date: Fri Nov 20 2015 - 08:13:58 CST

The IB cards are Mellanox, and the cluster is Sun (back in 2009).

Here is how our namd was compiled :

http://pastebin.com/dN4D19Pd

Do you see anything wrong (beside versions being old) ?
That was back in August 2013.

Maxime

Le 2015-11-20 09:02, Jim Phillips a écrit :
>
> The MPI version you have been building should work, and with replicas
> you probably won't see much of a performance difference.
>
> Who made your IB cards? They may now be supported directly, either in
> the released binaries or with a recompilation.
>
> The requirement for replicas is mpi, verbs, netlrts, or gni, so in
> your case you would want (copying from the release notes):
>
> Build and test the Charm++/Converse library (InfiniBand version):
> cd charm-6.7.0-pre
> ./build charm++ verbs-linux-x86_64 --with-production
> cd verbs-linux-x86_64/tests/charm++/megatest
> make pgm
> ./charmrun ++mpiexec +p4 ./pgm (uses mpiexec to launch processes)
> cd ../../../../..
>
> ./config Linux-x86_64-g++ --charm-arch verbs-linux-x86_64
> cd Linux-x86_64-g++
> make (or gmake -j4, which should run faster)
>
> If you have Intel compilers use those (verbs-linux-x86_64-iccstatic
> and Linux-x86_64-icc).
>
> Jim
>
>
> On Fri, 20 Nov 2015, Maxime Boissonneault wrote:
>
>> Hi,
>> A user of our cluster asked for us to install
>> Linux-x86_64-netlrts
>>
>> His need is to be able to perform replica exchanges, and he says that
>> only this version allowed him to do so. We have an older 2.9 version
>> of NAMD that we compiled, and apparently it does not support replica
>> exchanges.
>>
>> The thing is, we have a cluster with non-blocking QDR Infiniband. We
>> usually compile Namd from source, with MPI.
>>
>> What version would you recommend me to install, and if it's a
>> compilation from source, what should be the compilation options to
>> enable replica exchanges ?
>>
>> Thanks,
>>
>> --
>> ---------------------------------
>> Maxime Boissonneault
>> Analyste de calcul - Calcul Québec, Université Laval
>> Président - Comité de coordination du soutien à la recherche de
>> Calcul Québec
>> Team lead - Research Support National Team, Compute Canada
>> Instructeur Software Carpentry
>> Ph. D. en physique
>>
>> 

-- 
---------------------------------
Maxime Boissonneault
Analyste de calcul - Calcul Québec, Université Laval
Président - Comité de coordination du soutien à la recherche de Calcul Québec
Team lead - Research Support National Team, Compute Canada
Instructeur Software Carpentry
Ph. D. en physique

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