VMD-L Mailing List

From: YOGESH NARKHEDE (yogesh.pi.niper_at_gmail.com)
Date: Fri Dec 06 2019 - 20:26:01 CST

Hello Josh,
Many thanks for your reply. Here's the output of nvidia-smi on the CentOS
(problematic systems)
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 440.31 Driver Version: 440.31 CUDA Version: 10.2
  |
|-------------------------------+----------------------+----------------------+
| 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 RTX 2060 Off | 00000000:3B:00.0 On |
 N/A |
| 0% 35C P8 12W / 190W | 333MiB / 5934MiB | 0%
 Default |
+-------------------------------+----------------------+----------------------+
| 1 GeForce RTX 208... Off | 00000000:AF:00.0 Off |
 N/A |
| 27% 35C P8 1W / 250W | 1MiB / 11019MiB | 0%
 Default |
+-------------------------------+----------------------+----------------------+

>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) 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, 28 CPUs detected.
Info) 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 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) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384), Multitexture
(4)
Info) Detected 2 available TachyonL/OptiX ray tracing accelerators
Info) 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) 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, 80 CPUs detected.
Info) 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 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 <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
>
> +-----------------------------------------------------------------------------+
> | NVIDIA-SMI 430.50 Driver Version: 430.50 CUDA Version: 10.1
> |
>
> 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
>
>
> On 2019-12-06 14:09:35-07:00 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.
> 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