VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 22 2005 - 13:34:51 CDT

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/
> ------------------------------------------------------------------
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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