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

[George Patargias]

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