[gmx-users] strange GPU performance

[Mark Abraham]

Hi,

Why did you specify using 2 MPI ranks with 8 OpenMP threads per rank on a
node with 10 cores and 2 GPUs? You want something that fills all the cores
(and hyperthreads) e.g.

mpirun -np 2 gmx_mpi mdrun

or

mpirun -np 4 gmx_mpi mdrun

There are likely further improvements available along the lines Szilard
suggests.

Mark

On Mon, Jul 11, 2016 at 10:24 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).
> 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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