VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 24 2005 - 11:21:56 CDT

Oliver,
  Yes, this has strong implications for CAVE and stereo etc.
We'll have to find a way to avoid triggering the ATI driver crash, or
get you an updated SGI ATI driver so you can run VMD without having
this problem. Do you have an SGI support engineer over there? If so,
you should show them the crash you experience when you run VMD normally.
The crash occurs in the OpenGL shading language routines in
the ATI driver, that is definitely something I'd expect them to have
a strong interest in fixing.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 23, 2005 at 11:32:24AM +0100, Oliver Otto wrote:
> 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/
> ------------------------------------------------------------------
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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