Hi, The default changed in GROMACS 2018 - even if NVML is found, we do not link with it by default. Use cmake -DGMX_USE_NVML=on. Be advised that you may need to take care that the nvml library found at run time is compatible with the CUDA version used at compilation time. That can be non-trivial to automate, so we have left that issue to users who have the desire and ability to change the clocks (generally requires root privilege / sysadmin approval).
Mark On Fri, Jan 12, 2018 at 9:19 AM Jernej Zidar <jernej.zi...@gmail.com> wrote: > Hi, > > I have an interesting problem with the NVML library from CUDA 9 (and 9.1) > and Gromacs 2018. Namely, the NVML is reported as detected during cmake but > Gromacs 2018 is linked without it. > > This is the cmake command I would issue: > > m -rf * && CMAKE_PREFIX_PATH=/home/zidar/utils/fftw-3.3.6-gcc/ \ > > cmake ../gromacs-2018-rc1 -DGMX_GPU=on -DGMX_MPI=off > -DGMX_FFT_LIBRARY=fftw3 \ > > -DCMAKE_INSTALL_PREFIX=/home/zidar/utils/gromacs-2018-rc1-gcc > -DGMX_SIMD=AVX2_256 > > make install > > Relevant part from cmake: > > -- Looking for NVIDIA GPUs present in the system > > -- Number of NVIDIA GPUs detected: 3 > > -- Found CUDA: /usr/local/cuda (found suitable version "9.1", minimum > required is "6.5") > > -- Found NVML: /usr/lib/x86_64-linux-gnu/libnvidia-ml.so > > But when I run mdrun: > > NOTE: GROMACS was configured without NVML support hence it can not exploit > > application clocks of the detected Tesla K40c GPU to improve > performance. > > Recompile with the NVML library (compatible with the driver used) or > set application clocks manually. > > CUDA is installed in /usr/local/cuda-9.1 with a symlink to /usr/local/cuda. > The library file is physically present in /usr/lib/x86_64-linux-gnu/ > > Gromacs 2016.4 can be compiled without issues. The NVML library is detected > and properly linked: > > ldd /home/zidar/utils/gromacs-2016.4-gcc/bin/gmx > > linux-vdso.so.1 (0x00007ffc333ad000) > > libgromacs.so.2 => /home/zidar/utils/gromacs-2016.4-gcc/lib/libgromacs.so.2 > (0x00002ac6ada45000) > > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00002ac6b06c2000) > > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002ac6b08df000) > > librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00002ac6b0ae3000) > > libnvidia-ml.so.1 => /usr/lib/x86_64-linux-gnu/libnvidia-ml.so.1 > (0x00002ac6b0ceb000) > > libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 > (0x00002ac6b12c5000) > > libfftw3f.so.3 => /home/zidar/utils/fftw-3.3.6-gcc/lib/libfftw3f.so.3 > (0x00002ac6b1501000) > > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002ac6b1a2f000) > > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00002ac6b1d33000) > > libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00002ac6b20b5000) > > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002ac6b22e2000) > > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002ac6b24f9000) > > /lib64/ld-linux-x86-64.so.2 (0x00002ac6ad5df000) > > libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00002ac6b2898000) > > libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00002ac6b2aa3000) > > But not with neither Gromacs 2018 nor Gromacs 2018 rc1: > > ldd /home/zidar/utils/gromacs-2018-rc1-gcc/bin/gmx > > linux-vdso.so.1 (0x00007ffd2d5fd000) > > libgromacs.so.3 => > /home/zidar/utils/gromacs-2018-rc1-gcc/lib/libgromacs.so.3 > (0x00002aad09c56000) > > libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 > (0x00002aad0ca83000) > > libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002aad0ce05000) > > libgomp.so.1 => /usr/lib/x86_64-linux-gnu/libgomp.so.1 (0x00002aad0d109000) > > libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002aad0d336000) > > libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 > (0x00002aad0d54d000) > > libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002aad0d76a000) > > librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00002aad0db09000) > > libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002aad0dd11000) > > libcufft.so.9.1 => /usr/local/cuda/lib64/libcufft.so.9.1 > (0x00002aad0df15000) > > libhwloc.so.5 => /usr/lib/x86_64-linux-gnu/libhwloc.so.5 > (0x00002aad15402000) > > libfftw3f.so.3 => /home/zidar/utils/fftw-3.3.6-gcc/lib/libfftw3f.so.3 > (0x00002aad1563e000) > > /lib64/ld-linux-x86-64.so.2 (0x00002aad097ed000) > > libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 (0x00002aad15b6c000) > > libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00002aad15d77000) > > Any idea where to start looking ? > > Thanks, > Jernej > -- > 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.