Re: Compiling NAMD on Ranger

From: shayan_at_msu.edu
Date: Wed Apr 08 2009 - 12:51:26 CDT

Thanks for your suggestion Peter. I will be trying these options.
-Shayantani

Quoting "Peter Freddolino" <petefred_at_ks.uiuc.edu>:

> Hi Shayantani,
> try compiling using icc instead of gcc, and editing your .arch files
> to use the same compilation flags as we do (see
> http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdAtTexas).
> merging your code with the namd 2.7 tree, if possible without too
> much trouble, will also let you take advantage of sse loops which
> have made things even faster recently.
>
> Best,
> Peter
>
> shayan_at_msu.edu wrote:
>> 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.
>>
>> Thanks,
>> Shayantani
>>
>> Quoting "Axel Kohlmeyer" <akohlmey_at_cmm.chem.upenn.edu>:
>>
>>> On Wed, 2009-04-08 at 08:33 -0400, shayan_at_msu.edu 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   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
>>>    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
>> E-mail: shayan_at_msu.edu
>>
>
>

 

Shayantani Mukherjee
Postdoctoral Research Associate
Dept. of Biochemistry and Molecular Biology
Michigan State University
E-mail: shayan_at_msu.edu

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