Re: Compiling NAMD on Ranger

Date: Wed Apr 08 2009 - 10:09:11 CDT

Thanks Axel for your reply.
I have build using the 2.6 source, which, I beleive, is the same as the executable available on Ranger.
I need to compile NAMD myself since I have a code customized according to my need.
I have also compared the timing with the linux-amd64 binary available from NAMD home. The timing for 16cpus (1 node) are as follows:
16 CPU: 0.2533 s/step 1.4659 days/ns (executable from ~tg455591 on Ranger)
16 CPU: 0.9072 s/step 5.2504 days/ns (NAMD_2.6_Linux-amd64 binary from NAMD home)
16 CPU: 0.9850 s/step 5.7000 days/ns (my compiled version)
Using the right options might help me to get a better executable atleast close to the one in Ranger.


Quoting "Axel Kohlmeyer" <>:

> 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.
> axel.
>> 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.


Shayantani Mukherjee
Postdoctoral Research Associate
Dept. of Biochemistry and Molecular Biology
Michigan State University

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