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

[George Patargias]

Hi Szilard

Thanks for this tip; it was extremely useful. The problem was indeed the
incompatibility between the installed NVIDIA driver and the CUDA 5.0
runtime library. Installation of an older driver solved the problem. The
programs devideQuery etc can now detect the GPU.

GROMACS can also detect now the card but unfortunately aborts with the
following error

Fatal error: Incorrect launch configuration: mismatching number of PP MPI
processes and GPUs per node.
mdrun_mpi was started with 12 PP MPI processes per node, but only 1 GPU
were detected.

Here is my command line
mpirun -np 12 mdrun_mpi -s test.tpr -deffnm test_out -nb gpu

What can be the problem?

Thanks again

> 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,
> --
> Szil?rd
> 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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568