[gmx-users] Query regarding all-atom simulations on 980 Ti GPUs

[Suhani Nagpal]

Greetings

I have just recently started to work on this workstation (details as shown
below) and have employed all-atom simulation of 30,000 atoms with this
command (just for 1 micro-sec),

gmx mdrun -deffnm md -v -ntmpi 2 -ntomp 6 -gpu_id 01 -pin on


Running on 1 node with total 8 cores, 16 logical cores, 2 compatible GPUs
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Core(TM) i7-5960X CPU @ 3.00GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX2_256
  GPU info:
    Number of GPUs detected: 2
    #0: NVIDIA GeForce GTX 980 Ti, compute cap.: 5.2, ECC:  no, stat:
compatible
    #1: NVIDIA GeForce GTX 980 Ti, compute cap.: 5.2, ECC:  no, stat:
compatible

Reading file md.tpr, VERSION 5.1.2 (single precision)
Using 2 MPI threads
Using 6 OpenMP threads per tMPI thread

2 GPUs user-selected for this run.
Mapping of GPU IDs to the 2 PP ranks in this node: 0,1



I have just given the command,

and it shows:

step 126800, will finish Tue Jul 12 16:11:59 2016imb F  3%


and the imb F increases till 25-28%.

According to the time, this gives a performance of less 100 ns per day.
Because I have read other benchmarking studies, it should give above 200 ns
at least.

On another note (very strange),

when I subject more than 1 simulation (around 30,000 atoms) on this system,
the performance reduces a lot (~ 50 ns per day for the second trajectory). and
pin off when running more than one simulation.

What am I doing wrong? I have not worked on GPUs before.


Kindly help

Thanks a lot

Suhani