[gmx-users] strange GPU performance

[Albert]

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