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Old 07-24-10, 12:00 AM   #6
said
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Join Date: Jul 2010
Posts: 4
Default Re: vmd 1.8.7 crashed by TrueColor visual in ubuntu 10.04

Quote:
Originally Posted by AaronP View Post
That's very interesting... the glxinfo output from root looks fine. Does your user have access to the /dev/nvidia* device files?
The output for the permission of nvidia* files looks like:
$ ll /dev/nvidia*
crw-rw-rw- 1 root root 195, 0 2010-07-24 12:28 nvidia0
crw-rw-rw- 1 root root 195, 255 2010-07-24 12:28 nvidiactl

I think it is fine.

Quote:
Originally Posted by AaronP View Post
Actually, I take that back. Not having access to the device files would just result in indirect rendering. I suspect that something about your environment is causing OpenGL applications to use Mesa instead of the NVIDIA OpenGL library. Mesa has a bug that causes it to fail to fall back to indirect rendering correctly, and causes an error very much like the one you're seeing.

What does "ldd /usr/bin/glxinfo" show when you run it as root vs. non-root? Do you have LD_LIBRARY_PATH set in your environment?
$ ldd /usr/bin/glxinfo
linux-gate.so.1 => (0x4001d000)
libGL.so.1 => /usr/lib/mesa/libGL.so.1 (0x40020000)
libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0x40097000)
libX11.so.6 => /usr/lib/libX11.so.6 (0x400bd000)
libpthread.so.0 => /lib/tls/i686/cmov/libpthread.so.0 (0x401da000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0x401f3000)
libXext.so.6 => /usr/lib/libXext.so.6 (0x4034d000)
libXxf86vm.so.1 => /usr/lib/libXxf86vm.so.1 (0x4035e000)
libXdamage.so.1 => /usr/lib/libXdamage.so.1 (0x40364000)
libXfixes.so.3 => /usr/lib/libXfixes.so.3 (0x40368000)
libdrm.so.2 => /lib/libdrm.so.2 (0x4036e000)
libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0x40379000)
/lib/ld-linux.so.2 (0x40000000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x4037e000)
librt.so.1 => /lib/tls/i686/cmov/librt.so.1 (0x40398000)
libXau.so.6 => /usr/lib/libXau.so.6 (0x403a1000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x403a5000)
and
$ sudo ldd /usr/bin/glxinfo
linux-gate.so.1 => (0x00a25000)
libGL.so.1 => /usr/lib/nvidia-current/libGL.so.1 (0x005d9000)
libm.so.6 => /lib/tls/i686/cmov/libm.so.6 (0x00a4f000)
libX11.so.6 => /usr/lib/libX11.so.6 (0x006f2000)
libpthread.so.0 => /lib/tls/i686/cmov/libpthread.so.0 (0x00c9b000)
libc.so.6 => /lib/tls/i686/cmov/libc.so.6 (0x0024c000)
libnvidia-tls.so.256.35 => /usr/lib/nvidia-current/tls/libnvidia-tls.so.256.35 (0x00e8e000)
libnvidia-glcore.so.256.35 => /usr/lib/nvidia-current/libnvidia-glcore.so.256.35 (0x00e90000)
libXext.so.6 => /usr/lib/libXext.so.6 (0x00cd9000)
libdl.so.2 => /lib/tls/i686/cmov/libdl.so.2 (0x00110000)
/lib/ld-linux.so.2 (0x00da7000)
libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00ac5000)
libXau.so.6 => /usr/lib/libXau.so.6 (0x00114000)
libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00bbb000)

It seems normal users don't use libnvidia-tls.so.256.35 and libnvidia-glcore.so.256.35.

The 'echo $LD_LIBRARY_PATH' show that I used mesa at /usr/lib/mesa
If I get ride of this lib I can run vmd 1.8.7 now. But it required may resources.

$ vmd
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
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, 2 CPUs detected.
Info) Free system memory: 2529MB (84%)
Info) Detected 1 available CUDA accelerator:
Info) [0] Quadro NVS 140M 2 SM_1.1 @ 0.80 GHz, 127MB RAM, KTO, OIO
Info) Creating CUDA device pool and initializing hardware...
CUDA error: no CUDA-capable device is available, line 62
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Quadro NVS 140M/PCI/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)


################################################## ########
I suspect the high computer resource required by vmd should be related to the high nvidia driver. So I upgraded the nvidia driver.
$ aptitude show nvidia-current
Package: nvidia-current
State: installed
Automatically installed: no
Version: 195.36.24-0ubuntu1~10.04

Everything works fine except a warning of vmd 1.8.7

$ vmd
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
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, 2 CPUs detected.
Info) Free system memory: 2641MB (87%)
Info) Detected 1 available CUDA accelerator:
Info) [0] Quadro NVS 140M 2 SM_1.1 @ 0.80 GHz, 127MB RAM, KTO, OIO
Info) Creating CUDA device pool and initializing hardware...
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Quadro NVS 140M/PCI/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)

Last edited by said; 07-24-10 at 12:27 AM. Reason: upgrade nvidia driver
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