Hi, Short answer: use a profiler, e.g. nvprof.
Long answer: Unless you are running on a single GPU (i.e. no domain decomposition), due to CUDA limitations, we can not time internally the GPU kernels. However, you can easily do that using the "nvprof" tool that comes with the CUDA toolkit. If you simply prefix your regular GROMACS command with nvprof, you'll get a pretty usable trace of the GPU kernels, data movement, as well as CUDA API fucntions. Note that if you use DD the nvidia profiler will by default average the kernel time for all calls which will not give you the total per-step non-bonded kernel time (because with DD there will be a local and a non-local kernel called every step) - which what you typically want. In this case, you may want to get a full trace where every kernel call and its time is listed and calculate the average yourself. I hope that helps! Cheers, -- Szilárd On Fri, Sep 19, 2014 at 12:52 PM, xiexiao...@sjtu.edu.cn <xiexiao...@sjtu.edu.cn> wrote: > Thanks.Do you know how to calculate the time consuming of non-bonded force > that run on gpu? > > > > xiexiao...@sjtu.edu.cn > > From: Mark Abraham > Date: 2014-09-19 18:37 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] force > Hi, > > To which part of the log file do you refer? The "Force" part of the timing > breakdown does indeed refer to the combination of short-range non-bonded, > and bonded force + energy computation. > > Mark > > On Fri, Sep 19, 2014 at 11:11 AM, xiexiao...@sjtu.edu.cn < > xiexiao...@sjtu.edu.cn> wrote: > >> What does the force in log file mean?Does it include bonded force and >> non-bonded force? >> >> >> >> xiexiao...@sjtu.edu.cn >> -- >> 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.
