[gmx-users] trouble with -DGMX_BUILD_OWN_FFTW, crashing in m4?

Mark Abraham mark.j.abraham at gmail.com
Tue Jul 30 01:24:27 CEST 2013

Yes, this is a known problem. A race condition with parallel make
exists between the gmxfftw build target and the things that depend on
it. AFAIK, a second call to make will Just Work. There are known ways
for GROMACS to solve this by controlling the dependency properly, but
the leading candidates either do not work at all with a specific CMake
minor release, or require more invasive restructuring then we will do
in 4.6 series. A long discussion thread exists on gmx-developers for
those with nothing to do!

Do let us know how you go. I guess we should update the install guide


On Mon, Jul 29, 2013 at 11:59 PM, Jacob Pessin
<Jacob.Pessin at einstein.yu.edu> wrote:
> Hi all,
> I'm trying to compile 4.6.3 on my desktop, but have running into some issues with FFTW.
> Specifically with "-DGMX_BUILD_OWN_FFTW=ON" make seems to crash with M4 (if I'm reading it right)
> This is not dpkg install-info anymore, but GNU install-info
> See the man page for ginstall-info for command line arguments
> Making install in tools
>  /usr/bin/install -c fftw-wisdom-to-conf '/home/jacob/Desktop/gromacs-4.6.3/build-cmake/src/contrib/fftw/gmxfftw-prefix/bin'
>   /bin/bash ../libtool   --mode=install /usr/bin/install -c fftwf-wisdom '/home/jacob/Desktop/gromacs-4.6.3/build-cmake/src/contrib/fftw/gmxfftw-prefix/bin'
>  /usr/bin/install -c -m 644 /home/jacob/Desktop/gromacs-4.6.3/build-cmake/src/contrib/fftw/gmxfftw-prefix/src/gmxfftw/tools/fftw-wisdom-to-conf.1 fftwf-wisdom.1 '/home/jacob/Desktop/gromacs-4.6.3/build-cmake/src/contrib/fftw/gmxfftw-prefix/share/man/man1'
> libtool: install: /usr/bin/install -c fftwf-wisdom /home/jacob/Desktop/gromacs-4.6.3/build-cmake/src/contrib/fftw/gmxfftw-prefix/bin/fftwf-wisdom
> Making install in m4
> [ 57%] Completed 'gmxfftw'
> [ 57%] Built target gmxfftw
> make: *** [all] Error 2
> I've already have an AVX-compiled installed for other uses, building GMX of of that went fine aside from recommendations against using it in both the doc's and the build itself (upto 20% speed reduction, rather not thanks)
> Any suggestions, help or pointers, would be greatly appreciated.
> the only thing I can think of is create a separate build of FFTW and then direct cmake to use that one.
> I was able to build a new FFTW (--enable-sse2),  but couldn't figure out how to get cmake to prefer it over the others.
> I hope this is clear,
> thanks
> jacob
> machine in question
> Dell T3600 e5-1650 32gb ram (ECC) with nvidia quadro-600
> Xubuntu 13.04 (ubuntu, xfce spin)
> M4 ubuntu packaged 1.4.16-5
> command variations attempted:
> cmake ..-DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs4.6.3 2>&1|tee cmakeinitall.txt
>  cmake .. -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs4.6.3 2>&1|tee cmakeinitall.txt
> cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/include/cuda -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs4.6.3
>  cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs4.6.3 -DGMX_BUILD_OWN_FFTW=ON 2>&1|tee cmakeInitall.txt
>     All die as above after:
> make -j 12
>      BUT
> cmake .. -DGMX_GPU=OFF -DCMAKE_INSTALL_PREFIX=/opt/gromacs4.6.3avx
> make -j 12
> sudo make install
>      Runs fine, a full copy of the terminal text for gpu=off fftw=on can be found at:
> https://www.dropbox.com/s/367aji2x42w3ogz/cmakeinitall.txt
> https://www.dropbox.com/s/fmj5nszul3taczj/makej12.txt
> --
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