VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Aug 23 2015 - 19:59:56 CDT

Andrea,
  Thanks for sending the helpful followup email. I'm sure this will
be useful information for other Ubuntu users that run into similar
problems.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Aug 23, 2015 at 06:21:05PM +0200, Andrea Spitaleri wrote:
> 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) [1]http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to [2]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
> [3]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][4]http://www.iit.it/en/d3-people/andrea-spitaleri.html
> ORCID: [2][5]http://orcid.org/0000-0003-3012-3557
>
> References
>
> Visible links
> 1. [6]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. [7]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
> [8]http://www.iit.it/en/d3-people/andrea-spitaleri.html
> ORCID: [9]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
> [10]http://www.iit.it/en/d3-people/andrea-spitaleri.html
> ORCID: [11]http://orcid.org/0000-0003-3012-3557
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. mailto:vmd_at_ks.uiuc.edu
> 4. http://www.iit.it/en/d3-people/andrea-spitaleri.html
> 5. http://orcid.org/0000-0003-3012-3557
> 6. 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=
> 7. 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=
> 8. http://www.iit.it/en/d3-people/andrea-spitaleri.html
> 9. http://orcid.org/0000-0003-3012-3557
> 10. http://www.iit.it/en/d3-people/andrea-spitaleri.html
> 11. http://orcid.org/0000-0003-3012-3557 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/