Hi, Mixing versions of C++ compilers is never a good idea, precisely because there is no guarantee that linking can succeed, as here. Use gcc 4.8.5 for all compilation if you are forced to use such a dated distro for "stability." Bear in mind that that is often just code for "old, slow, and hasn't been changed." ;-)
You can/should investigate whether devtoolset-6 works well enough, since it contains a more recent gcc that is supported by that CUDA. Mark On Mon, May 7, 2018 at 7:38 PM Kevin Boyd <kevin.b...@uconn.edu> wrote: > Hi, > > I've been trying to install gromacs 2018 on a cluster running Centos7. > In keeping with the guidelines for maximizing performance, I'm > compiling with a recent (7.3.0) GCC version. However, Cuda 9.0 on > Centos 7.x needs to be compiled with GCC 4.8.5, so my cmake command > included -DCUDA_HOST_COMPILER=/path/to/gcc4.8.5. When installing, the > following error occurred. > > [ 98%] Built target libgromacs > [ 98%] Linking CXX executable ../../bin/template > ../../lib/libgromacs.so.4.0.0: undefined reference to > `gmx::formatString(char const*, ...)' > ../../lib/libgromacs.so.4.0.0: undefined reference to > `canDetectGpus(std::__cxx11::basic_string<char, > std::char_traits<char>, std::allocator<char> >*)' > ../../lib/libgromacs.so.4.0.0: undefined reference to > `gmx::getCudaRuntimeVersionString[abi:cxx11]()' > ../../lib/libgromacs.so.4.0.0: undefined reference to > `gmx::getCudaDriverVersionString[abi:cxx11]()' > > The same error (or at least part of the error) shows up trying Gromacs > 2018, 2018.1, and the current master branch. > > My full cmake configuration command was > > cmake .. -DCMAKE_INSTALL_PREFIX=/path/to/prefix \ > -DGMX_GPU=ON \ > -DGMX_SIMD=AVX2_256 \ > -DGMX_FFT_LIBRARY=fftw3 \ > -DCUDA_HOST_COMPILER=/path/to/gcc4.8.5 \ > -DCMAKE_PREFIX+PATH=/path/to/fftwlib > > > I can compile and run successfully if I turn off GPU support (with GCC > 7.3.0), or by using GCC 4.8.5 for the entire install (with GPUs), so > I'm assuming the issue has something to do with using both compilers. > > Has anyone else run into similar issues? > > Thanks, > > Kevin > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
