Hi Ryan, The issue you linked has been worked around in the build system, so my guess is that the issue you are seeing is not related.
I would recommend that you update your software stack to the latest version (both CUDA 9.1 and gcc 5 are a few years old). On Ubuntu 18.04 you should be able to get gcc 8 through the package manager. Together with upgrading to the latest CUDA might well solve your issues. Let us know if that worked! Cheers, -- Szilárd On Wed, Jan 29, 2020 at 12:14 AM Ryan Woltz <rlwo...@ucdavis.edu> wrote: > Hello Gromacs experts, > > First things first, I apologize for any double post but I just > joined the community so I'm very new and only found 1-2 posts related to my > problem but the solutions did not work. I have been doing MD for about > 6-months using NAMD but want to also try out Gromacs. That being said I am > slightly familiar with CPU modeling programs like Rosetta, but I am totally > lost when it comes to fixing errors using GPU accelerated code for CUDA. I > did find that at one point my error was fixed for an earlier version of > Gromacs but Gromacs-2020 may have resurfaced the same error again, here is > what I think my error is: > > https://redmine.gromacs.org/issues/1982 > > I am running Ubuntu 18.04.03 LTS, and gromacs-2020 I did initially have > the gcc/nvcc incompatible but I think installing and using gcc-5/g++-5 > version command in cmake has fixed that issue. I have a NVIDIA card with > CUDA-9.1 driver when I type nvcc --version. > > my cmake command is as follows: > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-5 -DCUDA_HOST_COMPILER=gcc-5 > -DCMAKE_CXX_COMPILER=g++-5 -DCMAKE_C_COMPILER=/usr/bin/gcc-5 > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug (I did > try adding -D_FORCE_INLINES= based on the link above in my running command > but it did not work). I did look at the error log but it is way over my > head. I have in addition deleted the CMakeCache.txt file or the unpacked > Gromacs and re-unzipped it to restart the cmake process to make sure it was > starting "clean". Is there any additional information I could provide? Does > anyone have a suggestion? Again I'm sorry if this is a duplicate, > everything I found on other sites was way over my head and I generally > understand what is going on but the forums I read on possible solutions > seem way over my head and I'm afraid I will break the driver if I attempt > them (which has happened to me already and the computer required a full > reinstall). > > here is last lines from the build: > > -- Found HWLOC: /usr/lib/x86_64-linux-gnu/libhwloc.so (found suitable > version "1.11.6", minimum required is "1.5") > -- Looking for C++ include pthread.h > -- Looking for C++ include pthread.h - found > -- Atomic operations found > -- Performing Test PTHREAD_SETAFFINITY > -- Performing Test PTHREAD_SETAFFINITY - Success > -- Adding work-around for issue compiling CUDA code with glibc 2.23 > string.h > -- Check for working NVCC/C++ compiler combination with nvcc > '/usr/local/cuda/bin/nvcc' > -- Check for working NVCC/C compiler combination - broken > -- /usr/local/cuda/bin/nvcc standard output: '' > -- /usr/local/cuda/bin/nvcc standard error: > '/home/rlwoltz/protein_modeling/gromacs-2020/build/gcc-5: No such file or > directory > ' > CMake Error at cmake/gmxManageNvccConfig.cmake:189 (message): > CUDA compiler does not seem to be functional. > Call Stack (most recent call first): > cmake/gmxManageGPU.cmake:207 (include) > CMakeLists.txt:577 (gmx_gpu_setup) > > > -- Configuring incomplete, errors occurred! > See also > > "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeOutput.log". > See also > > "/home/rlwoltz/protein_modeling/gromacs-2020/build/CMakeFiles/CMakeError.log". > -- > 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.