Re: mpirun compilation for NAMD

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Dec 03 2008 - 10:42:44 CST

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
> ~~~~~~~~~~~~~~~~~~~~
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:11 CST