[gmx-users] no CUDA-capable device is detected

Szilárd Páll szilard.pall at cbr.su.se
Thu Mar 28 11:39:33 CET 2013 

Hi,

If mdrun says that it could not detect GPUs it simply means that the GPU
enumeration found no GPUs, otherwise it would have printed what was found.
This is rather strange because mdrun uses the same mechanism the
deviceQuery SDK example. I really don't have a good idea what could be the
issue, but you could try recompiling or compiling with CUDA 4.2 to see if
any of that makes a difference.

Let us know if you figured out something.

Cheers,

--
Szilárd


On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess <gmx3 at hotmail.com> wrote:

>
> Hi,
>
> I am not the expert on GPU detection, so we'll need to wait until an
> expert replies.
> Maybe GPU 0 is ignored and the GPUs are renumbered, could you try:
> mdrun -ntmpi 1 -gpu_id 0
>
> Also your tpr file is from an older version. It will not run on a GPU.
> You need to set the mdp option:
> cutoff-scheme = Verlet
> and run grompp to get a new tpr file.
>
> Cheers,
>
> Berk
>
> > From: iitdckc at gmail.com
> > Date: Thu, 28 Mar 2013 14:57:16 +0530
> > Subject: Re: [gmx-users] no CUDA-capable device is detected
> > To: gmx-users at gromacs.org
> >
> > On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> >
> > >
> > > Hi,
> > >
> > > The code compiled, so the compiler is not the issue.
> > >
> > > I guess mdrun picked up GPU 0, which it should have ignored. You only
> want
> > > to use GPU 1.
> > >
> > > Could you try running:
> > > mdrun -ntmpi 1 -gpu_id 1
> > >
> >
> > $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr
> > Note: file tpx version 73, software tpx version 83
> >
> > NOTE: Error occurred during GPU detection:
> >       no CUDA-capable device is detected
> >       Can not use GPU acceleration, will fall back to CPU kernels.
> >
> >
> > No GPUs detected
> >
> >
> > -------------------------------------------------------
> > Program mdrun_461, VERSION 4.6.1
> > Source code file:
> > /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line:
> 580
> >
> > Fatal error:
> > Some of the requested GPUs do not exist, behave strangely, or are not
> > compatible:
> >     GPU #1: inexistent
> >
> > >
> > > Cheers,
> > >
> > > berk
> > >
> > > > Date: Thu, 28 Mar 2013 10:51:58 +0200
> > > > Subject: Re: [gmx-users] no CUDA-capable device is detected
> > > > From: gpat at bioacademy.gr
> > > > To: gmx-users at gromacs.org
> > > >
> > > > Hi Chandan
> > > >
> > > > Are you using the same version of GCC compiler that you used to
> compile
> > > > CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think
> > > there
> > > > was some kind of incompatibility between the two).
> > >
> >
> > There is an work around with gcc 4.7.2. Please see
> >
> http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html
> >
> > >
> > > > Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
> > > > worked in my system (MacOS/Darwin).
> > > >
> > > > Just make sure to set the variables CC and CXX to point to the right
> > > > compiler version when you run cmake.
> > > >
> > > > George
> > > >
> > > >
> > > > > Dear GMX Users,
> > > > >
> > > > > I am trying to execute Gromacs 4.6.1 on one of the GPU server:
> > > > > *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release)
> > > > > *gcc*: 4.7.2
> > > > >
> > > > > CUDA Library paths
> > > > > #CUDA-5.0
> > > > > export CUDA_HOME=/usr/local/cuda-5.0
> > > > > export PATH=$CUDA_HOME/bin:$PATH
> > > > > export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH
> > > > >
> > > > > The gromacs has been compiled with
> > > > >
> > > > > CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0
> > > cmake ..
> > > > > -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single
> > > > > -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461
> > > -DGMX_LIBS_SUFFIX=_461
> > > > > -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
> > > > >
> > > > > *Error on executing mdrun
> > > > > *
> > > > > *
> > > > > *
> > > > > *NOTE: Error occurred during GPU detection:
> > > > > no CUDA-capable device is detected
> > > > > Can not use GPU acceleration, will fall back to CPU kernels.
> > > > >
> > > > >
> > > > > Will use 24 particle-particle and 8 PME only nodes
> > > > > This is a guess, check the performance at the end of the log file
> > > > > Using 32 MPI threads
> > > > >
> > > > > No GPUs detected
> > > > >
> > > > > *I checked my cuda installation. I am able to compile and execute
> the
> > > > > sample programmes e.g., deviceQuery.
> > > > >
> > > > > Also executed *nvidia-smi *:
> > > > > +------------------------------------------------------+
> > > > > | NVIDIA-SMI 4.310.40 Driver Version: 310.40 |
> > > > >
> > >
> |-------------------------------+----------------------+----------------------+
> > > > > | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC |
> > > > > | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
> > > > >
> > >
> |===============================+======================+======================|
> > > > > | 0 NVS 300 | 0000:03:00.0 N/A | N/A |
> > > > > | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default |
> > > > >
> > >
> +-------------------------------+----------------------+----------------------+
> > > > > | 1 Tesla K20c | 0000:04:00.0 Off | Off |
> > > > > | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default |
> > > > >
> > >
> +-------------------------------+----------------------+----------------------+
> > > > >
> > > > >
> > >
> +-----------------------------------------------------------------------------+
> > > > > | Compute processes: GPU Memory |
> > > > > | GPU PID Process name Usage |
> > > > >
> > >
> |=============================================================================|
> > > > > | 0 Not Supported |
> > > > >
> > >
> +-----------------------------------------------------------------------------+
> > > > >
> > > > > What am I missing that Gromacs is not detecting the GPUs.
> > > > >
> > > > > Chandan
> > > > >
> > > > > --
> > > > > Chandan kumar Choudhury
> > > > > NCL, Pune
> > > > > INDIA
> > > > > --
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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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> >
> >
> >
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
> > --
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