[gmx-users] GPU version of GROMACS 4.6 in MacOS cluster

[Szilárd Páll]

Hi George,

As I said before, that just means that most probably the GPU driver is not
compatible with the CUDA runtime (libcudart) that you installed with the
CUDA toolkit. I've no clue about the Mac OS installers and releases, you'll
have to do the research on that. Let us know if you have further
(GROMACS-related) issues.

Cheers,

--
Szilárd


On Fri, Mar 1, 2013 at 2:48 PM, George Patargias <gpat at bioacademy.gr> wrote:

> Hi Szilαrd
>
> Thanks for your reply. I have run the deviceQuery utility and what I got
> back is
>
> /deviceQuery Starting...
>
>  CUDA Device Query (Runtime API) version (CUDART static linking)
>
> cudaGetDeviceCount returned 38
> -> no CUDA-capable device is detected
>
> Should I understand from this that the CUDA driver was not installed from
> the MAC OS  X CUDA 5.0 Production Release?
>
> George
>
>
> > HI,
> >
> > That looks like the driver does not work or is incompatible with the
> > runtime. Please get the SDK, compile a simple program, e.g. deviceQuery
> > and
> > see if that works (I suspect that it won't).
> >
> > Regarding your machines, just FYI, the Quadro 4000 is a pretty slow card
> > (somewhat slower than a GTX 460) so you'll hava a quite strong resource
> > imbalance: a lot of CPU compute power (2x Xeon 5xxx, right?) and little
> > GPU
> > compute power which will lead to the CPU idling while waiting for the
> GPU.
> >
> > Cheers,
> >
> > --
> > Szilαrd
> >
> >
> > On Thu, Feb 28, 2013 at 4:52 PM, George Patargias
> > <gpat at bioacademy.gr>wrote:
> >
> >> Hello
> >>
> >> We are trying to install the GPU version of GROMACS 4.6 on our own
> >> MacOS cluster. So for the cluster nodes that have the NVIDIA Quadro 4000
> >> cards:
> >>
> >> - We have downloaded and install the MAC OS  X CUDA 5.0 Production
> >> Release
> >> from here: https://developer.nvidia.com/cuda-downloads
> >>
> >> placing the libraries contained in this download in /usr/local/cuda/lib
> >>
> >> - We have managed to compile GROMACS 4.6 linking it statically with
> >> these
> >> CUDA libraries and the MPI libraries (with BUILD_SHARED_LIBS=OFF and
> >> GMX_PREFER_STATIC_LIBS=ON)
> >>
> >> Unfortunately, when we tried to run a test job with the generated
> >> mdrun_mpi, GROMACS reported that it cannot detect any CUDA-enabled
> >> devices. It also reports 0.0 version for CUDA driver and runtime.
> >>
> >> Is the actual CUDA driver missing from the MAC OS  X CUDA 5.0 Production
> >> Release that we installed? Do we need to install it from here:
> >>
> >> http://www.nvidia.com/object/cuda-mac-driver.html
> >>
> >> Or is something else that we need to do?
> >>
> >> Many thanks in advance.
> >> George
> >>
> >>
> >> Dr. George Patargias
> >> Postdoctoral Researcher
> >> Biomedical Research Foundation
> >> Academy of Athens
> >> 4, Soranou Ephessiou
> >> 115 27
> >> Athens
> >> Greece
> >>
> >> Office: +302106597568
> >>
> >>
> >> --
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>
>
> Dr. George Patargias
> Postdoctoral Researcher
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
>
> --
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