Re: [gmx-users] gromacs-2020 build gcc/nvcc error
Dear Ryan, On Thu, Jan 30, 2020 at 11:31 PM Ryan Woltz wrote: > Dear Szilárd, > > Thank you so much for your help. I performed the following steps > and it seems to have built successfully, I'll let you know if it does not > run correctly as well. > > rm -r gromacs-2020/ > sudo apt-get install gcc-8 g++-8 > tar -xvzf gromacs-2020.tar.gz > cd gromacs-2020/ > mkdir build > cd build > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release > Note that you are still using the _default_ gcc installation, that is gcc 7 on Ubuntu 18.04. You should see on the first line on the console when you run cmake something like: -- The C compiler identification is GNU 7.4.0 -- The CXX compiler identification is GNU 7.4.0 which will clearly indicate the version of the compiler detected. Unless you tell cmake to use the apt-get installed gcc-8, it will not use it (and you can also verify that by inspecting the CMAKE_CXX_COMPILER string in the CMakeCache.txt file). make > make check > sudo make install > source /usr/local/gromacs/bin/GMXRC > > Lastly, when I was building in default and ran into trouble I like to build > in debug so it gives details about building and helps me identify source of > the problems or identify relevant information to pass to you so you can > better help me. I appreciate your comment about not building in debugging > mode, but is there a way to run release in verbose mode? When I had > problems with other programs I'd usually build my first time in debugger > mode so I can monitor the process, then make clean and rebuild in default. > Is there a better way to do this? > A "Debug" build (i.e. when you use CMAKE_BUILD_TYPE=Debug), is useful to compile a program for running in a debugger (like gdb). You seem to instead want a way to "debug" build-time issues. A debug build will not help in that, you will not get additional information about compilation issues. You can run "make VERBOSE=1" (regadless of the build type) with makefiles generated by cmake to get a detailed information on the commands executed during the build, but unless you have a compile- or link-time failure that you want to track down that sea of output is generally not too useful. Configure-time errors are stored by cmake in files listed after the usual "-- Configuring incomplete, errors occurred!" error (files called CMakeOutput/CMakeError.txt). > Once again you help was greatly appreciated, > > Ryan > > PS again a few notes (if you have time to comment on anything incorrect) I > have for people needing a fix in the future and maybe myself if I do this > again in a few years and forget how. > > CUDA version (nvcc --version) is 9.1. This is a little confusing to me > because you referenced CUDA 10.1 and I completely rebuilt this computer in > September 2019, so unless there is a new driver since then it should be > 10.1? I grabbed the newest drivers I could find but my computer is > outputting 9.1 so I guess that is my version. > CUDA is not (just) the drivers, it is a number of software components that allow compiling for and runnig computation on the GPU: - the CUDA toolkit, latest of which is version 10.2 (as you can see here: https://developer.nvidia.com/cuda-downloads?target_os=Linux), but the Ubuntu 18.04 repositories seem to only have 9.1 - a display driver, confusingly versioned with numbers like 418.88 or 430.35, the Ubuntu packages are called "nvidia-driver-VERSION" These two of course have to be compatible, so if you decide to download the CUDA 10.2 installer from NVIDIA, this will include a compatible driver. Be careful to completely remove the NVIDIA drivers installed from the Ubuntu repositories prior to installing sofware with the NVIDIA installer! when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails > with the original error message regarding glibc 23.2. > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ > -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8 > -DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8 > -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release > Not sure, but if you want to investigate further, I suggest to start with installing a more recent CUDA toolkit version, 9.1 is already about two years old. Cheers, -- Szilárd > Do you know why this is? When I started this adventure I just had sudo > apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and > specified the version in the build step, which failed. after taking that > out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but > fails in "make". Based on your suggestions I ran the commands at the top of > the email to which then worked. Would this have worked if I had just > installed gcc-8 g++-8 from the beginning and ran CMAKE with no
Re: [gmx-users] gromacs-2020 build gcc/nvcc error
Dear Szilárd, Thank you so much for your help. I performed the following steps and it seems to have built successfully, I'll let you know if it does not run correctly as well. rm -r gromacs-2020/ sudo apt-get install gcc-8 g++-8 tar -xvzf gromacs-2020.tar.gz cd gromacs-2020/ mkdir build cd build CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release make make check sudo make install source /usr/local/gromacs/bin/GMXRC Lastly, when I was building in default and ran into trouble I like to build in debug so it gives details about building and helps me identify source of the problems or identify relevant information to pass to you so you can better help me. I appreciate your comment about not building in debugging mode, but is there a way to run release in verbose mode? When I had problems with other programs I'd usually build my first time in debugger mode so I can monitor the process, then make clean and rebuild in default. Is there a better way to do this? Once again you help was greatly appreciated, Ryan PS again a few notes (if you have time to comment on anything incorrect) I have for people needing a fix in the future and maybe myself if I do this again in a few years and forget how. CUDA version (nvcc --version) is 9.1. This is a little confusing to me because you referenced CUDA 10.1 and I completely rebuilt this computer in September 2019, so unless there is a new driver since then it should be 10.1? I grabbed the newest drivers I could find but my computer is outputting 9.1 so I guess that is my version. when building gromacs and I specify gcc/g++ verison 5, 8, or 9 it fails with the original error message regarding glibc 23.2. CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_GPLUSPLUS_PATH=/usr/bin/g++-8 -DCUDA_HOST_COMPILER=gcc-8 -DCMAKE_CXX_COMPILER=g++-8 -DCMAKE_C_COMPILER=/usr/bin/gcc-8 -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=release Do you know why this is? When I started this adventure I just had sudo apt-get install gcc g++ build-essentials. Then I used gcc-5 g++-5 and specified the version in the build step, which failed. after taking that out and running sudo apt-get install gcc-9 g++-9 it passes "CMAKE" but fails in "make". Based on your suggestions I ran the commands at the top of the email to which then worked. Would this have worked if I had just installed gcc-8 g++-8 from the beginning and ran CMAKE with no version specification? On Thu, Jan 30, 2020 at 5:50 AM Szilárd Páll wrote: > Dear Ryan, > > On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz wrote: > > > Dear Szilárd, > > > > Thank you for your quick response. You are correct, after > > issuing sudo apt-get install gcc-9 g++-9 CMake was run with: > > > > gcc 9 is not supported with CUDA, as far as I know version 8 is the latest > supported gcc in CUDA 10.2 (officially "native support" whatever they mean > by that is for 7.3 on Ubuntu 18.04.3, see > https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) > > CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON > > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug > > > > Don't use a Debug build unless you want to debug the GROMACS tools (it's > slow). > > Make sure that you cmake configuration does actually use the gcc version > you intend to use. The default invocation as above will pick up the default > compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by > opening the CMakeCache.txt file or using ccmake) -- and I think the lack of > proper AVX512 support in your default gcc 5 (which you are stil; using) is > the source of the issues you report below. > > You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the > configure step; for details see > > http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation > > Cheers, > -- > Szilárd > > > > However now I'm getting an error in make > > > > make VERBOSE=1 > > > > error: > > > > [ 25%] Building CXX object > > > > > src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o > > In file included from > > > > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0, > > from > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146, > > from > > > > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40, > > from > > > > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49: > > > > >
Re: [gmx-users] gromacs-2020 build gcc/nvcc error
Dear Ryan, On Wed, Jan 29, 2020 at 10:35 PM Ryan Woltz wrote: > Dear Szilárd, > > Thank you for your quick response. You are correct, after > issuing sudo apt-get install gcc-9 g++-9 CMake was run with: > gcc 9 is not supported with CUDA, as far as I know version 8 is the latest supported gcc in CUDA 10.2 (officially "native support" whatever they mean by that is for 7.3 on Ubuntu 18.04.3, see https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html) CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug > Don't use a Debug build unless you want to debug the GROMACS tools (it's slow). Make sure that you cmake configuration does actually use the gcc version you intend to use. The default invocation as above will pick up the default compiler toolchain (e.g. /us/bin/gcc in your case, you can verify that by opening the CMakeCache.txt file or using ccmake) -- and I think the lack of proper AVX512 support in your default gcc 5 (which you are stil; using) is the source of the issues you report below. You can explicitly set the compiler by passing CMAKE_CXX_COMPILER at the configure step; for details see http://manual.gromacs.org/current/install-guide/index.html?highlight=cxx%20compiler#typical-installation Cheers, -- Szilárd > However now I'm getting an error in make > > make VERBOSE=1 > > error: > > [ 25%] Building CXX object > > src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o > In file included from > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0, > from > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146, > from > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40, > from > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49: > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h: > In function ‘void gmx::gatherLoadTransposeHsimd(const float*, const float*, > const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2; > int32_t = int]’: > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28: > error: the last argument must be scale 1, 2, 4, 8 > tmp1 = _mm512_castpd_ps( > ^ > > /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28: > error: the last argument must be scale 1, 2, 4, 8 > tmp2 = _mm512_castpd_ps( > ^ > src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target > > 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o' > failed > make[2]: *** > > [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o] > Error 1 > CMakeFiles/Makefile2:2910: recipe for target > 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed > make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 > Makefile:162: recipe for target 'all' failed > make: *** [all] Error 2 > > after doing a 1 hour google I found discussions saying that the error > (Makefile:162: recipe for target 'all' failed) is too vague with no general > solution. I found fixes for headers and other files for other programs but > not fixes for this file. The fix linked below is for gromacs-2018 and a > different file but the general problem seems to suggest it still is a > gcc/g++ version compatibility error correct? Any suggestions for this > error? > > https://redmine.gromacs.org/issues/2312 > > > Thank you so much, > > Ryan > > PS Just to document for anyone else going through what I did for > Gromacs-2020 these were my steps. > > sudo apt-get install gcc g++ > cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON > > I then received multiple errors complaining about nvcc/C++ > incompatibility. After researching found errors for previous gromacs > versions suggesting to use gcc-5 (but as you suggested this error has been > patched). > > sudo apt-get install gcc-5 g++-5 > 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 > -D_FORCE_INLINES=OFF > > Received different error described in previous email and solved with your > suggested solution. The key might be to specifically install latest version > number i.e. > > sudo apt-get install gcc-X
Re: [gmx-users] gromacs-2020 build gcc/nvcc error
Dear Szilárd, Thank you for your quick response. You are correct, after issuing sudo apt-get install gcc-9 g++-9 CMake was run with: CMAKE_PREFIX_PATH=/usr/:/usr/local/cuda/ cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda/ -DCMAKE_BUILD_TYPE=Debug However now I'm getting an error in make make VERBOSE=1 error: [ 25%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o In file included from /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512.h:46:0, from /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/simd.h:146, from /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/nbnxm_simd.h:40, from /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp:49: /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h: In function ‘void gmx::gatherLoadTransposeHsimd(const float*, const float*, const int32_t*, gmx::SimdFloat*, gmx::SimdFloat*) [with int align = 2; int32_t = int]’: /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:422:28: error: the last argument must be scale 1, 2, 4, 8 tmp1 = _mm512_castpd_ps( ^ /home/rlwoltz/protein_modeling/gromacs-2020/src/gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_util_float.h:424:28: error: the last argument must be scale 1, 2, 4, 8 tmp2 = _mm512_castpd_ps( ^ src/gromacs/CMakeFiles/libgromacs.dir/build.make:13881: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o' failed make[2]: *** [src/gromacs/CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o] Error 1 CMakeFiles/Makefile2:2910: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2 Makefile:162: recipe for target 'all' failed make: *** [all] Error 2 after doing a 1 hour google I found discussions saying that the error (Makefile:162: recipe for target 'all' failed) is too vague with no general solution. I found fixes for headers and other files for other programs but not fixes for this file. The fix linked below is for gromacs-2018 and a different file but the general problem seems to suggest it still is a gcc/g++ version compatibility error correct? Any suggestions for this error? https://redmine.gromacs.org/issues/2312 Thank you so much, Ryan PS Just to document for anyone else going through what I did for Gromacs-2020 these were my steps. sudo apt-get install gcc g++ cmake ../ -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON I then received multiple errors complaining about nvcc/C++ incompatibility. After researching found errors for previous gromacs versions suggesting to use gcc-5 (but as you suggested this error has been patched). sudo apt-get install gcc-5 g++-5 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 -D_FORCE_INLINES=OFF Received different error described in previous email and solved with your suggested solution. The key might be to specifically install latest version number i.e. sudo apt-get install gcc-X g++-X (with X being the largest number available). On Wed, Jan 29, 2020 at 2:05 AM Szilárd Páll wrote: > 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 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 >
Re: [gmx-users] gromacs-2020 build gcc/nvcc error
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 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.
[gmx-users] gromacs-2020 build gcc/nvcc error
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.
