Hi, I'm trying to install GROMACS 2018.1 and getting errors during "make check" which Google has never heard of. My computer is nothing particularly unusual: a laptop with an Nvidia GTX 1050, Intel i7-8550U CPU, and running Ubuntu 18.04.
The problem has something to do with the GPU: - Building goes fine when I don't include GPU (specifying -DGMX_GPU=off for cmake) - When I built for OpenCL, using -DGMX_GPU=on -DGMX_USE_OPENCL=on, "make" and "make check" were successful, although the mdrun failed with a message about CL_OUT_OF_HOST_MEMORY (see message at the bottom).- When I build for CUDA, with just -DGMX_GPU=on, I get four failures in "make check". I ran the following: cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DCMAKE_C_COMPILER=gcc-6 -DCMAKE_CXX_COMPILER=g++-6 make make check (The compiler options are because CUDA requires older compilers. I also tried it with gcc-5/g++-5. Either way,) "make" succeeds, but "make check" fails four tests: 7/39 Test #7: EwaldUnitTests ...................***Failed 0.00 sec [...]/gromacs-2018.1/build/bin/ewald-test: symbol lookup error: [...]/gromacs-2018.1/build/bin/ewald-test: undefined symbol: _Z13pme_gpu_solvePK6PmeGpuP9t_complex12GridOrderingb 9/39 Test #9: GpuUtilsUnitTests ................***Failed 0.00 sec [...]/gromacs-2018.1/build/bin/gpu_utils-test: symbol lookup error: [...]/gromacs-2018.1/build/bin/gpu_utils-test: undefined symbol: _Z18isHostMemoryPinnedPv 32/39 Test #32: MdrunTests .......................***Failed 0.00 sec [...]/gromacs-2018.1/build/bin/mdrun-test: symbol lookup error: [...]/gromacs-2018.1/build/bin/mdrun-test: undefined symbol: _Z16resetGpuProfilerv 33/39 Test #33: MdrunMpiTests ....................***Failed 0.00 sec [...]/gromacs-2018.1/build/bin/mdrun-mpi-test: symbol lookup error: [...]/gromacs-2018.1/build/bin/mdrun-mpi-test: undefined symbol: _Z16resetGpuProfilerv And at the bottom of the output: Errors while running CTest CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target 'CMakeFiles/run-ctest-nophys' failed make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 CMakeFiles/Makefile2:1385: recipe for target 'CMakeFiles/run-ctest-nophys.dir/all' failed make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 CMakeFiles/Makefile2:1165: recipe for target 'CMakeFiles/check.dir/rule' failed make[1]: *** [CMakeFiles/check.dir/rule] Error 2 Makefile:626: recipe for target 'check' failed make: *** [check] Error 2 You can see the full outputs here: make_check.log: https://gist.githubusercontent.com/sssheridan/10b7c045aff58b782e6a0fc5c4d2f833/raw/f1ba6b024d32e75d64ef4e4af75e57d3b22e1954/make_check.log make.log: https://gist.githubusercontent.com/sssheridan/10b7c045aff58b782e6a0fc5c4d2f833/raw/f1ba6b024d32e75d64ef4e4af75e57d3b22e1954/make.log So, my questions are: 1) Is this a failure to be concerned about, or can I go ahead and use this GROMACS build? 2) Is there something I can/should do to fix it? Just to try, I'm running with the CUDA build right now and, well, it's lasted longer than the OpenCL build without a crash (currently on step 740000). I appreciate any advice or assistance you can offer! Steve ----------------- Here's the error in mdrun from the OpenCL build: [...] Using 1 MPI thread Using 8 OpenMP threads 1 GPU auto-selected for this run. Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node: PP:0 starting mdrun 'Protein in water' 5000000 steps, 10000.0 ps. ------------------------------------------------------- Program: gmx mdrun, version 2018.1 Source file: src/gromacs/gpu_utils/oclutils.h (line 165) Function: void gpuStreamSynchronize(cl_command_queue) Assertion failed: Condition: CL_SUCCESS == cl_error Error caught during clFinish:CL_OUT_OF_HOST_MEMORY For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- I have 8GB of RAM, and the GPU has 4GB of video memory, and wasn't running much else at the time. -- 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 [email protected].
