Re: Compiling NAMD on Ranger

From: Axel Kohlmeyer (
Date: Wed Apr 08 2009 - 08:15:51 CDT

On Wed, 2009-04-08 at 08:33 -0400, wrote:
> Hello NAMD users,
> I need to have a NAMD executable that can run on 16cpus of 1 node on
> Ranger without using the MPI environment. Can anyone tell me about the
> optimal build options for Ranger?
> I have tried to compile using the following options:
> build charm++ net-linux-amd64 -O -DCMK_OPTIMIZE=1
> config tcl fftw Linux-amd64-g++
> I have used the fftw-linux-amd64 and tcl-linux-amd64 libraries from
> the NAMD home.
> But, the compiled version is several times slower than the executable
> from the directory ~tg455591/Linux-amd64-MVAPICH-icc/namd2.
> Any suggesstion that will help me to compile and get close to the
> optimal timing would be greatly helpful.

before getting in way over your head, did you try the precompiled
amd64 version from the namd homepage? you should also make sure that
you compare executables generated from the same sources, i.e. that you
don't mix the recent beta release with the 2.6 version.


> Thanking all,
> Shayantani
> Shayantani Mukherjee
> MSU.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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