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

Jernej Zidar jernej.zidar at gmail.com
Thu Jun 13 10:13:46 CEST 2013

  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
2. Compile Gromacs 4.6 using instructions from Gromacs' page:
cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \

  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.
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.

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

Thanks in advance,

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