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

Ryan Woltz rlwoltz at ucdavis.edu
Wed Jan 29 00:14:04 CET 2020


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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