[gmx-users] optimize cpu with gpu node for gromacs

[Szilárd Páll]

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 <rahuldhakne89 at 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
> -
> --
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