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 accordingly. Mark On Mon, Jul 29, 2013 at 11:59 PM, Jacob Pessin <jacob.pes...@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 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/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 > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
