Our cluster offers users a number of visual applications that our users are loading as Linux software modules and running on the Mate Desktop. Most of these are running without issue, but we have discovered that one such application, Visual Molecular Dynamics (VMD 1.9.3) is not using the NVIDIA driver and is reporting the following error when the application is started from the terminal shell window:
/hpc/applications/vmd/1.9.3/ogl/lib/vmd/vmd_LINUX64: /lib64/libGL.so.1: no version information available (required by /hpc/applications/vmd/1.9.3/ogl/lib/vmd/vmd_LINUXAMD64)
The application still produces a display, but the message would seem to mean that it is trying to use the libGL.so.1 library (actually a symlink to the libGL.so.1.7.0 library) that is supplied by the libglvnd-glx package rather than using the NVIDIA driver. We saw something similar a couple of years ago when we were installing the DCV product from NICE Software. They had us deal with it by copying a custom libGL.so.9999.9999.9999 to the system and then recreating the libGL.so.1 and libGL.so symlinks with links to the custom library. (I tried copying that same file to my Mate Desktop system, but no dice!) Is anyone else using this application in a Mate Desktop accessed via OOD?
Our environment:
VMD 1.9.3 (OpenGL)
Open OnDemand 1.5.5
CentOS 7.4 / 7.5 (have tried both)
Linux Kernel 3.10.0-693.21.1.el7.x86_64 / 3.10.0-862.14.4.el7.x86_64
NVIDIA Quaddro M5000 with x86_64 drivers 390.116, 418.43, 440.44, and 440.59 (have tried each)
Full text output when running VMD:
$ vmd
/hpc/applications/vmd/1.9.3/ogl/lib/vmd/vmd_LINUX64: /lib64/libGL.so.1: no version information available (required by /hpc/applications/vmd/1.9.3/ogl/lib/vmd/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@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, 36 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 247GB (98%)
Info) Creating CUDA device pool and initializing hardware…
Info) Detected 1 available CUDA accelerator:
Info) [0] Quadro M5000 16 SM_5.2 @ 1.04 GHz, 7.9GB RAM, AE2, 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: Gallium 0.4 on llvmpipe (LLVM 3.9, 256 bits)
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (512x512x512), Multitexture (8)
Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
Info) Compiling 1 OptiX shaders on 1 target GPU…
Info) Dynamically loaded 2 plugins in directory:
Info) /hpc/applications/vmd/1.9.3/ogl/lib/vmd/plugins/LINUXAMD64/molfile
vmd >