VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Nov 18 2015 - 09:45:12 CST

Hi Katrine,

In my limited experience compiling for Mac, everything goes wrong all
the time, and I run back to my linux box for all of its python-infused
goodies. That being said, it looks like you've gotten reasonably far.
What happens if you try to run VMD from the command line? Say:
./MACOSXX86_64/vmd_MACOSXX86_64 -dispdev text? Or better yet:
./MACOSXX86_64/vmd_MACOSXX86_64 -dispdev text -python

When I do that, VMD complains about certain environment variables not
being set, but will otherwise behave more or less normally. With regard
to your specific questions:

1.) This might be the evil filechooser problem. John has addressed this
in past posts, and while it was originally a Yosemite problem, I don't
think El Capitan did anything to solve it. Quoting John:
"

The solution is to set an environment variable to tell VMD not to
use the MacOS-provided file browser window, and to instead use the
FLTK-based file chooser. This is done by setting the environment variable
"VMDFILECHOOSER" to the value "FLTK". This can be done in VMD itself
in the text console, in the user's .vmdrc file, in the global .vmdrc
file in the VMD.app bundle, or by setting the environment variable in the
user's Unix shell .bashrc, etc.

To set the variable in VMD or .vmdrc etc, run this command:
      set env(VMDFILECHOOSER) FLTK

To set the variable in bash, add this to .bashrc etc:
   VMDFILECHOOSER=FLTK
   export VMDFILECHOOSER

After the environment variable is set, VMD will use the alternative
file selector window in the graphical interface, and this should prevent
the problems you've been encountering.

"

2.) I think this is why there aren't any official VMD64 bit builds for
Mac. Something about FLTK not playing nice. An intermediate workaround
might be to load from a script passed along to -e. Its not ideal, but it
would work, and more importantly, can now be a python script because you
baked in python support! The three line version would be this:

from Molecule import *
mol=Molecule()
mol.load("filenamegoeshere")

3.) Ick. I think it might be related to 1, but I'm not familiar enough
with compiling for Mac to know the best way of getting around it. :(

Good luck!
-Josh Vermaas

On 11/18/2015 08:29 AM, kskeby wrote:
> Hi
>
> I have been trying to compile VMD 1.9.2 with python on my mac running
> OSX El Capitan (10.11.1). I have managed to make a build, but VMD is
> not behaving as it should.
> 1. When I open the molecule file browser and go to browse for a file,
> I am not able to actually select a file, they are inactive.
> 2. I can load files using the tk console, but the console is not
> behaving properly. It seems like it does not alway register when a key
> is pressed, and when I type letters too fast it does not catch all the
> letters.
> 3. When I load a pdf-file and dcd on top of that, no molecule is shown
> in the OpenGL display.
>
> Here are the steps I took to build the binaries:
>
> 1. Install fltk
> I tried doing this with Homebrew, however that does not work with El
> Capitan, and I eventually found this post
> (https://github.com/mikepurvis/ros-install-osx/issues/12
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_mikepurvis_ros-2Dinstall-2Dosx_issues_12&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=XQ8fa5_HEjkMzUCubp0b7rsWcoT7fRBqgUChTcYjuUA&s=oynDKUVxrRrPOCCGdUsp-1XfFUeveRVTboIc3TjshT8&e=>)
> that said that you can use the following to install fltk:
> |> brew reinstall --devel
> https://raw.githubusercontent.com/dpo/homebrew/ec46018128dde5bf466b013a6c7086d0880930a3/Library/Formula/fltk.rb
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__raw.githubusercontent.com_dpo_homebrew_ec46018128dde5bf466b013a6c7086d0880930a3_Library_Formula_fltk.rb&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=XQ8fa5_HEjkMzUCubp0b7rsWcoT7fRBqgUChTcYjuUA&s=rslGEKdfoL3PI3dyCHLKJY55A04b-4Yz8LAjrHzxX_I&e=>|
>
> 3. I already had Xcode (7.1.1 7B1005) and Command line tools
> installed, so no need to install Tcl, Tk and OpenGL.
> I am running Tcl8.5, Tk8.5 and Python2.7.
>
> 4. I also had XQuartz (X11, http://www.xquartz.org/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.xquartz.org_&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=XQ8fa5_HEjkMzUCubp0b7rsWcoT7fRBqgUChTcYjuUA&s=qFtc9v6nVMPt0YDROcyBF2ExWY_93ug0Kv3KY5vhR4U&e=>)
> installed, which should also be done manually, because it is not
> included with OS X anymore (https://support.apple.com/en-us/HT201341
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.apple.com_en-2Dus_HT201341&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=XQ8fa5_HEjkMzUCubp0b7rsWcoT7fRBqgUChTcYjuUA&s=_6phZeaNsP0OFWQMvNKDEPKqy5pUyUJ6sBJDMBNyDzY&e=>).
>
> 5. Extract the VMD tarball
> > cd /Applications/vmd
> > tar xvfz vmd-1.9.2.src.tar.gz
>
> 6. Compile plugins
> > cd /Applications/vmd/vmd-1.9.2
> > mv ../plugins .
> > cd plugins
> > export TCLINC=-I/usr/local/include
> > export TCLLIB=-L/usr/local/lib
> > make MACOSXX86_64 TCLINC=$TCLINC TCLLIB=$TCLLIB
>
> > export PLUGINDIR=/Applications/vmd/vmd-1.9.2/plugins
>
> I commented out the following lines in the Makefile:
> #-mkdir -p $(PLUGINDIR)/include
> #for header in $(PLUGINHEADERS); do cp -p $(INCLUDEDIR)/$$header
> $(PLUGINDIR)/include || exit 1 ; done
> Because I was getting the following error when I tried to do make distrib:
> Populating distribution directory with compiled plugins
> cp: /Applications/vmd/plugins/include/vmdplugin.h and
> include/vmdplugin.h are identical (not copied).
> make: *** [distrib] Error 1
>
> > make distrib
>
> 7. Compile VMD
> > cd /Applications/vmd/vmd-1.9.2/
>
> Changed the configure.options file so that it only contained:
> MACOSXX86_64 FLTKOPENGL FLTK TK TCL PYTHON PTHREADS LP64
>
> > ./configure
> > cd src
>
> This is where I really ran into problems. I had a lot of error when I
> typed make depend, so I have to change the INCDIRS, LIBS, and LIBDIRS
> in the Makefile. This is what I ended up with which didn’t give me any
> error in the dependencies:
> INCDIRS =
> -F/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/System/Library/Frameworks
> -I../plugins/include -I../plugins/MACOSXX86_64/molfile -I.
> -I/usr/local/include -I/usr/X11/include
> -I/usr/local/Cellar/fltk/1.3.3-r10866_1/include
>
> LIBS = -lfltk_gl -lfltk -framework ApplicationServices -ldl
> -framework OpenGL -framework AGL -framework Cocoa -framework Python
> -lpthread -framework Tk -framework Tcl -lmolfile_plugin -framework
> Carbon $(VMDEXTRALIBS)
>
> LIBDIRS = -Wl,-executable_path . -lmx
> -L../plugins/MACOSXX86_64/molfile -L/usr/local/lib
> -L/usr/local/Cellar/fltk/1.3.3-r10866_1/lib
>
> > make
> I get this error at the end of the make call:
> Linking vmd_MACOSXX86_64 ...
> /Developer/Tools/Rez -t APPL -o ./MACOSXX86_64/vmd_MACOSXX86_64 vmdmac.r
> make: /Developer/Tools/Rez: No such file or directory
> make: *** [vmd_MACOSXX86_64] Error 1
>
> > make install
>
> Even though there was an error when running the make command, the make
> install command is able to run, and executable files are created in
> /usr/local/lib/vmd.
>
> 8. In order to open VMD I had to create a symbolic link to
> /usr/local/Cellar/fltk/1.3.3-r10866_1 in /usr/local/opt
> > cd /usr/local/opt
> > ln -s /usr/local/Cellar/fltk/1.3.3-r10866_1 fltk
>
> I tried attaching some files with the output from the different
> commands, but my email seemed not to make it on to the mailing list.
>
> Is there anyone who can help me figure out what is going on? I would
> really appreciate it. And please let me know if there is any
> additional information that you need.
>
> Thanks,
> Katrine
>