Re: mpirun compilation for NAMD

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Dec 04 2008 - 20:34:35 CST

Thanks for the discussion. To get back to your point made in the earlier
mail,

"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."

We do have mpirun in our cluster. In fact, all programs other than NAMD are
being run using mpirun.

For some reason, NAMD is extremely slow in our cluster, using only ~20% of
the CPU. The clocktimes are far slower than my previous experience on
another machine.

Since other programs seem to run fine with mpirun, we think it may be
because charm++ is not suited for this machine.
Please let me know what you think.
Regards,
Neelanjana

On Thu, Dec 4, 2008 at 11:43 PM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>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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