VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jun 30 2008 - 13:17:20 CDT

On Mon, 30 Jun 2008, James Irving wrote:

JI> Hi,

james,

JI> I was wondering whether anyone else has had this problem.

i don't have a mac and thus never seen this, but it reminds me
of a discussion on this list recently. it most likely is some
underlying issue of the operating system itself, but if it is
limited to the file chooser dialog, you could try to work around
it by setting the environment variable VMDFILECHOOSER to FLTK
before starting VMD, or in your .vmdrc file as

set env(VMDFILECHOOSER) FLTK

JI> I've been using VMD 1.8.6 for a couple of months on my OSX leopard
JI> macbook pro, and recently VMD 1.8.7(CUDA). Both have worked fine.
JI>
JI> Two obvious changes to my system: an auto-upgrade from OSX10.5.2 to
JI> OSX10.5.3, and installation of ActiveTcl 8.4.16 followed by 8.5.2
JI>
JI> VMD opens OK from the Applications folder
JI> When I bring up the 'load molecule' dialog at some point VMD crashes -
JI> either straight away, or after I've loaded a coordinate set, or after
JI> loading a trajectory, but always by loading a second trajectory.
JI> The error on crash is either 'Bus error' or 'Segmentation fault'
JI> This happens on both versions of VMD
JI> ActiveTcl version made no difference
JI>
JI> When I run VMD from within gdb, the error messages produced are typically:
JI>
JI> Program received signal EXC_BAD_ACCESS, Could not access memory.
JI> Reason: KERN_INVALID_ADDRESS at address: 0xa099b00c
JI> 0xffff1281 in __longcopy ()
JI>
JI> or
JI>
JI> Program received signal EXC_BAD_ACCESS, Could not access memory.
JI> Reason: KERN_INVALID_ADDRESS at address: 0x440b0004
JI> 0x92d8daba in _CFDoExceptionOperation ()

no clue where this is coming from, but i would suspect
the graphics driver. this looks like it is an error about
copying data from the kernel to userspace or vice versa
and graphics is a prime candidate for that...

cheers,
   axel.

JI>
JI> Thanks for any assistance,
JI> James
JI> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.