Hi, In this case you can't do much, the GPU is simply not fast enough to finish its job before the CPU does. What you can try is: - decrease nstlist - especially if it has been increased by mdrun (hint use GMX_NSTLIST) - try running in mixed GPU+CPU non-bonded mode, e.g. mdrun -ntmpi 2 -gpu_id 00 -nb gpu_cpu or to "push" more work to the CPU: mdrun -ntmpi 4 -gpu_id 0000 -nb gpu_cpu This will require domain decomposition, though, so it may not help.
Cheers, -- Szilárd On Fri, Jun 6, 2014 at 9:15 AM, rahul dhakne <rahuldhakn...@gmail.com> wrote: > Dear all Gromacs User, > I am using one GPU node (NVIDIA Tesla C2050, 2.5 Gb ,6 core ) > for simulation purpose on Intel(R) core I7 (3.0 *GHz, 16gb*) system. I did > tested on this workstation with Gromacs 4.6. It seems from these that > performance of GPU is imbalanced with CPU. It was showing shorter cut_off > but I am using least of it. > > Using 1 MPI thread > Using 8 OpenMP threads > > 1 GPU detected: > #0: NVIDIA Tesla C2050, compute cap.: 2.0, ECC: yes, stat: compatible > > 1 GPU auto-selected for this run. > Mapping of GPU to the 1 PP rank in this node: #0 > > starting mdrun 'Protein ' > 500000 steps, 1000.0 ps. > > Writing final coordinates. > > > NOTE: The GPU has >20% more load than the CPU. This imbalance causes > performance loss, consider using a shorter cut-off and a finer PME > grid. > > Core t (s) Wall t (s) (%) > Time: 26585.222 3827.438 694.6 > 1h03:47 > (ns/day) (hour/ns) > Performance: 22.574 1.063 > > How to optimize this mdrun to get maximum use of GPU and accelerate the > performance?. How many thread to be given? What to be optimized so that I > can use for simulation purpose? Please let me know this is enough > information. > > > > -- with regard > Rahul > - > -- > 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.