> Yes CentOS 6 would be worse in the same way that using a horse would be > worse than driving a Model T in 2018. :-)
I totally agree, but unfortunately my home cluster still uses RHEL 6.7 and another cluster we have an allocation for uses Centos 6.7. ¯\_(ツ)_/¯ Thanks for the help! On Tue, May 8, 2018 at 10:01 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > On Tue, May 8, 2018 at 3:54 PM Kevin Boyd <kevin.b...@uconn.edu> wrote: > >> Thanks for the reply. >> >> The distro is actually relatively up to date, from what I can tell gcc >> 4.8.5 is all that CUDA supports for the most recent versions of RHEL >> and Centos. > > > CUDA is just supporting the stock compiler for CentOS. That such distros by > design ship such a compiler that is 5 years old is part of what makes them > stable, and therefore dated. ;-) It's a perfectly reasonable approach to > deploying servers, but it's not consistent with also wanting high > performance from them on hardware that wasn't designed when the compiler > was shipped. > > Older versions (6.x series) of both only support version >> 4.4.7, so to install Gromacs 2018 with GPUs I'd need to use clang or >> icc with those distros, which is a bummer. >> > > Yes CentOS 6 would be worse in the same way that using a horse would be > worse than driving a Model T in 2018. :-) > > Mark > > I'll look into devtoolset-6, thanks. >> >> Kevin >> >> On Mon, May 7, 2018 at 4:36 PM, Mark Abraham <mark.j.abra...@gmail.com> >> wrote: >> > 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. >> -- >> 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. -- 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.