Re: NAMD infiniband performance

From: Guanglei Cui (amber.mail.archive_at_gmail.com)
Date: Tue May 19 2009 - 11:06:09 CDT

Hi Axel,

apologies for the typo in your name.

Guanglei

On Tue, May 19, 2009 at 11:00 AM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Tue, 2009-05-19 at 09:56 -0400, Guanglei Cui wrote:
>> Hi Lev,
>
> dear guanglei,
>
>
>> Thanks for the reply. I have not tried to compile Charm++ with any MPI
>> implementations, and been using the net- option. Is there any
>> advantage of using MPI (just any MPI)vs. using the net- option?
>
> yes there is an advantage. the net version always uses tcp/ip,
> which has a high communication overhead. now for a small number
> of nodes or a large system this does not matter much, as NAMD
> can hide communication latencies through the ingenuity of charm++
> over plain MPI. however, if you have an infiniband network, the
> low latency that the infiniband communication offers, is only
> available if you use a charm++ installation that uses MPI for
> lowlevel communication or even the ibverbs layer directly.
>
> the difference between the two approaches will be larger the
> more nodes you can use in your tests. the net version will scale
> out _much_ faster than the custom compile.
>
> cheers,
>   axel.
>
>>
>> Best regards,
>> Guanglei
>>
>> On Tue, May 19, 2009 at 2:31 AM, Lev Lafayette <lev_at_vpac.org> wrote:
>> > Hi Guanglei,
>> >
>> > Although I am no NAMD expert, I would suggest compiling from source and creating an application. As a binary you probably won't be picking up the performance benefits, which should be determined by whatever you're using as message parsing interface (OpenMPI?). Then you should seem some real gains.
>> >
>> > All the best,
>> >
>> > --
>> > Lev Lafayette (03) 9925 4909, Systems Administrator, Victorian Partnership for Advanced Computing
>> > "If you are sending a reply to a message or a posting be sure you summarize the original at the top of the message, or include just enough text of the original to give a context. This will make sure readers understand when they start to read your response."
>> > RFC 1855
>> >
>> >
>
> --
> =======================================================================
> Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>   Center for Molecular Modeling   --   University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
>

-- 
Guanglei Cui

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