The error you saw is clear evidence of a bug. There's a few things you might try to help narrow things down. * Is the error reproducible on each run of mdrun?
Yes * 2018.3 was not designed or tested on CUDA 10, which was released rather later. If you have an earlier CUDA, please see if building with it alleviates the error No I have only CUDA 10.0 installed. Taking into account that I made that running (see replies to the next questions) please let me know whether should I go with CUDA 9. * The error message could be triggered by multiple parts of the code; what do you get with mdrun -nb gpu -pme cpu? This way I get MD running, no crash. All 72 cores (dual Xeon Gold 6140) with my system I got $mdrun -deffnm md -v -nb gpu -pme cpu (ns/day) (hour/ns) Performance: 56.867 0.422 $nvidia-smi | 0 Quadro P5000 On | 00000000:D5:00.0 On | Off | | 35% 56C P0 63W / 180W | 1400MiB / 16256MiB | 37% Default | * Do you get any more diagnostics from running with a build with cmake -DCMAKE_BUILD_TYPE=Debug? Interesting comes here. Gromacs with Debug = ON allows to stably run MD with no additional params. I mean $ gmx mdrun -deffnm md -v runs with no crash. However, only half of the Xeon cores are used (monitored with htop) (ns/day) (hour/ns) Performance: 69.577 0.345 $nvidia-smi | 0 Quadro P5000 On | 00000000:D5:00.0 On | Off | | 38% 62C P0 68W / 180W | 1430MiB / 16256MiB | 56% Default | If I run $ gmx mdrun -deffnm md -v -nb gpu -pme cpu Then all CPU cores are busy but performancs is poor (ns/day) (hour/ns) Performance: 20.249 1.185 $nvidia-smi | 0 Quadro P5000 On | 00000000:D5:00.0 On | Off | | 37% 57C P0 58W / 180W | 1408MiB / 16256MiB | 22% Default | Finally, If I run same MD with no GPU at all (i.e. -nb cpu) then I got performance (ns/day) (hour/ns) Performance: 47.536 0.505 Does this help? Dmytro From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark Abraham <mark.j.abra...@gmail.com> Sent: Wednesday, November 14, 2018 1:37 PM To: gmx-us...@gromacs.org Cc: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Running GPU issue Hi, I expect that that warning is fine (for now). The error you saw is clear evidence of a bug. There's a few things you might try to help narrow things down. * Is the error reproducible on each run of mdrun? * 2018.3 was not designed or tested on CUDA 10, which was released rather later. If you have an earlier CUDA, please see if building with it alleviates the error * The error message could be triggered by multiple parts of the code; what do you get with mdrun -nb gpu -pme cpu? * Do you get any more diagnostics from running with a build with cmake -DCMAKE_BUILD_TYPE=Debug? Mark On Wed, Nov 14, 2018 at 1:09 PM Kovalskyy, Dmytro <kovals...@uthscsa.edu> wrote: > I forgot to add. While compiling gromacs I got following error at the very > beggining: > > > [ 3%] Built target gpu_utilstest_cuda > /usr/local/tmp/gromacs-2018.3/src/gromacs/gpu_utils/gpu_utils.cu: In > function ?int do_sanity_checks(int, cudaDeviceProp*)?: > /usr/local/tmp/gromacs-2018.3/src/gromacs/gpu_utils/gpu_utils.cu:258:28: > warning: ?cudaError_t cudaThreadSynchronize()? is deprecated > [-Wdeprecated-declarations] > if (cudaThreadSynchronize() != cudaSuccess) > ^ > /usr/local/cuda/include/cuda_runtime_api.h:947:46: note: declared here > extern __CUDA_DEPRECATED __host__ cudaError_t CUDARTAPI > cudaThreadSynchronize(void); > > > But make has completed its job without falling down. > > > > > ________________________________________ > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Mark > Abraham <mark.j.abra...@gmail.com> > Sent: Tuesday, November 13, 2018 10:29 PM > To: gmx-us...@gromacs.org > Cc: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Running GPU issue > > Hi, > > It can share. > > Mark > > On Mon, Nov 12, 2018 at 10:19 PM Kovalskyy, Dmytro <kovals...@uthscsa.edu> > wrote: > > > Hi, > > > > > > > > To perform GPU with Gromacs does it require exclusive GPU card or > Gromacs > > can share the video card with X-server? > > > > > > Thank you > > > > > > Dmytro > > -- > > 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. > -- > 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. -- 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.