[gmx-users] Gromacs-4.6 on two Titans GPUs

James Starlight jmsstarlight at gmail.com
Tue Nov 5 12:16:49 CET 2013


My suggestions:

1) During compilstion using -march=corei7-avx-i I have obtained error that
somethng now found ( sorry I didnt save log) so I compile gromacs without
this flag

2) I have twice as better performance using just 1 gpu by means of

mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v  -deffnm md_CaM_test

than using of both gpus

mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v  -deffnm md_CaM_test

in the last case I have obtained warning

WARNING: Oversubscribing the available 12 logical CPU cores with 24 threads.
         This will cause considerable performance loss!

How it could be fixed?
All gpu are recognized correctly


2 GPUs detected:
  #0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
compatible
  #1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC:  no, stat:
compatible


James


2013/11/4 Szilárd Páll <pall.szilard at gmail.com>

> You can use the "-march=native" flag with gcc to optimize for the CPU
> your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
> CPUs.
> --
> Szilárd Páll
>
>
> On Mon, Nov 4, 2013 at 12:37 PM, James Starlight <jmsstarlight at gmail.com>
> wrote:
> > Szilárd, thanks for suggestion!
> >
> > What kind of CPU optimisation should I take into account assumint that
> I'm
> > using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12
> > nodes in Debian).
> >
> > James
> >
> >
> > 2013/11/4 Szilárd Páll <pall.szilard at gmail.com>
> >
> >> That should be enough. You may want to use the -march (or equivalent)
> >> compiler flag for CPU optimization.
> >>
> >> Cheers,
> >> --
> >> Szilárd Páll
> >>
> >>
> >> On Sun, Nov 3, 2013 at 10:01 AM, James Starlight <
> jmsstarlight at gmail.com>
> >> wrote:
> >> > Dear Gromacs Users!
> >> >
> >> > I'd like to compile lattest 4.6 Gromacs with native GPU supporting on
> my
> >> i7
> >> > cpu with dual GeForces Titans gpu mounted. With this config I'd like
> to
> >> > perform simulations using cpu as well as both gpus simultaneously.
> >> >
> >> > What flags besides
> >> >
> >> > cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5
> >> >
> >> >
> >> > should I define to CMAKE for compiling optimized gromacs on such
> >> workstation?
> >> >
> >> >
> >> > Thanks for help
> >> >
> >> > James
> >> > --
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