Re: mpirun compilation for NAMD

From: Warner Yuen (wyuen_at_apple.com)
Date: Thu Dec 04 2008 - 12:54:37 CST

My confusion... I'm still somewhat fuzzy on the details from what I
did in the past with NAMD and charm++. But I recall that straight charm
++ for the parallelization was supposed to faster than MPI? But maybe
this was only for Myrinet-MX?

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

On Dec 4, 2008, at 10:13 AM, Giacomo Fiorin wrote:

> NAMD always uses charm++. You wouldn't be able to compile it
> otherwise.
>
> Using NAMD with MPI means that the charm++ communication runs over the
> MPI protocol, instead of the "regular" TCP/IP Internet protocol. In
> that case, charmrun becomes interchangeable with mpirun, but the
> charm++ functions (with load balancing and all the other goodies) are
> always inside the executable.
>
> 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 Thu, Dec 4, 2008 at 1:08 PM, Warner Yuen <wyuen_at_apple.com> wrote:
>> 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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