[gmx-users] strange GPU performance

[Szilárd Páll]

On Mon, Jul 11, 2016 at 10:23 AM, Albert <mailmd2011 at gmail.com> wrote:
> Hello:
>
> I submitted Gromacs GPU job with the following command line:
>
> mpirun -np 2 gmx_mpi mdrun -s 7.tpr -v -g 7.log -c 7.gro -x 7.xtc -gpu_id 01
> -ntomp 8 >& 7.info
>
> I obtained the following log file:
>
>
> Number of logical cores detected (20) does not match the number reported by
> OpenMP (2).

This note means that an external tool (MPI or job launcher) set core
affinities and as it was not told to use 8 cores per rank it placed
all 16 threads on  four cores. Along the cores/rank  you should also
tell the launcher to bind to socket.

Alternatively, you can turn off binding in that external tool and use
mdrun -pin on. However, as you have 2x10 cores the second rank will be
spanning across the two CPUs which is not ideal.

BTW, you can try running with 4 ranks, it could be faster.

--
Szilárd

> Consider setting the launch configuration manually!
>
> Running on 1 node with total 10 cores, 20 logical cores, 2 compatible GPUs
> Hardware detected on host cudaA.europe.actelion.com (the node of MPI rank
> 0):
>   CPU info:
>     Vendor: GenuineIntel
>     Brand:  Intel(R) Xeon(R) CPU E5-2690 v2 @ 3.00GHz
>     SIMD instructions most likely to fit this hardware: AVX_256
>     SIMD instructions selected at GROMACS compile time: AVX_256
>   GPU info:
>     Number of GPUs detected: 2
>     #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat:
> compatible
>     #1: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC:  no, stat:
> compatible
>
> Reading file 7.tpr, VERSION 5.1.2 (single precision)
> Changing nstlist from 20 to 40, rlist from 1.009 to 1.064
>
> Using 2 MPI processes
> Using 8 OpenMP threads per MPI process
>
>
> In principle, there should be 2x8=16 CPU occupied. However, I noticed that
> there is only 4 CPU was using but it generated 16 Gromacs process. The speed
> of GPU is very slow.... I am just wondering how to solve this problem?
>
> Thanks a lot
>
> Albert
>
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