Re: NAMD infiniband performance

From: Guanglei Cui (amber.mail.archive_at_gmail.com)
Date: Mon Jun 01 2009 - 15:15:23 CDT

Dear Axel,

Thanks for the suggestion. It took me a while to work on this again.
After some fiddling, I was able to compile 2.7b1 with openmpi-1.3.2
and the Intel compiler 11 with libraries (intel and openmpi)
dynamically loaded. However, I couldn't figure out how to build a
static executable. The linker always complains about some undefined
openmpi symbols even with -lmpi -lmpi_cxx -lopen-pal -lopen-rte -lote
specified. Did I miss anything?

Regards,
Guanglei

On Tue, May 19, 2009 at 6:13 PM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Tue, 2009-05-19 at 12:04 -0400, Guanglei Cui wrote:
>> Dear Alex,
>>
>> I guess it's difficult to justify the cost of infiniband without
>> infiniband :-) Anyways, I'll give MPI a try. Is there any particular
>> implementation you recommend? And a related question ... how does
>
> my personal preference is OpenMPI because of its flexibility
> and convenience, but there also is MVAPICH. if you have an OFED
> installation, you should have both already available.
>
>> charm++ handle a heterogeneous system setup with core-core and
>> node-node interfaces? Thanks a lot for the input.
>
> yes, you have to adjust the compilation to add SMP or multi-core
> support and provide some topology information through arguments
> (e.g. +ppn). i have not experimented with it very much, but i am
> certain, it is explained somewhere in the charm++ or namd2
> documentation.
>
> cheers,
>   axel.
>>
>> Regards,
>> 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.
>> >
>> >
>
> --
> =======================================================================
> 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.
>
>

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