Hi, If mdrun claims it's using the GPU and you see no errors (and results look reasonable), the GPU is likely being used. That nvidia-smi is not showing it is admittedly strange. However, this truncated log output does not confirm much, e.g. it does not show the performance table and the final performance.
Could you please run again and look at (and share if approapriate): - the entire log, not just parts, in particular we want to see the header, perf table - the output of nvidia-smi dmon executing *during* mdrun's execution (this monitors the device continuously) Cheers, -- Szilárd On Thu, Jul 14, 2016 at 8:28 PM, Vito Spadavecchio <spadavecc...@gmail.com> wrote: > Hello > > After building GROMACS with GPU support and running some simple MD, I am > only getting ~20ns/day (which is what I would expect to get out of my > i7-6700k cpu only. My machine currently has a 1080 GTX in it, which should > even on moderately large systems, be getting ~100ns/day) > > I've tried launching a mdrun with with the following command: > > gmx mdrun -deffnm md_0_1 -gpu_id 0 -nb gpu > > > > With the following in my md.mdp file: > > ; Neighborsearching > > cutoff-scheme = Verlet > > > > The top of the log file for the mdrun notes: > > Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU >> Hardware detected: >> CPU info: >> Vendor: GenuineIntel >> Brand: Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz >> SIMD instructions most likely to fit this hardware: AVX2_256 >> SIMD instructions selected at GROMACS compile time: AVX2_256 >> GPU info: >> Number of GPUs detected: 1 >> #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC: no, stat: >> compatible >> Reading file md_0_1.tpr, VERSION 5.1.2 (single precision) >> Changing nstlist from 10 to 40, rlist from 1 to 1.099 >> Using 1 MPI thread >> Using 8 OpenMP threads >> 1 GPU user-selected for this run. >> Mapping of GPU ID to the 1 PP rank in this node: 0 >> > > The output of *nvidia-smi *on my machine is: > > hu Jul 14 11:25:04 2016 >> >> +-----------------------------------------------------------------------------+ >> | NVIDIA-SMI 367.27 Driver Version: 367.27 >> | >> >> |-------------------------------+----------------------+----------------------+ >> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. >> ECC | >> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute >> M. | >> >> |===============================+======================+======================| >> | 0 GeForce GTX 1080 Off | 0000:01:00.0 On | >> N/A | >> | 30% 41C P8 7W / 180W | 730MiB / 8113MiB | 3% >> Default | >> >> +-------------------------------+----------------------+----------------------+ >> >> >> >> +-----------------------------------------------------------------------------+ >> | Processes: GPU >> Memory | >> | GPU PID Type Process name Usage >> | >> >> |=============================================================================| >> | 0 1035 G /usr/lib/xorg/Xorg >> 424MiB | >> | 0 2132 G compiz >> 103MiB | >> | 0 5296 G ...s-passed-by-fd --v8-snapshot-passed-by-fd >> 59MiB | >> | 0 14079 G ...s-passed-by-fd --v8-snapshot-passed-by-fd >> 31MiB | >> | 0 14234 G ...ing<BrotliEncoding --disable-features=Doc >> 108MiB | >> >> +-----------------------------------------------------------------------------+ > > > and output of *nvcc --version* is: > > nvcc: NVIDIA (R) Cuda compiler driver >> Copyright (c) 2005-2015 NVIDIA Corporation >> Built on Tue_Aug_11_14:27:32_CDT_2015 >> Cuda compilation tools, release 7.5, V7.5.17 > > > Does anyone have any ideas what the problem might be? > > Thanks! > -- > 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.