Running GROMACS on an AMD GPU using OpenCL

Philip Fowler,

I first used an Apple Mac when I was eight. Apart from a brief period in the 1990s when I had a PC laptop I’ve used them ever since.

Until last year I had an old MacPro which had four PCI slots so you could add a GPU-capable NVIDIA card, although you were limited by the power supply. A GPU can accelerate the molecular dynamics code I use, GROMACS, by up to 2-3 times.

Unfortunately, when Apple designed the new MacPro, they put in AMD FirePro GPUs so although it is a lovely machine, you can’t run CUDA applications.

But this morning I saw that the next release candidate of GROMACS 5.1 supported OpenCL. Although OpenCL applications are usually a bit slower than CUDA applications, this would, in theory, allow me to accelerate GROMACS on my MacPro.

So I downloaded the code, compiled it with the appropriate OpenCL flag and it just works! I benchmarked the code on an atomistic and a coarse-grained benchmark that I use. Running on a single core, using a single AMD FirePro D300 accelerated GROMACS by 2.0 and 2.5x for the atomistic and coarse-grained benchmarks, respectively.

Here’s looking forward to the final release of GROMACS 5.1!fig-gromacs-5.1-amd

computing GPUs molecular dynamics

Related Posts

Comments (10)

  1. Compiling the official release of Gromacs 5.1 as I type this. Very excited for the potential of independence from only one manufacturer. Lots of hope for the future of GPU acceleration with the recent release of the new Fury AMD chips.

    Reply

  2. Compiling the official release of Gromacs 5.1 as I type this. Very excited for the potential of independence from only one manufacturer. Lots of hope for the future of GPU acceleration with the recent release of the new Fury AMD chips.

    Reply

  5. Is it possible to have a step-by-step instruction for such an installation as I am not really familiar with the coding part but rather an user of Gromacs?

    Reply

  6. Is it possible to have a step-by-step instruction for such an installation as I am not really familiar with the coding part but rather an user of Gromacs?

    Reply

  7. Which system you think would work better , is it reasonable to buy a mac pro or , hp server, or assembling cpu+gpu ? what is your prediction for ns/day ?

    1-
    2.7GHz 12-core with 30MB of L3 cache
    64GB (4x16GB) of 1866MHz DDR3 ECC
    1TB PCIe-based flash storage
    Dual AMD FirePro D700 GPUs with 6GB of GDDR5 VRAM each
    User’s Guide (English)
    $ 9600

    2-
    2.7GHz 12-core with 30MB of L3 cache
    16GB (4x4GB) of 1866MHz DDR3 ECC
    1TB PCIe-based flash storage
    Dual AMD FirePro D700 GPUs with 6GB of GDDR5 VRAM each
    $ 8400

    3-
    3.5GHz 6-core with 12MB of L3 cache
    16GB (4x4GB) of 1866MHz DDR3 ECC
    1TB PCIe-based flash storage
    Dual AMD FirePro D500 GPUs with 3GB of GDDR5 VRAM each
    $ 4800
    regards
    y
    ?

    Reply

  8. Which system you think would work better , is it reasonable to buy a mac pro or , hp server, or assembling cpu+gpu ? what is your prediction for ns/day ?

    1-
    2.7GHz 12-core with 30MB of L3 cache
    64GB (4x16GB) of 1866MHz DDR3 ECC
    1TB PCIe-based flash storage
    Dual AMD FirePro D700 GPUs with 6GB of GDDR5 VRAM each
    User’s Guide (English)
    $ 9600

    2-
    2.7GHz 12-core with 30MB of L3 cache
    16GB (4x4GB) of 1866MHz DDR3 ECC
    1TB PCIe-based flash storage
    Dual AMD FirePro D700 GPUs with 6GB of GDDR5 VRAM each
    $ 8400

    3-
    3.5GHz 6-core with 12MB of L3 cache
    16GB (4x4GB) of 1866MHz DDR3 ECC
    1TB PCIe-based flash storage
    Dual AMD FirePro D500 GPUs with 3GB of GDDR5 VRAM each
    $ 4800
    regards
    y
    ?

    Reply

Leave a Reply

Your email address will not be published. Required fields are marked *

This site uses Akismet to reduce spam. Learn how your comment data is processed.