[gmx-users] no CUDA-capable device is detected
Chandan Choudhury
iitdckc at gmail.com
Thu Mar 28 12:03:34 CET 2013
Hi !!
I problem with the permission of /dev/nvidia*
changed it to 0666 /dev/nvidia*
Everything resolved. mdrun can be executed as normal user.
Thanks everyone.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury <iitdckc at gmail.com>wrote:
>
> On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll <szilard.pall at cbr.su.se>wrote:
>
>> 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,
>>
>
> Thanks Szilárd for the eye opening comment.
>
> I just tried running gromacs as root. I recalled I had executed
> deviceQuery as root. While executing as user it produces the same error :
>
> */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery
> Starting...
>
> CUDA Device Query (Runtime API) version (CUDART static linking)
>
> cudaGetDeviceCount returned 38
> -> no CUDA-capable device is detected*
>
> Now, running gromacs as root, it is running successfully (I suppose).
>
> Output of 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 48C N/A N/A / N/A | 3% 17MB / 511MB | N/A
> Default |
>
>
> +-------------------------------+----------------------+----------------------+
> | 1 Tesla K20c | 0000:04:00.0 Off |
> Off |
> | 50% 62C P0 106W / 225W | 2% 87MB / 5119MB | 76%
> Default |
>
>
> +-------------------------------+----------------------+----------------------+
>
>
>
> +-----------------------------------------------------------------------------+
> | Compute processes: GPU
> Memory |
> | GPU PID Process name
> Usage |
>
> |=============================================================================|
> | 0 Not
> Supported |
> | 1 9127 mdrun_461
> 72MB |
>
> +-----------------------------------------------------------------------------+
>
> Output of md.log
>
> 2 GPUs detected:
> #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: no, stat: compatible
> #1: NVIDIA NVS 300, compute cap.: 1.2, ECC: no, stat: incompatible
>
> 1 GPU auto-selected for this run: #0
>
>
> I think there is something relate to permissions. Though nvcc has 755
> permission, something else might require additional permissions.
>
> Chandan
>
>
>> --
>> 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
>> > > > > > --
>> > > > > > gmx-users mailing list gmx-users at gromacs.org
>> > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > > > > > * Please search the archive at
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>> > posting!
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>> > > > > > www interface or send it to gmx-users-request at gromacs.org.
>> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> > > > > >
>> > > > >
>> > > > >
>> > > > > 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
>> > > > > * Please search the archive at
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>> > > > --
>> > > > gmx-users mailing list gmx-users at gromacs.org
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>> > > >
>> > >
>> > >
>> > >
>> > > --
>> > > Chandan kumar Choudhury
>> > > NCL, Pune
>> > > INDIA
>> > > --
>> > > gmx-users mailing list gmx-users at gromacs.org
>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
>> > > * Please search the archive at
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>> > --
>> > gmx-users mailing list gmx-users at gromacs.org
>> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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>> --
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>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
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