[gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

[Johnny Lu]

Try -nt, -ntmpi, -ntomp, -np  (one at a time) ?
I forget about what I tried now.... But I just stop the mdrun, and then
read the log file.
Also can look for the mdrun page in the offical manual (pdf) and try this
page:
http://www.gromacs.org/Documentation/Gromacs_Utilities/mdrun?highlight=mdrun


On Mon, Sep 22, 2014 at 6:46 PM, Siva Dasetty <sdasett at g.clemson.edu> wrote:

> Dear  All,
>
> I am trying to run NPT simulations using GROMACS version 5.0.1 of a system
> of size 140k atoms (protein+water systems) with 2 or more GPU's
> (model=k20); 8 cores (or more); and 1 or more nodes. I am trying to
> understand how to run simulations using multiple gpus on more than one
> node. I  get the following errors/output when I run the simulation using
> the following commands:-
>
> Note: time-step used = 2 fs and total number of steps = 20000
>
> First 4 cases are using single GPU and cases 5-8 are using 2 GPU's.
>
> 1. 1 node, 8 cpus, 1 gpu
> export OMP_NUM_THREADS = 8
> command used-  mdrun -s topol.tpr  -gpu_id 0
> Speed - 5.8 ns/day
>
> 2.  1 node, 8 cpus, 1 gpu
> export OMP_NUM_THREADS = 16
> command used-  mdrun -s topol.tpr   -gpu_id 0
> Speed - 4.7 ns/day
>
> 3. 1 node, 8cpus, 1gpu
> mdrun -s topol.tpr -ntomp 8  -gpu_id 0
> Speed- 5.876 ns/day
>
> 4. 1 node, 8cpus, 1gpu
> mdrun -s topol.tpr -ntomp 16  -gpu_id 0
> Fatal Error: Environment variable OMP_NUM_THREADS (8) and the number of
> threads requested on  the command line (16) have different values. Either
> omit one, or set them both
>  to the same value.
>
> Question for 3 and 4 : Do I need to always use OMP_NUM_THREADS or is there
> a way ntomp overwrites the environment settings?
>
>
> 5. 1 node, 8cpus , 2gpus
> export OMP_NUM_THREADS = 8
> mpirun -np 2 mdrun -s topol.tpr -pin on  -gpu_id 01
> Speed - 4.044 ns/day
>
> 6. 2 nodes, 8cpus , 2 gpus
> export OMP_NUM_THREADS = 8
> mpirun -np 2 mdrun -s topol.tpr -pin on  -gpu_id 01
> Speed - 3.0 ns/day
>
> Are the commands that I used for 5 and 6 correct?
>
> 7. I also used (1node, 8 cpus, 2 gpus)
>  mdrun -s topol.tpr -ntmpi 2 -ntomp 8  -gpu_id 01
> but this time I get a fatal error: thread mpi's are requested but gromacs
> is not compiled with thread MPI.
>
> Question: Isn't thread MPI enabled by default?
>
> 8. Finally, I recompiled Gromacs without OpenMP and re-ran case 1 but this
> time there is a fatal error "More than 1 OpenMP thread requested, but
> Gromacs was compiled without OpenMP support."
> command : mdrun -s topol.tpr  (no environment settings)  -gpu_id 0
> Question: Here again, I assumed thread MPI is enabled by default and I
> think Gromacs still assumes OpenMp thread settings. Am i doing something
> wrong here?
>
> Thanks in advance for your help
>
> --
> Siva
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