[gmx-users] Groms 2019.0, simulations using 2 GPUs: RTX 2080Ti

[Pragati Sharma]

Hi Paul,

The option -pme gpu works when I give pme order = 4 in mdp file instead of
3. but it gives me an increase of 6-7 ns/day.

@Dave M : I am also getting same observation. "If I run just one
simulation, I get almost double performance compared to when I run two
simulations in two GPUs as follows.

mdrun -ntomp 12 -gpu_id 0 -nb gpu
mdrun -ntomp 12  -gpu_id 1  -nb gpu

I am seeing various benchmarks, and the performance should not reduce to
half with two simulations.

I need a command line with mdrun for maximal use of CPU and gpu.













On Fri, Dec 13, 2019 at 1:14 PM Dave M <dave.gromax at gmail.com> wrote:

> Hi Paul,
>
> I just jumped in this discussion. But I am wondering is
> CUDA_VISIBLE_DEVICES  equivalent to providing gpu_id in mdrun?
> Also, my multiple simulations run slower in the same node with multiple
> gpus. e.g. in a node with 4 GPU and 64 CPU
> mpirun -np 1 mdrun -ntomp 24 -gpu_id 0 -pin on
> mpirun -np 1 mdrun -ntomp 24 -gpu_id 2 -pin on
>
> If I run just one simulation I get almost double performance (with same
> command as above).
>
> Dave
>
> On Thu, Dec 12, 2019 at 11:22 PM Paul bauer <paul.bauer.q at gmail.com>
> wrote:
>
> > Hello,
> >
> > the error you are getting in the end means that your simulation likely
> > does not use PME, or uses it in a way that is not implemented to run on
> > the GPU.
> > You can still run the nonbonded calculations on the GPU, just remove the
> > -pme gpu flag.
> >
> > For running different simulations on your GPUs, you need to set the
> > environment variable CUDA_VISIBLE_DEVICES so that each simulation only
> > sees on of the available GPUs.
> >
> > Cheers
> >
> > Paul
> >
> > On 13/12/2019 06:22, Pragati Sharma wrote:
> > > Hello all,
> > >
> > > I am running a polymer melt with 100000 atoms, 2 fs time step, PME, on
> a
> > > workstation with specifications:
> > >
> > > 2X Intel Xeon 6128 3.4 2666 MHz 6-core CPU
> > > 2X16B DDR4 RAM
> > > 2XRTX 2080Ti 11 GB
> > >
> > > I have installed *GPU and thread_mpi *enabled gromacs 2019.0 version
> > using:
> > >
> > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > > *-DGMX_THREAD_MPI=ON
> > > -DGMX_GPU=ON*
> > >
> > > While running a single job with below command, I am getting a
> performance
> > > of *65 ns/day. *
> > >
> > > *gmx_tmpi mdrun -v -s t1.tpr -c t1.pdb -gpu_id 0 -ntmpi 1 -ntomp 24*
> > >
> > > *Q. However I want to run two different simulations at a time using CPU
> > > cores and one GPU for each, Can somebody help me with mdrun command
> (what
> > > combination of ntmpi and ntomp) I should use to run two simulations
> with
> > > efficient utilization of CPU cores and 1 GPU each.*
> > >
> > > *Q.* I have also tried utilising GPU for PME calculations using -pme
> GPU,
> > > as in the command
> > >
> > > gmx_tmpi mdrun -v -s t1.tpr -c t1.pdb -ntmpi 1 -ntomp 24  -gputasks 01*
> > -nb
> > > gpu -pme gpu*
> > >
> > > but i get the below error,
> > >
> > >
> > > *"Feature not implemented:The input simulation did not use PME in a way
> > > that is supported on the GPU."*
> > >
> > > why is this error coming? Should I put extra attributes while compiling
> > > gromacs.
> > >
> > > Thanks
> >
> >
> > --
> > Paul Bauer, PhD
> > GROMACS Release Manager
> > KTH Stockholm, SciLifeLab
> > 0046737308594
> >
> > --
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