[gmx-users] gromacs-2020 build gcc/nvcc error

[Szilárd Páll]

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 <rlwoltz at 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".
> --
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