Re: Compile NAMD on Bluegene

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Thu Jun 15 2006 - 12:16:40 CDT

I don't remember we used BGL_HOME, I thought it should be BL_INSTALL
it should be the path prefix that has bglsys/include and bglsys/lib,
typically it is /bgl/BlueLight/ppcfloor/

Gengbin

Dong Luo wrote:

>This Blue Gene machine is located at Boston
>University. As far as I know, NAMD is not installed.
>Since NAMD requires single precision fftw to do the
>PME calculation and I found the preinstalled fftw with
>the machine has this version, I will use that fftw
>first. It it failed again, I will try to compile it as
>Gengbin suggested.
>I have another question as mentioned in previous post,
>ie, what BL_HOME variable should I define to be able
>to use charm++?
>
>--- Gengbin Zheng <gzheng_at_ks.uiuc.edu> wrote:
>
>
>
>>I think most Blue Gene machines already have NAMD
>>installed, you may
>>want to find out.
>>
>>To compile your own version, please check out the
>>following web site for
>>how to compile fftw for NAMD
>>
>>
>>
>http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdCompile
>
>
>>Gengbin
>>
>>Mgr. Lubos Vrbka wrote:
>>
>>
>>>hi,
>>>
>>>
>>>
>>>>This time, after compiled for a while, the new
>>>>
>>>>
>>problem
>>
>>
>>>>came out as:
>>>>"src/ComputePme.C", line 8.10: 1540-0836 (S) The
>>>>#include file <sfftw.h> is not found.
>>>>"src/ComputePme.C", line 9.10: 1540-0836 (S) The
>>>>#include file <srfftw.h> is not found.
>>>>I checked the fftw directory and find out there
>>>>
>>>>
>>are
>>
>>
>>>>only fftw.h and rfftw.h in the include directory.
>>>>As the fftw libary are downloaded from the
>>>>
>>>>
>>website as
>>
>>
>>>>suggested (I downloaded the file
>>>>fftw-bluegene.tar.gz), I now have no idea how to
>>>>
>>>>
>>fix
>>
>>
>>>>this problem.
>>>>Please give some hints. Thanks.
>>>>
>>>>
>>>i don't have any experience with namd compilation,
>>>
>>>
>>but this error
>>
>>
>>>means that you are trying to use single precision
>>>
>>>
>>version of the fftw
>>
>>
>>>binary that is apparently missing on your
>>>
>>>
>>computer. maybe there is
>>
>>
>>>some switch you can use to specify that you want
>>>
>>>
>>to use double
>>
>>
>>>precision fftw instead of single precision (in
>>>
>>>
>>configure scripts the
>>
>>
>>>switch is usually --enable-float/--disable float).
>>>
>>>
>>i don't know what
>>
>>
>>>is the situation for namd, though...
>>>
>>>regards,
>>>lubos
>>>
>>>
>>>
>
>
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