Re: mpirun compilation for NAMD

From: Warner Yuen (wyuen_at_apple.com)
Date: Thu Dec 04 2008 - 12:08:37 CST

Is MPI the best way to use NAMD? I thought that the use of charm++ was
the more efficient way to go. I haven't run NAMD in quite a while, but
I recall building it with Myrinet support with charm++

Warner Yuen
Scientific Computing
Consulting Engineer
Apple Computer
email: wyuen_at_apple.com
Tel: 408.718.2859
Fax: 408.715.0133

On Dec 3, 2008, at 8:42 AM, Giacomo Fiorin wrote:

> Hi Neelanjana, the instructions on the NAMD release notes are generic,
> but on the charm++ documentation it is written quite clearly that
> "mpi-linux" is one of the modes of compilation for charm++, in which
> the library (charm++) uses MPI instead of the "basic" Internet
> protocol to transfer data across processors.
>
> But beware: if you want to compile charm++ (and later, namd2) to use
> MPI it means that you already have mpirun, and the rest of one of the
> many MPI libraries, already installed. Needless to say, you must make
> sure that you compile charm++ to use that one, and none other. You
> may have special network hardware, so you could need to add extra
> flags for that.
>
> In summary, once you've gathered info on how the machine you intend to
> run is organized, try to find instructions about similar machines on
> the pertinent webpage (charm.cs.uiuc.edu), in the Charm++ Wiki, and in
> the NAMD Wiki.
>
> There's just a tiny bit more information than in notes.txt.
>
> Giacomo
>
>
> ---- -----
> Giacomo Fiorin
> Center for Molecular Modeling at
> University of Pennsylvania
> 231 S 34th Street, Philadelphia, PA 19104-6323
> phone: (+1)-215-573-4773
> fax: (+1)-215-573-6233
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_<at>_gmail.com
> web: http://www.cmm.upenn.edu/
> ---- ----
>
>
>
> On Wed, Dec 3, 2008 at 8:46 AM, Neelanjana Sengupta <senguptan_at_gmail.com
> > wrote:
>> Hello all,
>>
>> I am trying to compile NAMD (from the source) for mpirun usage.
>> Now, the
>> instructions given in "notes.txt" is the foll:
>> ---------
>> If you're building an MPI version you will probably need to edit
>> compiler flags or commands in the Charm++ src/arch directory. The
>> file charm/src/arch/mpi-linux/conv-mach.sh contains the definitions
>> that select the mpiCC compiler for mpi-linux, while other compiler
>> choices are defined by files in charm/src/arch/common/.
>> ----------
>> I edited the conv-mach.sh file. Since there is no specific
>> instruction for
>> mpirun compilation, I did the foll:
>>
>> ./build charm++ net-linux --no-shared -O -DCMK_OPTIMIZE=1
>> This built charm++, and not mpirun.
>>
>> This did not get me the mpirun compilation either:
>> ./build mpirun net-linux --no-shared -O -DCMK_OPTIMIZE=1
>>
>> Can someone point out what I should be doing here?
>>
>> Thanks,
>> Neela
>> --
>> ~~~~~~~~~~~~~~~~~~~~
>> Neelanjana Sengupta, PhD
>> Physical and Materials Chemistry Division
>> National Chemical Laboratory
>> Dr. Homi Bhaba Road
>> Pune 411008, India
>> Phone: +91-20-2590 2087
>> ~~~~~~~~~~~~~~~~~~~~
>>
>

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