VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 18 2003 - 12:57:00 CDT

Kelvin,
  I suspect that the environment variables are the source of your problem,
specifically this one:
DYLD_LIBRARY_PATH=/Applications/OpenOffice.org1.0.1/program:/Applications/OpenOffice.org1.0.1/program/filter:/usr/X11R6/lib

Try taking that out of your .cshrc/.login files (or other scripts that they
source) and I bet that VMD runs fine from then on.

I suspect that the "/usr/X11R6/lib" is what is actually causing the OpenGL
dynamic linkage failure you're seeing. At the very least, I'd recommend
taking that part out of the DYLD_LIBRARY_PATH variable.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 18, 2003 at 01:05:25PM -0400, Kelvin Chu wrote:
> Hi John;
>
> Thanks for your mail.
>
> I don't know what other OpenGL programs have run. Here's what "About
> this mac" looks like:
>
> OpenGL.framework 1.2.4 20 may 2003 08:12 AM OpenGL1.2.4.4.0
>
> Here's the terminal window for 1.8:
>
> /var/tmp/tmp.0.SgQJLr; exit
> Welcome to Darwin!
> [chipotle:~] kelvin% /var/tmp/tmp.0.SgQJLr; exit
> Info) vmd for MACOSX, version 1.8 (December 9, 2002)
> Info) VMD WWW Page: http://www.ks.uiuc.edu/Research/vmd/
> Info) Please email all comments and bug reports to vmd_at_ks.uiuc.edu
> Info) The authors request that any published work which utilizes
> Info) VMD please include the following reference:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> dyld: /Applications/VMD
> 1.8.app/Contents/Resources/vmd/../VMD_MACOSX.app/Contents/MacOS/
> vmd_MACOSX Undefined symbols:
> OpenGL undefined reference to _gll_noop expected to be defined in
> /usr/X11R6/lib/libGL.dylib
> OpenGL undefined reference to _gll_pkey expected to be defined in
> /usr/X11R6/lib/libGL.dylib
> Trace/BPT trap
> logout
> [Process completed]
>
> And here's the terminal window for 1.8.1
>
> Last login: Wed Jun 18 13:02:05 on ttyp1
> /Applications/VMD\ 1.8.1.app/Contents/MacOS/VMD.stWelcome to Darwin!
> artup; exit
> [chipotle:~] kelvin% /Applications/VMD\
> 1.8.1.app/Contents/MacOS/VMD.startup; exit
> Info) VMD for MACOSX, version 1.8.1 (June 15, 2003)
> 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.
> dyld: /Applications/VMD
> 1.8.1.app/Contents/Resources/VMD.app/Contents/MacOS/VMD Undefined
> symbols:
> OpenGL undefined reference to _gll_noop expected to be defined in
> /usr/X11R6/lib/libGL.dylib
> OpenGL undefined reference to _gll_pkey expected to be defined in
> /usr/X11R6/lib/libGL.dylib
> Trace/BPT trap
> logout
> [Process completed]
>
> Just in case I have something wacky in my environment, here is "setenv"
>
> [chipotle:~] kelvin% setenv
> PWD=/Users/kelvin
> USER=kelvin
> SHLVL=1
> SHELL=/bin/tcsh
> HOME=/Users/kelvin
> PATH=/sw/bin:/sw/sbin:/Users/kelvin/bin:/usr/local/bin:/bin:/sbin:/usr/
> bin:/usr/local/bin:/usr/sbin:/usr/local/teTeX/bin/powerpc-apple-darwin-
> current:/usr/local/bin:/usr/X11R6/bin
> __CF_USER_TEXT_ENCODING=0x1F5:0:0
> _=/usr/bin/open
> TERM=vt100
> TERMCAP=\277\377\331\300
> TERM_PROGRAM=Apple_Terminal
> TERM_PROGRAM_VERSION=81
> LOGNAME=kelvin
> HOSTTYPE=macintosh
> VENDOR=apple
> OSTYPE=darwin
> MACHTYPE=powerpc
> GROUP=staff
> HOST=chipotle
> PYTHONPATH=/Users/kelvin/code/Local
> PYTHONSTARTUP=/Users/kelvin/code/Local/Startup.py
> DYLD_LIBRARY_PATH=/Applications/OpenOffice.org1.0.1/program:/
> Applications/OpenOffice.org1.0.1/program/filter:/usr/X11R6/lib
> VMDSCRSIZE=500 500
> ono=/usr/local/o/bin
> ODAT=/usr/local/o/data
> MANPATH=/sw/share/man:/sw/man:/usr/local/share/man:/usr/local/man:/usr/
> share/man:/usr/X11R6/man
> INFOPATH=/sw/share/info:/sw/info:/usr/local/share/info:/usr/local/lib/
> info:/usr/local/info:/usr/share/info
> PERL5LIB=/sw/lib/perl5
>
> -------
>
> Ok, got it.
>
> I commented out the DYLD_LIBRARY_PATH for Openoffice and it runs just
> fine now.
>
> sorry for bothering you with this.
>
> (Whew.)
>
> -k
>
> On Wednesday, June 18, 2003, at 11:55 AM, John Stone wrote:
>
> >
> >
> >Kelvin,
> > Wow, this is a new one. I've never seen this error before.
> >Since you are running MacOS X 10.2.6, I'm puzzled why you would
> >get the errors below. Have you run any other OpenGL programs on your
> >Mac recently? The MacOS X builds of VMD 1.8 were actually done on
> >a MacOS X 10.1 machine, and so they don't even use any of the new
> >OpenGL features found in Jaguar etc. The new VMD 1.8.1 builds were
> >done on a MacOS X 10.2.6 box with the most recent updates applied.
> >I'm very curious about this. Can you tell me what your Mac says in the
> >"About this mac" app (top menu item in the apple menu). Open the
> >menu and select the "Frameworks" tab, and tell me what it says
> >for the version of OpenGL on your machine??
> >
> >Do you get exactly the same error with both VMD 1.8.1 and with VMD
> >1.8??
> >I assume that you're starting them by clicking on them in the finder
> >right,
> >not by some other means? Also, these versions are NOT X11 versions of
> >VMD, they are _native_ versions, so they should have no need for the
> >X11
> >libraries, as such, its puzzling to me that you are getting this
> >linkage
> >error against the X11 OpenGL libraries. If you have the same problem
> >with both VMD 1.8 and VMD 1.8.1, this would be very interesting.
> >
> >Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> >On Wed, Jun 18, 2003 at 11:37:55AM -0400, Kelvin Chu wrote:
> >>Hi All;
> >>
> >>I'm writing because I'm encountering an error I haven't seen before.
> >>
> >>System:
> >>Apple iMac, 0.8GHz running MacOSX 10.2.6.
> >>VMD 1.8, 1.8.1, 1.8.1 beta 4.
> >>
> >>When I start VMD, a Terminal wiindow opens with the following output:
> >>
> >>/var/tmp/tmp.0.VQRlD2; exit
> >>Info) vmd for MACOSX, version 1.8 (December 9, 2002)
> >>Info) VMD WWW Page: http://www.ks.uiuc.edu/Research/vmd/
> >>Info) Please email all comments and bug reports to vmd_at_ks.uiuc.edu
> >>Info) The authors request that any published work which utilizes
> >>Info) VMD please include the following reference:
> >>Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> >>Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> >>Info) -------------------------------------------------------------
> >>dyld: /Applications/VMD
> >>1.8.app/Contents/Resources/vmd/../VMD_MACOSX.app/Contents/MacOS/
> >>vmd_MACOSX Undefined symbols:
> >>OpenGL undefined reference to _gll_noop expected to be defined in
> >>/usr/X11R6/lib/libGL.dylib
> >>OpenGL undefined reference to _gll_pkey expected to be defined in
> >>/usr/X11R6/lib/libGL.dylib
> >>Trace/BPT trap
> >>logout
> >>[Process completed]
> >>
> >>Thinking this was an X11 error, I dl'd and installed the Apple X11 and
> >>X11SDK packages. No change in the errors.
> >>
> >>I haven't seen this before and a scan of the threads in the VMD
> >>mailing
> >>list hasn't turned up anything pertinent yet.
> >>
> >>Any help would be greatly appreciated.
> >>
> >>-k
> >>
> >>--
> >>Kelvin Chu, Physics Department, Cook Building
> >>82 University Place, University of Vermont, Burlington, VT 05405-0125
> >>http://www.uvm.edu/~kchu/; (802) 656-0064; Fax: (802) 656-0817
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
> --
> Kelvin Chu, Physics Department, Cook Building
> 82 University Place, University of Vermont, Burlington, VT 05405-0125
> http://www.uvm.edu/~kchu/; (802) 656-0064; Fax: (802) 656-0817 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078