Installing VMD with Python options on a Mac

Backstory: To simplify my workflow, I’ve been learning Python so that I’m not constantly switching between Matlab, C, Perl, and Tcl.  I use a Mac, and due to the rather baroque set of options in Mac software development the VMD developers have sensibly chosen to not provide Python functionality in their binary distributions for Mac.  This week, I spent some time figuring out how to build it.

The biggest help by far was Reid Van Lehn’s (RVL’s) detailed post on the VMD mailing list.

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/16171.html

My system:

  • MacBook Air running OS X 10.7.5
  • MacPorts gcc 4.2.1 with SciencePorts ( https://bitbucket.org/seanfarley/scienceports )… I would like to give a shout out to my friend and colleague Sean Farley, who is my go-to expert on all things Mac and especially MacPorts.
  • For Python, I used the 64-bit Enthought Python Distribution for access to SciPy and many other packages.

It is likely that this installation process could be simplified further.  I don’t quite have time at the moment.

Happy to post more system details if people ask for them; off the top of my head, I don’t know what else might be relevant.

1. My build directory is
~/tmp/vmdsrc/

and it holds

fltk-1.3.2-source.tar.gz
tcl8.5.13-src.tar.gz
tk8.5.13-src.tar.gz
vmd-1.9.1.src.tar.gz

2. cd ~/tmp/vmdsrc/ ; mkdir fltk ; mkdir tcltk

3. tar -xzvf *.gz

4. Build and install FLTK to the place you want it (dummy directory here)
cd ~/tmp/vmdsrc/fltk-1.3.2
./configure –prefix=/Users/jbardhan/tmp/vmdsrc/fltk
make
make install

5. Build and install Tcl to the place you want (perhaps not in a system directory…)
cd ~/tmp/vmdsrc/tcl8.5.13/unix
./configure –prefix=/Users/jbardhan/tmp/vmdsrc/tcltk –disable-64bit –disable-corefoundation
make
make test
make install

Note 5.0: Notes on compiling Tcl/Tk are at http://www.tcl.tk/doc/howto/compile.html

Note 5.1: I disabled 64 bit following the earlier instructions from RVL, but I’m
not sure what this does since everything else was built 64 bit, and
nothing died.

Note 5.2: I built with corefoundation disabled because I was hoping to use this
Tcl/Tk installation to build PyMOL from scratch. That turned out to be impossible,
so this is probably unnecessary.

Note 5.3: A number of Tcl tests fail: httpold-4.12, exec-9.7, platform. Googling
wasn’t so helpful, except to see that other people have the same problems.

6. Build and install Tk
cd ~/tmp/vmdsrc/tk8.5.13/unix

./configure –prefix=/Users/jbardhan/tmp/vmdsrc/tcltk –with-tcl=/Users/jbardhan/tmp/vmdsrcd/tcl8.5.13/unix/ –disable-xft –disable-64bit –disable-corefoundation
make
make test
make install

Note 6.1: I disabled xft because it was giving me problems. The fonts
in the resulting VMD are definitely a step down, so this would be a
good problem to fix.

Note 6.2: A bunch of things fail during the test. clipboard-6.2,
focus-5.1, font-21.15 crashes the test suite.

7. Now on to the actual VMD side of things. Plugins are compiled first.

cd ~/tmp/vmdsrc/vmd-1.9.1/plugins
export TCLINC=”-I/Users/jbardhan/tmp/vmdsrc/tcltk/include”
export TCLLIB=”-L/Users/jbardhan/tmp/vmdsrc/tcltk/lib”
make MACOSXX86_64 TCLINC=$TCLINC TCLLIB=$TCLLIB
export PLUGINDIR=/Users/jbardhan/tmp/vmdsrc/vmd-1.9.1/plugins
make distrib

Note 7.1: Big difference from RVL’s instructions: I actually used
MACOSXX86_64 architecture, whereas he said to use MACOSXX86.

Note 7.2: The last two lines copy all the needed compiled plugins into
the VMD source directory. I didn’t understand RVL’s Steps 8 and 9 a
at first, but do now; the above instructions do what he said.

8. Time to start the pain.

cd ~/tmp/vmdsrc/vmd-1.9.1

edit configure.options to read
MACOSXX86_64 FLTKOPENGL FLTK TK TCL PYTHON PTHREADS

edit configure for the final destination of your VMD scripts and files:
$install_name = “vmdpy”;
$install_bin_dir=”/Users/jbardhan/tmp/bin”;
$install_library_dir=”/Users/jbardhan/tmp/lib/$install_name”;

./configure

cd src

edit the Makefile so that
a) I commented out VMD_OTHER_EXE and VMD_OTHER_NAMES because I don’t use those

b) INCDIRS = -F/System/Library/Frameworks -I../lib/tcl/include -I../lib/tk/lib_MACOSXX86_64/Tk.framework/Versions/8.5/Headers -I../plugins/include -I../plugins/MACOSXX86_64/molfile -I../lib/fltk/fltk -I. -I/Users/jbardhan/tmp/vmdsrc/fltk/include -I/Users/jbardhan/tmp/vmdsrc/tcltk/include -I/Library/Frameworks/EPD64.framework/Versions/7.3/include/python2.7 -I/Library/Frameworks/EPD64.framework/Versions/7.3/include/python2.7

c) LIBS = -lfltk_gl -lfltk -framework ApplicationServices -framework Cocoa -framework OpenGL -frameemacwork AGL -L/Library/Frameworks/EPD64.framework/Versions/7.3/lib/python2.7/config -ldl -framework CoreFoundation /Library/Frameworks/EPD64.framework/Versions/7.3/Python -lpthread -lpthread -ltk8.5 -ltcl8.5 -lmolfile_plugin -framework Carbon $(VMDEXTRALIBS)

d) LIBDIRS = -F../lib/tcl/lib_MACOSXX86_64 -F../lib/tk/lib_MACOSXX86_64 -Wl,-executable_path . -lmx -L../plugins/MACOSXX86_64/molfile -L../lib/fltk/MACOSXX86_64 -L/Users/jbardhan/tmp/vmdsrc/fltk/lib -L/Users/jbardhan/tmp/vmdsrc/tcltk/lib

e) remove “-m32″ from CFLAGS and CPPFLAGS
make depend

make

make install

Note 8.0: I’m using a different install_name so that I know which vmd
is a standard binary download from their website, and which is my
custom build with Python.

Note 8.1: I’m not sure about pthreads, but everything else seems
essential…

Note 8.2: At one point with a different set of configuration options,
I needed to add a space at the end of the line, otherwise the script
would not identify the last word/option on the line (it would truncate
by one character, e.g. complain about PTHREAD not being a valid
option).

Note 8.3: I did not have problems with VMD hanging upon startup, so
I skipped RVL’s step 14, but that may be because I’m building with a
new Tcl/Tk/FLTK rather than with those from MacPorts, see

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/15280.html

Note 8.4: The link stage when you run just “make” will seem to crash!
“””
/Developer/Tools/Rez -t APPL -o ../MACOSXX86/vmd_MACOSXX86 vmdmac.r
### /Developer/Tools/Rez – SysError -120 during create of “../MACOSXX86/vmd_MACOSXX86″.
### /Developer/Tools/Rez – Fatal error trying to open the resource file “../MACOSXX86/vmd_MACOSXX86″ for writing.
Fatal Error!
### /Developer/Tools/Rez – Fatal Error, can’t recover.
### /Developer/Tools/Rez – Since errors occurred, ../MACOSXX86/vmd_MACOSXX86′s resource fork was not written.
“””

However, the binary is written and seems to run fine. This is the
most worrisome part of the build =) Without “-framework Cocoa” I
always found at the link stage weird things happening. Undefined
symbols for architecture x86_64: “_objc_msgSend” , “_NSApp”,
“_NSFilenamesPboardType” and the FLTK examples all include Cocoa,
unsurprisingly.

9. Edit the script install_name (here vmdpy) which has been copied to your
install_bin directory. Change MACOSX to MACOSXX86.

10. Check if you’ve gotten everything up and running:

a) run the install_name script, which should bring up your standard
two windows.

b) type “gopython” to enter python mode.

c) if you see “module VMD not found” you have a problem.

d) check you have the version of python you want, by running
import sys
print sys.version
Other notes:
1. You _have_ to compile the VMD plugins directory before you try the
main directory. This wasn’t clear to me from stepping into the
vmd-1.9.1 directory, but it is clear once the configure dies and you
start Googling.

2. FLTK is _required_ for the familiar VMD interface. This wasn’t clear
from the installation/configuration options, but again it’s clear from
a moment’s Googling.

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One Response to Installing VMD with Python options on a Mac

  1. When I follow your instructions I manage to compile a 64bit VMD 1.9.1 including python support. However, when i try to load any molecule data, the file dialog will not let me select any files. Also, when I try to open the built-in tcl-console, the app crashes.

    Do you also experience that, and if so, did you manage to solve the issue?

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