VMD-L Mailing List

From: Maria Dimitrova (maria.dimitrova_at_helsinki.fi)
Date: Thu Jan 21 2021 - 05:22:57 CST

Hello,

I have a fresh installation of Ubuntu 20.04 and running the proprietary
drivers by NVidia for my 980 Ti GPU. I have installed vmd locally and it
renders fine, the GPU and CUDA are available.

Then I connect over ssh to our cluster and suddenly I get issues with
OpenGL. Visualisation over ssh works from other computers, so there is
something wrong about mine. It looks like the driver is supposedly
working fine. Maybe something regarding X.org?

The startup output over ssh to the cluster:

$ vmd

/opt/vmd-1.9.4a51/build/lib//vmd_LINUXAMD64: /lib64/libGL.so.1: no
version information available (required by
/opt/vmd-1.9.4a51/build/lib//vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020)
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, 192 CPUs detected.
Info)   CPU features: SSE2 SSE4.1 AVX AVX2 FMA F16 AVX512F AVX512CD HT
Info) Free system memory: 1391GB (92%)
Info) No CUDA accelerator devices available.
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.
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
XRequest.152: BadValue (integer parameter out of range for operation) 0x0
XRequest.152: GLXBadContext 0x165
XRequest.152: GLXBadContext 0x0
Info) OpenGL renderer: ErrorUnknown
Info)   Features:
Info)   GLSL rendering mode is NOT available.
XRequest.152: GLXBadDrawable 0x5400105
Info) Dynamically loaded 3 plugins in directory:
Info) /opt/vmd-1.9.4a51/build/lib/plugins/LINUXAMD64/molfile
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
XRequest.152: GLXBadDrawable 0x5400105
XRequest.152: GLXBadContext 0x5400105
XRequest.152: GLXBadContext 0x0
/opt/vmd-1.9.4a51/build/lib/scripts/tcl8.5
/opt/vmd-1.9.4a51/build/lib/scripts /opt/vmd-1.9.4a51/build/lib
/Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
/opt/vmd-1.9.4a51/build/lib/scripts/tk8.5
/opt/vmd-1.9.4a51/build/lib/scripts/tk8.5/ttk
/opt/vmd-1.9.4a51/build/lib//scripts/vmd
/opt/vmd-1.9.4a51/build/lib/plugins/LINUXAMD64/tcl
/opt/vmd-1.9.4a51/build/lib/plugins/noarch/tcl
/trunk/opt/vmd-1.9.1/vmd/scripts/orient
/opt/vmd-1.9.4a51/build/lib/scripts/tcl8.5
/opt/vmd-1.9.4a51/build/lib/scripts /opt/vmd-1.9.4a51/build/lib
/Projects/johns/tcl/8.5.6/lib_LINUXAMD64/lib
/opt/vmd-1.9.4a51/build/lib/scripts/tk8.5
/opt/vmd-1.9.4a51/build/lib/scripts/tk8.5/ttk
/opt/vmd-1.9.4a51/build/lib//scripts/vmd /opt/vmd-1.9.4a51/build/lib/plug

But on my computer:

$ vmd
/usr/local/lib/vmd/vmd_LINUXAMD64: /lib/x86_64-linux-gnu/libGL.so.1: no
version information available (required by
/usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020)
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, 4 CPUs detected.
Info)   CPU features: SSE2 SSE4.1 AVX F16 HT
Info) Free system memory: 12GB (67%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator::
Info) [0] GeForce GTX 980 Ti   22 SM_5.2 1.2 GHz, 5.9GB RAM SP32 KT AE2 ZC
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 GTX 980 Ti/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) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info)   Compiling  OptiX shaders on 1 target GPU...
Info) Dynamically loaded 3 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
vmd > Info) VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020)
Info) Exiting normally.

Details about my computer:

# uname -a
Linux XXXX 5.8.0-38-generic #43~20.04.1-Ubuntu SMP Tue Jan 12 16:39:47
UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

$ glxinfo | grep -i opengl
OpenGL vendor string: NVIDIA Corporation
OpenGL renderer string: GeForce GTX 980 Ti/PCIe/SSE2
OpenGL core profile version string: 4.6.0 NVIDIA 460.32.03
OpenGL core profile shading language version string: 4.60 NVIDIA
OpenGL core profile context flags: (none)
OpenGL core profile profile mask: core profile
OpenGL core profile extensions:
OpenGL version string: 4.6.0 NVIDIA 460.32.03
OpenGL shading language version string: 4.60 NVIDIA
OpenGL context flags: (none)
OpenGL profile mask: (none)
OpenGL extensions:
OpenGL ES profile version string: OpenGL ES 3.2 NVIDIA 460.32.03
OpenGL ES profile shading language version string: OpenGL ES GLSL ES 3.20
OpenGL ES profile extensions:

# nvidia-smi
Thu Jan 21 12:53:46 2021
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 460.32.03    Driver Version: 460.32.03    CUDA Version:
11.2     |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile
Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util
Compute M. |
|                               | |               MIG M. |
|===============================+======================+======================|
|   0  GeForce GTX 980 Ti  Off  | 00000000:01:00.0  On
|                  N/A |
|  0%   62C    P0    83W / 325W |   1863MiB /  6082MiB | 14%      Default |
|                               | |                  N/A |
+-------------------------------+----------------------+----------------------+

+-----------------------------------------------------------------------------+
| Processes: |
|  GPU   GI   CI        PID   Type   Process name GPU Memory |
|        ID   ID Usage      |
|=============================================================================|
|    0   N/A  N/A      2504      G /usr/lib/xorg/Xorg              
1587MiB |
|    0   N/A  N/A      2811      G /usr/bin/gnome-shell             
185MiB |
|    0   N/A  N/A   1314497      G ...lib/vmware/bin/vmware-vmx      
17MiB |
+-----------------------------------------------------------------------------+

Best regards,

Maria