VMD-L Mailing List

From: Oliver Otto (O.Otto_at_salford.ac.uk)
Date: Thu Jun 23 2005 - 05:32:24 CDT

John,

VMD is working now when I use setenv VMDSIMPLEGRAPHICS 1
Do you think this will have implications on the later use of stereo and
even CAVE usage?

Thanks,
Oliver

John Stone wrote:

>Oliver,
> Ok, that looks like a broken ATI driver, same problem that I've
>been seeing on other Linux platforms. Try doing this before running VMD:
> setenv VMDSIMPLEGRAPHICS 1
>
>See if that works any better...
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>On Wed, Jun 22, 2005 at 06:28:13PM +0100, Oliver Otto wrote:
>
>
>>Hello John,
>>
>>please find below the output I get when I follow your instructions (and
>>further down for Intel 8.1 libs):
>>
>>[103]prism2> ./vmd -debug
>>***
>>*** Running VMD in debugger, type 'run' at debugger prompt
>>***
>>GNU gdb Red Hat Linux (6.1post-1.20040607.52rh)
>>Copyright 2004 Free Software Foundation, Inc.
>>GDB is free software, covered by the GNU General Public License, and you are
>>welcome to change it and/or distribute copies of it under certain
>>conditions.
>>Type "show copying" to see the conditions.
>>There is absolutely no warranty for GDB. Type "show warranty" for details.
>>This GDB was configured as "ia64-redhat-linux-gnu"...Using host libthread_db
>>library "/lib/tls/libthread_db.so.1".
>>
>>(gdb) run
>>Starting program: /home/demos/VMD/lib/vmd/vmd_LINUXIA64
>>[Thread debugging using libthread_db enabled]
>>[New Thread 2305843009213892944 (LWP 6115)]
>>Info) VMD for LINUXIA64, version 1.8.4a5 (June 21, 2005)
>>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, 1 CPU detected.
>>Info) OpenGL renderer: Fire GL X2 (FireGL) (GNU_ICD)
>>Info) Features: STENCIL RN MDE CVA MTX PP PS GLSL(OVF)
>>
>>Program received signal SIGSEGV, Segmentation fault.
>>[Switching to Thread 2305843009213892944 (LWP 6115)]
>>0x40000000006dbdf1 in aligned ()
>>(gdb) where
>>#0 0x40000000006dbdf1 in aligned ()
>>#1 0x2000000000586bb0 in std::string::append ()
>> from /opt/intel/cc/9.0/lib/libcprts.so.6
>>#2 0x2000000001a44ef0 in TInfoSinkBase::append ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#3 0x2000000001c048e0 in TATICompiler::internalError ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#4 0x2000000001be9940 in TATICompiler::TraverseBinaryNode ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#5 0x2000000001bdcde0 in TATICompiler::TraverseNode ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#6 0x2000000001a43480 in TATIVertexCompiler::compile ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#7 0x2000000001a07b60 in ShCompile ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#8 0x2000000000efe8f0 in __glslATICompileShader ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#9 0x2000000000eff510 in __glslATICompileVertexShader ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#10 0x20000000010892c0 in __glim_CompileShaderARB ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#11 0x2000000000ea0640 in __fgl_glCompileShaderARB ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>---Type <return> to continue, or q <return> to quit---
>>#12 0x4000000000026c80 in OpenGLShader::CompileShaders ()
>>#13 0x40000000000267f0 in OpenGLShader::LoadShader ()
>>#14 0x4000000000018820 in OpenGLRenderer::setup_initial_opengl_state ()
>>#15 0x4000000000012a90 in OpenGLDisplayDevice::open_window ()
>>#16 0x4000000000013400 in OpenGLDisplayDevice::init ()
>>#17 0x40000000001cd560 in VMDApp::VMDinit ()
>>#18 0x40000000002014c0 in main ()
>>(gdb) q
>>The program is running. Exit anyway? (y or n) y
>>
>>
>>#############################
>>*and if I use the libraries of the Intel compiler 8.1 I get a very
>>similar output*
>>
>>[root_at_prism2 bin]# ./vmd -debug
>>***
>>*** Running VMD in debugger, type 'run' at debugger prompt
>>***
>>GNU gdb Red Hat Linux (6.1post-1.20040607.52rh)
>>Copyright 2004 Free Software Foundation, Inc.
>>GDB is free software, covered by the GNU General Public License, and you are
>>welcome to change it and/or distribute copies of it under certain
>>conditions.
>>Type "show copying" to see the conditions.
>>There is absolutely no warranty for GDB. Type "show warranty" for details.
>>This GDB was configured as "ia64-redhat-linux-gnu"...Using host libthread_db
>>library "/lib/tls/libthread_db.so.1".
>>
>>(gdb) run
>>Starting program: /home/demos/VMD/lib/vmd/vmd_LINUXIA64
>>[Thread debugging using libthread_db enabled]
>>[New Thread 2305843009213892944 (LWP 6460)]
>>Info) VMD for LINUXIA64, version 1.8.4a5 (June 21, 2005)
>>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, 1 CPU detected.
>>Info) OpenGL renderer: Fire GL X2 (FireGL) (GNU_ICD)
>>Info) Features: STENCIL RN MDE CVA MTX PP PS GLSL(OVF)
>>
>>Program received signal SIGSEGV, Segmentation fault.
>>[Switching to Thread 2305843009213892944 (LWP 6460)]
>>0x40000000006dbdf1 in aligned ()
>>(gdb) where
>>#0 0x40000000006dbdf1 in aligned ()
>>#1 0x2000000000559db0 in std::char_traits<char>::copy ()
>> from /opt/intel_cc_80/lib/libcprts.so.6
>>#2 0x2000000000585e00 in std::string::append ()
>> from /opt/intel_cc_80/lib/libcprts.so.6
>>#3 0x2000000001a44ef0 in TInfoSinkBase::append ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#4 0x2000000001c048e0 in TATICompiler::internalError ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#5 0x2000000001be9940 in TATICompiler::TraverseBinaryNode ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#6 0x2000000001bdcde0 in TATICompiler::TraverseNode ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#7 0x2000000001a43480 in TATIVertexCompiler::compile ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#8 0x2000000001a07b60 in ShCompile ()
>>---Type <return> to continue, or q <return> to quit---
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#9 0x2000000000efe8f0 in __glslATICompileShader ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#10 0x2000000000eff510 in __glslATICompileVertexShader ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#11 0x20000000010892c0 in __glim_CompileShaderARB ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#12 0x2000000000ea0640 in __fgl_glCompileShaderARB ()
>> from /usr/X11R6/lib/modules/dri/fglrx_dri.so
>>#13 0x4000000000026c80 in OpenGLShader::CompileShaders ()
>>#14 0x40000000000267f0 in OpenGLShader::LoadShader ()
>>#15 0x4000000000018820 in OpenGLRenderer::setup_initial_opengl_state ()
>>#16 0x4000000000012a90 in OpenGLDisplayDevice::open_window ()
>>#17 0x4000000000013400 in OpenGLDisplayDevice::init ()
>>#18 0x40000000001cd560 in VMDApp::VMDinit ()
>>#19 0x40000000002014c0 in main ()
>>(gdb) q
>>The program is running. Exit anyway? (y or n) y
>>
>>Oliver
>>
>>John Stone wrote:
>>
>>
>>
>>>Oliver,
>>> The Linux builds of VMD don't support the CAVE, so there's no use in
>>>trying -dispdev cave on the Prism at the moment. Since the executable
>>>runs ok without OpenGL, it would appear that your Prism has libraries that
>>>are compatible with the machine I biult the binary on, so now we need to
>>>figure out what's up with this OpenGL issue. Can you run VMD in a debugger
>>>like this, and tell me what happens:
>>> vmd -debug
>>> when the debugger prompt appears, just type "run"
>>> when VMD terminates, type "where" and email me all of the output...
>>>
>>>Thanks,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>>On Wed, Jun 22, 2005 at 11:34:37AM +0100, Oliver Otto wrote:
>>>
>>>
>>>
>>>
>>>>Hello,
>>>>
>>>>I have tried this version on our Prism system and got the following results:
>>>>- running ./vmd -dispdev win or ./vmd -dispdev cave creates two
>>>>windows (vmd console and vmd OpenGL display) but both disappear after 1 sec
>>>>
>>>>- starting with ./vmd -dispdev text starts vmd in the console mode
>>>>[root_at_prism2 bin]# ./vmd -dispdev text
>>>>Info) VMD for LINUXIA64, version 1.8.4a5 (June 21, 2005)
>>>>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, 1 CPU detected.
>>>>vmd > q
>>>>Info) VMD for LINUXIA64, version 1.8.4a5 (June 21, 2005)
>>>>Info) Exiting normally.
>>>>
>>>>[root_at_prism2 bin]# uname -a
>>>>Linux prism2 2.4.21-sgi305rp05060914_10173 #1 SMP Thu Jun 9 14:16:44 PDT
>>>>2005 ia64 ia64 ia64 GNU/Linux
>>>>
>>>>Any idea why the OpenGL window disappears?
>>>>
>>>>Oliver
>>>>
>>>>John Stone wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>Hi,
>>>>>I've built a test version of VMD for Linux running on Itanium.
>>>>>In theory it will work on any reasonably current Linux distribution
>>>>>running on Itanium, but I've only tested it on the NCSA Teragrid
>>>>>thus far. It ought to work on the SGI Prism, Altix, and similar
>>>>>machines too, so feel free to give it a spin:
>>>>>http://www.ks.uiuc.edu/Research/vmd/alpha/vmd-1.8.4a5.bin.LINUXIA64.opengl.tar.gz
>>>>>
>>>>>A few other test binaries are also posted here as time allows:
>>>>>http://www.ks.uiuc.edu/Research/vmd/alpha/
>>>>>
>>>>>John Stone
>>>>>vmd_at_ks.uiuc.edu
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>--
>>>>------------------------------------------------------------------
>>>>Oliver Otto, M.Sc., Dipl-Ing. (FH)
>>>>
>>>>Ph.D. Student and System Admin at
>>>>The Centre for Virtual Environments,
>>>>Business House, University Road,
>>>>University of Salford,
>>>>Manchester M5 4WT
>>>>------------------------------------------------------------------
>>>>Email: O.Otto_at_salford.ac.uk
>>>>Tel: +44 (0)161 29 55078
>>>>Fax: +44 (0)161 29 52925
>>>>WWW: http://www.OliverOtto.de
>>>>PGP: http://www.OliverOtto.de/Oliver_Otto.asc
>>>>------------------------------------------------------------------
>>>>Project web-site: http://www.nicve.salford.ac.uk/
>>>>------------------------------------------------------------------
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>--
>>------------------------------------------------------------------
>>Oliver Otto, M.Sc., Dipl-Ing. (FH)
>>
>>Ph.D. Student and System Admin at
>>The Centre for Virtual Environments,
>>Business House, University Road,
>>University of Salford,
>>Manchester M5 4WT
>>------------------------------------------------------------------
>>Email: O.Otto_at_salford.ac.uk
>>Tel: +44 (0)161 29 55078
>>Fax: +44 (0)161 29 52925
>>WWW: http://www.OliverOtto.de
>>PGP: http://www.OliverOtto.de/Oliver_Otto.asc
>>------------------------------------------------------------------
>>Project web-site: http://www.nicve.salford.ac.uk/
>>------------------------------------------------------------------
>>
>>
>>
>
>
> 

-- 
------------------------------------------------------------------
Oliver Otto, M.Sc., Dipl-Ing. (FH)
Ph.D. Student and System Admin at
The Centre for Virtual Environments,
Business House, University Road,
University of Salford,
Manchester M5 4WT
------------------------------------------------------------------
Email: O.Otto_at_salford.ac.uk
Tel:   +44 (0)161 29 55078
Fax:   +44 (0)161 29 52925
WWW:   http://www.OliverOtto.de
PGP:   http://www.OliverOtto.de/Oliver_Otto.asc
------------------------------------------------------------------
Project web-site:    http://www.nicve.salford.ac.uk/
------------------------------------------------------------------