Re: mpirun compilation for NAMD

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Thu Dec 04 2008 - 12:13:14 CST

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
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 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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