VMD-L Mailing List
From: kskeby (kks_at_chem.au.dk)
Date: Wed Nov 18 2015 - 08:29:45 CST
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://github.com/mikepurvis/ros-install-osx/issues/12>) 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://raw.githubusercontent.com/dpo/homebrew/ec46018128dde5bf466b013a6c7086d0880930a3/Library/Formula/fltk.rb>
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/ <http://www.xquartz.org/>) installed, which should also be done manually, because it is not included with OS X anymore (https://support.apple.com/en-us/HT201341 <https://support.apple.com/en-us/HT201341>).
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
> 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
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.