VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Dec 07 2019 - 10:53:26 CST

Hi,
  I'm still catching up on emails after being out of the office, but I'll have to dig into
the details of your emails to give you the right answer. I can summarize what is needed
to get VMD to use your new RTX GPUs however:
  VMD itself is compiled against particular versions of CUDA and OptiX, and
  they both have minimum driver version requirements.
  OptiX versions prior to OptiX 6 work fine on GPUs up to Volta, but to support the latest
  Turing GPUs, you need to use VMD versions built with OptiX 6 and later.

VMD 1.9.3 was built with OptiX 4.0.1, which is way too old for Turing GPUs, so
that's never going to work on Turing GPUs.

VMD 1.9.4 versions are currently compiled against OptiX 5.x and OptiX 6.x.
I'm still tracking an issue with OptiX 6 that can cause a crash (or a memory leak,
so the current builds have a memory leak to avoid the crash). Once these are totally
resolved, all of the VMD 1.9.4 test builds will be done with OptiX 6.x or later.

Now, on Ubuntu it seems like you've got things working, so the question is
why it isn't working on CentOS. Here I'm assuming that the CentOS driver
distribution has failed to include the OptiX components, and this causes the
OptiX code in VMD to fail at runtime. You can check this by looking to see if
your CentOS machine has these files installed or not, they should be part of your
driver install:
  /usr/lib64/libnvoptix.so.1
  /usr/lib64/libnvoptix.so.440.31

Have a look at your CentOS machine and see if those exist or if they are missing.
If they are missing, you might also see if other driver components are there or
not, such as:
  /usr/lib64/libnvidia-glcore.so.440.31
  /usr/lib64/libnvidia-eglcore.so.440.31
  /usr/lib64/libnvidia-ml.so
  /usr/lib64/libnvidia-ml.so.1
  /usr/lib64/libnvidia-ml.so.440.31

Best,
  John Stone

On Fri, Dec 06, 2019 at 06:26:01PM -0800, YOGESH NARKHEDE wrote:
> Hello Josh,
> Many thanks for your reply. Here's the output of nvidia-smi on the CentOS
> (problematic systems)
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 440.31 Â Â Â Driver Version: 440.31 Â Â Â CUDA Version:
> 10.2 Â Â |
> |-------------------------------+----------------------+----------------------+
> | GPU  Name     Persistence-M| Bus-Id     Disp.A | Volatile
> Uncorr. ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap|     Memory-Usage | GPU-Util
> Â Compute M. |
> |===============================+======================+======================|
> |  0  GeForce RTX 2060   Off  | 00000000:3B:00.0  On |    Â
> Â Â Â Â Â N/A |
> | Â 0% Â 35C Â Â P8 Â Â 12W / 190W | Â Â 333MiB / Â 5934MiB | Â Â
> Â 0% Â Â Â Default |
> +-------------------------------+----------------------+----------------------+
> |  1  GeForce RTX 208... Off  | 00000000:AF:00.0 Off |    Â
> Â Â Â Â Â N/A |
> | 27% Â 35C Â Â P8 Â Â 1W / 250W | Â Â Â 1MiB / 11019MiB | Â Â
> Â 0% Â Â Â Default |
> +-------------------------------+----------------------+----------------------+
> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
> From the comparison of the systems where OPTIX works and where it does
> not, it seems that the vmd binary detects the OPTIX shaders on Ubuntu
> whereas it does not in CentOS. Please note the output of vmd in 2 systems:
> ############################
> Ubuntu 18.04 LTS 64 bit
> #############################
> /opt/vmd-1.9.3/lib//vmd_LINUXAMD64: /usr/lib/x86_64-linux-gnu/libGL.so.1:
> no version information available (required by
> /opt/vmd-1.9.3/lib//vmd_LINUXAMD64)
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info) [1]http://www.ks.uiuc.edu/Research/vmd/ Â Â Â Â Â Â Â Â Â
> Â Â Â
> Info) Email questions and bug reports to [2]vmd_at_ks.uiuc.edu     Â
> Info) Please include this reference in published work using VMD: Â
> Info) Â Â Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Â
> Info) Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 28 CPUs detected.
> Info) Â CPU features: SSE2 AVX AVX2 FMA KNL:AVX-512F+CD+ER+PF
> Info) Free system memory: 29GB (93%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 2 available CUDA accelerators:
> Info) [0] GeForce RTX 2080 Ti 68 SM_7.5 @ 1.65 GHz, 11GB RAM, AE3, ZCP
> Info) [1] GeForce RTX 2060 Â 30 SM_7.5 @ 1.75 GHz, 5.8GB RAM, KTO, AE3,
> ZCP
> 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 RTX 2060/PCIe/SSE2
> Info) Â Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info) Â Full GLSL rendering mode is available.
> Info) Â Textures: 2-D (32768x32768), 3-D (16384x16384x16384),
> Multitexture (4)
> Info) Detected 2 available TachyonL/OptiX ray tracing accelerators
> Info) Â Compiling 1 OptiX shaders on 2 target GPUs...
> Info) Dynamically loaded 2 plugins in directory:
> Info) /opt/vmd-1.9.3/lib/plugins/LINUXAMD64/molfile
> vmd >
> and
> ####################
> CentOS
> ####################
> /software/repo/moleculardynamics/vmd/1.9.3/lib/vmd_LINUXAMD64:
> /lib64/libGL.so.1: no version information available (required by
> /software/repo/moleculardynamics/vmd/1.9.3/lib/vmd_LINUXAMD64)
> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
> Info) [3]http://www.ks.uiuc.edu/Research/vmd/ Â Â Â Â Â Â Â Â Â
> Â Â Â
> Info) Email questions and bug reports to [4]vmd_at_ks.uiuc.edu     Â
> Info) Please include this reference in published work using VMD: Â
> Info) Â Â Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Â
> Info) Â Â Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 80 CPUs detected.
> Info) Â CPU features: SSE2 AVX AVX2 FMA KNL:AVX-512F+CD+ER+PF
> Info) Free system memory: 88GB (94%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 2 available CUDA accelerators:
> Info) [0] GeForce RTX 2080 Ti 68 SM_7.5 @ 1.54 GHz, 11GB RAM, AE3, ZCP
> Info) [1] GeForce RTX 2060 Â 30 SM_7.5 @ 1.83 GHz, 5.8GB RAM, KTO, AE3,
> ZCP
> Info) Dynamically loaded 2 plugins in directory:
> Info)
> /software/repo/moleculardynamics/vmd/1.9.3/lib/plugins/LINUXAMD64/molfile
> vmd >
>
> i hope this information is helpful for John and the community to debug.
> With warm regards,
> Yogesh
> On Fri, Dec 6, 2019 at 3:57 PM Vermaas, Joshua
> <[5]Joshua.Vermaas_at_nrel.gov> wrote:
>
> Hi Yogesh,
>
> Not a developer, but I've seen this happen if you have a cuda version
> that isn't supported by the driver. Then it will start normally, but
> specific GPU-dependent analysis and rendering routines just don't show
> up. What is the output of nvidia-smi? Mine looks something like this:
>
> nvidia-smi
> Fri Dec  6 16:51:55 2019    Â
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 430.50 Â Â Â Driver Version: 430.50 Â Â Â CUDA
> Version: 10.1 Â Â |
> And while you say that VMD gives no errors, I don't think anyone can say
> something more concrete without seeing startup output VMD spits out to
> the terminal.
>
> -Josh
> Â
>
> On 2019-12-06 14:09:35-07:00 [6]owner-vmd-l_at_ks.uiuc.edu wrote:
>
> Hello vmd developers,
> We recently installed vmd-1.9.3 with cuda, OPTIX and ospray support on
> centos 7 systems (total 4 systems, 64 bit os, Intel Xeon, Nvidia
> rtx2060 and rtx2080ti) via the module system. On all systems, the
> latest cuda version (cuda 10.1) is installed along with the latest
> display driver from NVIDIA. The startup of vmd also gives no errors.
> However, when we attempt to ray trace the loaded molecule, the option
> to use Tachyon+OPTIX is simply missing from the systems. Installing
> the latest vmd-1.9.4 alpha build locally have the same results.Â
> The issue that vexes us is that on an identical system with same gpus,
> cuda version but only ubuntu-18.04 64 bit LTS version, the Tachyon+
> OPTIX/ospray works.
> Can the developers please aid us in this matter to get the OPTIX ray
> tracing working properly?
> With warm regards,
> Yogesh
>
> --
> YOGESH B.NARKHEDE, Ph.D.
> Ph: +91 8600081096
>
> References
>
> Visible links
> 1. http://www.ks.uiuc.edu/Research/vmd/
> 2. mailto:vmd_at_ks.uiuc.edu
> 3. http://www.ks.uiuc.edu/Research/vmd/
> 4. mailto:vmd_at_ks.uiuc.edu
> 5. mailto:Joshua.Vermaas_at_nrel.gov
> 6. mailto:owner-vmd-l_at_ks.uiuc.edu 

-- 
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/