[gmx-users] Problem compiling Gromacs 4.6 on BlueGene/Q

Mark Abraham mark.j.abraham at gmail.com
Thu Jun 13 11:00:31 CEST 2013

On Thu, Jun 13, 2013 at 10:13 AM, Jernej Zidar <jernej.zidar at gmail.com>wrote:

> Hi,
>   I'm trying to compile Gromacs 4.6 on a BlueGene cluster but I've
> stumbled upon something that looks like a bug.
>   Here's how I'm trying:
> 1. Compile FFTW-3.3.2:
> ./configure --prefix=/scratch/home/user/fftw-3.3.2
> make && make install

This does not compile a single-precision FFTW (per generic GROMACS
installation instructions).

> 2. Compile Gromacs 4.6 using instructions from Gromacs' page:
> cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \
>   -DCMAKE_PREFIX_PATH=/scratch/home/user/fftw-3.3.2
>   The cmake process completes without any error but make fails stating:
> Could not find fftw3f library named libfftw3f, please specify its
> location in CMAKE_PREFIX_PATH or FFTWF_LIBRARY by hand (e.g.
> -DFFTWF_LIBRARY='/path/to/libfftw3f.so')
> CMake Error at CMakeLists.txt:922 (MESSAGE):
>   Cannot find FFTW 3 (with correct precision - libfftw3f for
> single-precision
>   GROMACS or libfftw3 for double-precision GROMACS).  Either choose the
> right
>   precision, choose another FFT(W) library, enable the advanced option to
> let
>   GROMACS build FFTW 3 for you, or use the really slow GROMACS built-in
>   fftpack library.
> CMake Error: The following variables are used in this project, but
> they are set to NOTFOUND.
> Please set them or make sure they are set and tested correctly in the
> CMake files:
>   Problem 1: no shared objects are generated during the make phase of FFTW.

You probably want a static FFTW - the suggested solution is generic, though.

  Problem 2: even when setting the paths as instructed, the make fails
> with the same error. Looks like cmake is unable to "read" the path in

I'd say it's more likely the single-precision libfftw3f.a file is not
there, so it can't be read :-)

>   I compiled Cmake myself using GNU compilers. Could this be the problem?



> Thanks in advance,
> Jernej
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