VMD-L Mailing List

From: Joshua Anderson (joaander_at_umich.edu)
Date: Thu Feb 04 2010 - 07:26:10 CST

No, the vmdmac.r file wasn't in the src directory. The one you
attached seems identical to the one I found online, trying it
anyways....

It of course solves the file not found error, but doesn't do anything
to help the GUI to respond to mouse events. Tcl (and python) commands
work from the terminal where I launched vmd from. I can resize the
display with "display resize", molecules load and display, etc... It
even runs my .vmdrc file. But the mouse just displays a spinning
colorwheel when I move it over any vmd gui element and there is no
response to clicks. Popping up a Tk window from python with root =
Tk() even works, but like the other VMD gui windows, it does not
respond to any input events.

I can confirm that the resource fork is being written:
$ xattr -p com.apple.ResourceFork ../MACOSXX86/vmd_MACOSXX86
66`?&?????
About FLTK-ZMBARMENU&carb2?????2Apple

Interestingly, I can get a very similar behavior with the VMD 1.8.7
application bundle downloaded from the VMD web page if I run it like so:
cd /Applications/VMD\ 1.8.7.app/Contents/vmd/
./vmd_MACOSXX86
The only difference is that running the packaged vmd that way,
my .vmdrc is not run.
The packaged VMD app bundle of course works perfectly if I run
cd ~/
/Applications/VMD\ 1.8.7.app/Contents/vmd/vmd_MACOSXX86
(or one of the startup scripts that do the same thing)
That suggests to me that path identification issues may cause the non-
updating GUI, but in both cases I see what appear to be all the same
*DIR variables set when I run "env": didn't check them exhaustively.

However, I'm not very familiar with the VMD source and how the input
event loop is launched.

Any hints on how to narrow down root cause that I can debug locally?
Even a simple explanation of why the 1.8.7 bundle gives the same
behavior when launched as above would help me narrow it down.

Josh

On Feb 3, 2010, at 4:55 PM, John Stone wrote:

> Hi,
> Do you have a copy of vmdmac.r in your vmd/src/ directory?
> The resource compiler is looking for it there, but seems not
> to be finding it in your case. I've attached a copy of it
> to this email.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Feb 03, 2010 at 04:39:52PM -0500, Joshua Anderson wrote:
>> I'm attempting to create a build of VMD on my mac linked with a
>> specific python I have installed (via macports if you must know, not
>> that it matters). The system is a recent intel iMac running Mac OS X
>> 10.5.8.
>>
>> The configuration I'm using to build is:
>> MACOSXX86 FLTKOPENGL FLTK TK CUDA IMD LIBTACHYON NETCDF TCL PYTHON
>> PTHREADS NUMPY SILENT
>>
>> I've navigated the VMD compiling docs, built the plugins without
>> problems, modified the configure scripts to point to the macports
>> libraries and am now compiling vmd proper. Everything compiles, but I
>> get the following errors in the linking phase.
>>
>> $ make
>> Linking vmd_MACOSXX86 ...
>> ln: ./foobar: File exists
>> failed to find vmdmac/vmdmac.r
>> ### /Developer/Tools/Rez - SysError 0 during open of "vmdmac.r".
>> Fatal Error!
>> ### /Developer/Tools/Rez - Fatal Error, can't recover.
>> vmdmac.r: ### /Developer/Tools/Rez - Since errors occurred, ../
>> MACOSXX86/vmd_MACOSXX86's resource fork was not written.
>> make: *** [vmd_MACOSXX86] Error 3
>>
>> The vmdmac.r file does not show up in the source tarball. I found
>> this
>> ancient post regarding it:
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/0678.html .
>> If I
>> use the vmdmac.r file from that post, vmd does compiles and link
>> successfully, but I still have problems at that point.
>>
>> I then make install VMD to a test dir to try it out. Running bin/vmd
>> errors out with vmd_MACOSX not existing. OK, update that to
>> MACOSXX86,
>> run bin/vmd again and VMD loads, but the menus, opengl display,
>> etc...
>> do not respond to any mouse clicks. I can quit by typing quit in the
>> terminal window I used to launch it, though.
>>
>> Any ideas what am I doing wrong?
>>
>> I don't think the problem is due to any library mismatching. I've
>> triple checked that all include and library directories are pointing
>> to Tcl, Tk, and FLTK installed by macports. otool confirms that all
>> those libraries are linked from macports (/opt/local/*)
>> $ otool -L vmd_MACOSXX86
>> vmd_MACOSXX86:
>> /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version
>> 292.4.0)
>> /System/Library/Frameworks/OpenGL.framework/Versions/A/OpenGL
>> (compatibility version 1.0.0, current version 1.0.0)
>> /System/Library/Frameworks/AGL.framework/Versions/A/AGL
>> (compatibility version 1.0.0, current version 1.0.0)
>> @rpath/libcudart.dylib (compatibility version 1.1.0, current version
>> 3.0.0)
>> /opt/local/Library/Frameworks/Python.framework/Versions/2.6/Python
>> (compatibility version 2.6.0, current version 2.6.0)
>> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
>> version 111.1.4)
>> /opt/local/lib/libtk8.5.dylib (compatibility version 8.5.0, current
>> version 8.5.8)
>> /opt/local/lib/libtcl8.5.dylib (compatibility version 8.5.0, current
>> version 8.5.8)
>> /opt/local/lib/libnetcdf.4.dylib (compatibility version 5.0.0,
>> current version 5.0.0)
>> /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon
>> (compatibility version 2.0.0, current version 136.0.0)
>> /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current
>> version 7.4.0)
>> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current
>> version 1.0.0)
>> /System/Library/Frameworks/CoreServices.framework/Versions/A/
>> CoreServices (compatibility version 1.0.0, current version 32.0.0)
>> /System/Library/Frameworks/CoreFoundation.framework/Versions/A/
>> CoreFoundation (compatibility version 150.0.0, current version
>> 476.19.0)
>> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/
>> ApplicationServices (compatibility version 1.0.0, current version
>> 34.0.0)
>>
>> --------
>> Joshua A. Anderson, Ph.D.
>> Chemical Engineering Department, University of Michigan
>
> --
> 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
> <vmdmac.r.gz>