Hi Paul,
Firstly let me caution you on running any GPU calculations with your version of AMBER until it has been fully patched. There are a number of bug fixes for the GPU code in addition to the MPI support and I would caution anyone who tried to use an earlier version.
> So I've successfully compiled the cuda variants with SDK 3.2: hybrid,
> mpi-hybrid, DPDP, and mpi-DPDP.
>
> A quick question because I've not fully (nor would I dare at the
> moment)
> delved into the CUDA code. What happens if I have two GPU devices but
> set
> the number of MPI processes to more than 2 (let's say 4); how is the
> work
> load divided and how is the GPU memory shared?
>
> What would be the optimal DO_PARALLEL setting given that I have a
> system
> with 16 CPU cores and 2x C2070s?
For the CPU code with 16 cores you should use 'mpirun -np 16' for the GPU code you should use 'mpirun -np 2' - That is you should specify 1 MPI thread per GPU present in the machine that you want to run on. See
http://ambermd.org/gpus/ (read the whole page) for instructions on running in parallel. If you run more threads than you have GPUs you will run multiple instances on a single GPU and then be in for a whole world of hurt performance wise.
But please please please start from a clean copy of AMBER 11 and AMBERTools 1.5 and apply ALL the bugfixes before proceeding.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 25 2011 - 22:30:02 PDT
