[gmx-users] Compiling gromacs 4.6.5 on cray XT5m

[Gmx QA]

Hello again

Problem solved, I think. At least it's compiling now. I downloaded fftw
myself and built it with --enable-static --disable-fortran, and that seems
to have worked.

Thanks
/PK



2014-05-13 9:06 GMT+02:00 Gmx QA <gmxquestions at gmail.com>:

> Dear users
>
> I am having problems compiling gromacs 4.6.5 on a (rather ancient) Cray
> XT5m machine.
>
> My approach has been the following, but it stops during the make stage
> when processing fftw.
>
> 1. Download gromacs-4.6.5 tar ball
> tar -xvg gromacs-4.6.5.tar
> cd gromacs-4.6.5
> mkdir build
> cd build
>
> Then swap some modules
> module swap PrgEnv-pgi PrgEnv-gnu
> module swap gcc/4.4.4 gcc/4.6.1
>
> I now have the following modules loaded:
>
> ~/gromacs-4.6.5/build> module list
> Currently Loaded Modulefiles:
>   1) modules/3.2.6.6
>   2) portals/2.2.0-1.0301.26633.6.9.ss
>   3) nodestat/2.2-1.0301.25918.4.1.ss
>   4) sdb/1.0-1.0301.25929.4.88.ss
>   5) MySQL/5.0.64-1.0301.2899.20.1.ss
>   6)
> lustre-cray_ss_s/1.8.4_2.6.27.48_0.12.1_1.0301.5943.18.1-1.0301.27524.1.24
>   7) Base-opts/1.0.2-1.0301.25878.4.1.ss
>   8) xtpe-network-seastar
>   9) PrgEnv-gnu/3.1.72
>  10) atp/1.4.4
>  11) xt-asyncpe/5.10
>  12) pmi/2.1.4-1.0000.8596.15.1.ss
>  13) xt-mpich2/5.3.5
>  14) xt-libsci/10.5.02
>  15) gcc/4.6.1
>
> Then my cmake line is:
> cmake .. -DGMX_GPU=OFF -DGMX_MPI=ON  -DGMX_PREFER_STATIC_LIBS=ON
>  -DBUILD_SHARED_LIBS=OFF -DCMAKE_INCLUDE_PATH=/opt/fftw/
> 3.3.0.0/x86_64/include/ -DCMAKE_LIBRARY_PATH=/opt/fftw/3.3.0.0/x86_64/lib/
>
> Which proceeds fine through the configuring stage, but then during make I
> get this:
>
> <snip>
> -- Performing Test GNU_SSE2_CFLAG
> -- Performing Test GNU_SSE2_CFLAG - Success
> -- Looking for emmintrin.h
> -- Looking for emmintrin.h - found
> -- Enabling SSE2 Gromacs acceleration
> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.23")
> -- checking for module 'fftw3f'
> --   package 'fftw3f' not found
> -- pkg-config could not detect fftw3f, trying generic detection
> -- Looking for fftwf_plan_r2r_1d in /opt/fftw/
> 3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so
> -- Looking for fftwf_plan_r2r_1d in /opt/fftw/
> 3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so - not found
> CMake Error at cmake/FindFFTW.cmake:97 (message):
>   Could not find fftwf_plan_r2r_1d in
>   /opt/fftw/3.3.0.0/x86_64/lib/fftw3f.so;/usr/lib/libm.so, take a look at
> the
>   error message in
>   /home/users/pela3247/gromacs-4.6.5/build/CMakeFiles/CMakeError.log to
> find
>   out what went wrong.  If you are using a static lib (.a) make sure you
> have
>   specified all dependencies of fftw3f in FFTWF_LIBRARY by hand (e.g.
>   -DFFTWF_LIBRARY='/path/to/libfftw3f.so;/path/to/libm.so') !
> Call Stack (most recent call first):
>   CMakeLists.txt:895 (find_package)
>
>
> -- Configuring incomplete, errors occurred!
>
>
> Clearly there is something screwy with fftw, but I am not experienced
> enough with cray to tell what it is. Trying to do what the message suggest
> (adding -DFFTWF_LIBRARY=''') only results in exactly the same error.
>
> Could you please provide some pointers to where I go wrong?
>
> Thanks
> /PK
>
>