VMD-L Mailing List

From: Andrea Spitaleri (andrea.spitaleri_at_iit.it)
Date: Sun Aug 23 2015 - 11:21:05 CDT

Hi all,

a quick update for the future. The X update screw up my system ... and
so after a fresh installation I went in deep to understand why
installing nvidia and cuda-toolkit from repository was not enough to
use GPU capability (i.e. mismatch of drivers). The problem was present
in gromacs too (not able to use GPU). The trick was to install by hand
nvidia-modprobe package, which is responsible to load the nvidia_uvm
driver and allow to use the GPU. Few kb of package ... Wondering why
ubuntu did not install it ...

hope it helps

and

On 19/08/2015 09:02, Andrea Spitaleri wrote:
> Hi John,
>
> I was able to force the upgrade to 346.59-updates (before was 346.59)
> on my ubuntu 15.04 and with cuda-6.5.14-1 from repository. Now the
> things changed in better:
>
> Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 8 CPUs detected.
> Info) Free system memory: 13752MB (87%)
> *Info) Creating CUDA device pool and initializing hardware...**
> **Info) Detected 1 available CUDA accelerator:**
> **Info) [0] GeForce GT 740M 2 SM_3.5 @ 1.03 GHz, 2.0GB RAM, KTO,
> AE1, ZCP**
> **Info) Detected 1 available TachyonL/OptiX ray tracing accelerator*
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Info) OpenGL renderer: GeForce GT 740M/PCIe/SSE2
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048),
> Multitexture (4)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
>
> nvidia-smi give back:
>
> NVIDIA-SMI 346.59 Driver Version: 346.59
>
> as before but with the "update" version of the 346.59 release.
>
> best
>
> and
>
> On 18/08/2015 21:02, John Stone wrote:
>> Hi,
>> I wonder if your distro has left out some driver component
>> that's needed. Can you please send me the complete startup
>> messages that VMD prints on your machine, and also the output you
>> get when you run nvidia-smi on your system? That should be helpful
>> in giving you some concrete suggestions to try next.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Tue, Aug 18, 2015 at 11:10:24AM +0200, Andrea Spitaleri wrote:
>>> Hi,
>>>
>>> thanks to all for the kind reply. My nvidia-smi give me back:
>>>
>>> NVIDIA-SMI 346.59 Driver Version: 346.59
>>>
>>> so as mentioned by John my version and system should fulfil the minimum
>>> requirement in order to use GPU-acceleration for rendering.
>>>
>>> I use to update my nvidia drivers and cuda by using apt-get and the latest
>>> driver for NVIDIA is 346.59
>>>
>>> best
>>>
>>> and
>>>
>>> On 13/08/2015 22:27, Josh Vermaas wrote:
>>>
>>> Hi Andrea,
>>>
>>> VMD in principle doesn't care which driver version you use (save for
>>> really old ones), so long as the driver matches the cuda runtime
>>> version. To figure out what is being detected on your machine, run
>>> nvidia-smi. On my computer, which is running Ubuntu 14.04, this is my
>>> output:
>>>
>>> nvidia-smi
>>> Thu Aug 13 15:21:27 2015
>>> +------------------------------------------------------+
>>> | NVIDIA-SMI 346.59 Driver Version: 346.59
>>> |
>>> |-------------------------------+----------------------+----------------------+
>>> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile
>>> Uncorr. ECC |
>>> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
>>> Compute M. |
>>> |===============================+======================+======================|
>>> | 0 GeForce GTX 980 Off | 0000:0C:00.0 N/A
>>> | N/A |
>>> | 46% 77C P2 N/A / N/A | 2731MiB / 4095MiB | N/A
>>> Default |
>>> +-------------------------------+----------------------+----------------------+
>>>
>>> +-----------------------------------------------------------------------------+
>>> | Processes: GPU
>>> Memory |
>>> | GPU PID Type Process name
>>> Usage |
>>> |=============================================================================|
>>> | 0 C+G Not
>>> Supported |
>>> +-----------------------------------------------------------------------------+
>>>
>>> The important part is at the top (I've bolded it). Those numbers need to
>>> match, or else nothing cuda-related is going to work. Odds are one of
>>> those two is ahead of or behind the other, which is causing a mismatch
>>> between the cuda runtime (the first number), and the driver version. I
>>> *think* the runtime is hidden in the libcuda package, but I've been
>>> known to misremember things.
>>>
>>> -Josh
>>>
>>> On 08/13/2015 10:58 AM, andrea spitaleri wrote:
>>>
>>> Hi all,
>>>
>>> I have configured my new machine bearing Geforce 740M Optimus
>>> technology, Ubuntu 15.04 installed, nvidia proprietary driver version
>>> 346.59 (from Ubuntu repository) and nvidia-cuda-toolkit 6.5.14.-1
>>> version installed from Software Center. I have installed vmd 1.9.2
>>> 64bit OpenGL, CUDA, TachyonL-Optix.
>>> When vmd starts, I got that my nvidia and cuda drivers have a mismatch
>>> version. Not sure what kind of driver nvidia version I need to install
>>> to make vmd happy :)
>>>
>>> thanks
>>>
>>> and
>>>
>>> --
>>> Andrea Spitaleri PhD
>>> D3 - Drug Discovery & Development
>>> Istituto Italiano di Tecnologia
>>> Via Morego, 30 16163 Genova
>>> cell: +39 3485188790
>>> [1]http://www.iit.it/en/d3-people/andrea-spitaleri.html
>>> ORCID: [2]http://orcid.org/0000-0003-3012-3557
>>>
>>> References
>>>
>>> Visible links
>>> 1.https://urldefense.proofpoint.com/v2/url?u=http-3A__www.iit.it_en_d3-2Dpeople_andrea-2Dspitaleri.html&d=AwMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=36zvnmXtWv5UM_HCAeUybkKd534kFQS3ThHvFGb-DG8&s=rcG2AuleURX-4If9aiUOuB1vDfUaK_MmnFnesN7QtmM&e=
>>> 2.https://urldefense.proofpoint.com/v2/url?u=http-3A__orcid.org_0000-2D0003-2D3012-2D3557&d=AwMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=36zvnmXtWv5UM_HCAeUybkKd534kFQS3ThHvFGb-DG8&s=kEBBrNDq0tGf4bdSX3S3zZtIjr452qiin69Y5ymwG3Y&e=
>
> --
> Andrea Spitaleri PhD
> D3 - Drug Discovery & Development
> Istituto Italiano di Tecnologia
> Via Morego, 30 16163 Genova
> cell: +39 3485188790
> http://www.iit.it/en/d3-people/andrea-spitaleri.html
> ORCID:http://orcid.org/0000-0003-3012-3557 

-- 
Andrea Spitaleri PhD
D3 - Drug Discovery & Development
Istituto Italiano di Tecnologia
Via Morego, 30 16163 Genova
cell: +39 3485188790
http://www.iit.it/en/d3-people/andrea-spitaleri.html
ORCID: http://orcid.org/0000-0003-3012-3557