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 >
[gmx-users] Cell Membrane Potential
Hi, I am undergraduate student wanting to learn and use GROMACS for a project on membrane proteins. Is altering membrane potential in a simulation possible using GROMACS? I do apologize if this is trivial. I tried looking at the documentation, but most of the information are currently too challenging for me. Any guidance would be greatly appreciated. kind regards, Frank -- 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] gmx dens charge
Dear users, I need to know for charge density calculation specially for water, should we use -center /-symm option or not and if not why? Since I tried the option (-center/-symm) for charge density calculation of water and gmx dens module was not reading frame. I used the gromacs version 5.1.4 for the analysis. I will be highly thankful if any one can suggest me regarding this. -- 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] ERROR DURING INSTALLATION
I am using Linux to install gromacs and have installed all the prerequisites and programs and packages as per my knowledge. In the build directory, after using the command - 'cmake ..' I have received the following error message. Please help me out with this. ERROR - CMake Error at CMakeLists.txt:63 (include): include could not find load file: gmxManageCcache CMake Warning at CMakeLists.txt:69 (find_package): By not providing "FindLibStdCpp.cmake" in CMAKE_MODULE_PATH this project has asked CMake to find a package configuration file provided by "LibStdCpp", but CMake did not find one. Could not find a package configuration file provided by "LibStdCpp" with any of the following names: LibStdCppConfig.cmake libstdcpp-config.cmake Add the installation prefix of "LibStdCpp" to CMAKE_PREFIX_PATH or set "LibStdCpp_DIR" to a directory containing one of the above files. If "LibStdCpp" provides a separate development package or SDK, be sure it has been installed. CMake Error at CMakeLists.txt:75 (include): include could not find load file: gmxBuildTreeInfo CMake Error at CMakeLists.txt:76 (include): include could not find load file: gmxVersionInfo CMake Error at CMakeLists.txt:85 (include): include could not find load file: gmxBuildTypeReference CMake Error at CMakeLists.txt:86 (include): include could not find load file: gmxBuildTypeProfile CMake Error at CMakeLists.txt:87 (include): include could not find load file: gmxBuildTypeTSAN CMake Error at CMakeLists.txt:88 (include): include could not find load file: gmxBuildTypeASAN CMake Error at CMakeLists.txt:89 (include): include could not find load file: gmxBuildTypeMSAN CMake Error at CMakeLists.txt:90 (include): include could not find load file: gmxBuildTypeReleaseWithAssert CMake Error at CMakeLists.txt:112 (include): include could not find load file: gmxCTestUtilities CMake Error at CMakeLists.txt:113 (gmx_ctest_init): Unknown CMake command "gmx_ctest_init". -- Configuring incomplete, errors occurred! See also "/home/sakshi/Downloads/gromacs-2020/CMakeFiles/CMakeOutput.log".\ Regards, Sakshi Arora -- 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.
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.
