"Previous Section"_Section_intro.html - "Pizza.py WWW Site"_pws -
"Pizza.py Documentation"_pd - "Pizza.py Tools"_pt - "Next
Section"_Section_basics.html :c

:link(pws,http://pizza.sandia.gov)
:link(pd,Manual.html)
:link(pt,Section_tools.html)

:line

2. Installing Pizza.py :h3

Unpack the Pizza.py distribution by typing the following:

gunzip pizza.tar.gz
tar xvf pizza.tar :pre

The Pizza.py main directory should then contain the following
directories:

README:			   initial instructions
LICENSE:		   the GNU open-source license
doc:			   HTML documentation for Pizza.py
examples:		   scripts and data sets that exercise Pizza.py tools
scripts:		   various Pizza.py script files
src:			   source code for Pizza.py and its tools :tb(s=:)

Because Python is an interpreted language, there is no need to compile
or "make" Pizza.py.  You run Pizza.py by executing the src/pizza.py
file directly, as described below.  However there are 3 issues to
consider: (a) you must have Python installed on your machine, (b) some
Pizza.py tools require your Python to be extended with additional
Python packages, and (c) some Pizza.py tools are wrappers on other
software which needs to be available on your system.

If you don't plan to use a particular Pizza.py tool, you don't need to
install additional Python packages or other software it requires.

2.1 "Installing Python"_#2_1
2.2 "Running Pizza.py"_#2_2
2.3 "Setting up the DEFAULTS.py file"_#2_3
2.4 "Installing additional Python packages"_#2_4
2.5 "Installing other software"_#2_5 :all(b)

Note that we cannot provide help on installing the various software
packages described here.  If you have problems, you'll need to talk to
a local expert who can help you with your machine.  If you find that
instructions on this page are incorrect or incomplete or you can
provide a better description of the install procedure, please send an
email to sjplimp@sandia.gov.

:line

Installing Python :h4,link(2_1)

Python is open-source software available for Unix, Macintosh, and
Windows machines.  If you have a Linux box or Mac it is probably
already installed.  If the python executable is in your path, typing
"python" should give you a Python prompt ">>>" and tell you what
version you are running.  Version 2.4 or newer is sufficiently current
to run Pizza.py, though older versions may work as well.

If Python is not installed on your machine, go to
"www.python.org"_http://www.python.org to download a binary or
source-code version and then build and/or install it.

On my Linux box, this was as easy as

./configure; make; sudo make install :pre

To use the Pizza.py tools that have GUIs, you need to insure your
Python supports Tcl/Tk via the Tkinter module.  You can test if this
is the case by typing the following from your Python prompt:

>>> import Tkinter
>>> Tkinter._test() :pre

If this fails, see further instructions below for Tkinter.

IMPORTANT NOTE: If you are installing a new version of Python, read
the Tkinter section first, since it describes how to make sure the
Tcl/Tk and Togl libraries are installed.  If you want to use the
Pizza.py tools that require them, you need to do this step before
building Python.

:line

Running Pizza.py :h4,link(2_2)

Typically Pizza.py should be run from the directory where your LAMMPS
or other data files are.  Like any Python program, Pizza.py can be run
in one of 2 ways, by typing either

python -i ~/pizza/src/pizza.py
~/pizza/src/pizza.py :pre

where the last argument is the full pathname of the pizza.py file.

The -i switch leaves Python in interactive mode (instead of exiting)
after the pizza.py script is run.  In the 2nd case, if the src dir is
in your path, just pizza.py could be typed.  For the 2nd case, you
must also set src/pizza.py to be an executable file (chmod +x
pizza.py) and edit the 1st line of pizza.py to reflect where Python
lives on your system (find it by typing "which python"), e.g.

#!/usr/local/bin/python -i :pre

Putting a definition like one of the following in your .cshrc file (or
equivalent syntax for other Unix shell start-up files) will let you
simply type "pizza" at the command-line to start Pizza.py.

alias pizza python -i ~/pizza/src/pizza.py
alias pizza ~/pizza/src/pizza.py

Pizza.py accepts several command-line options; they are described in
"this section"_Section_basics.html of the documentation.

When Pizza.py starts, it reads a few values from the src/DEFAULTS.py
file (described below) and imports the *.py files from the src
directory as Python modules.  These are the Pizza.py tools.  Error
messages will be printed if your Python has not been extended with a
Python package that a tool requires.  If you don't plan to use the
tool you can ignore the message, or exclude that tool via the
command-line switch "-x".

Once all tools have been loaded and any initial scripts and commands
have been run (via command-line arguments) you should see the Pizza.py
">" prompt.  From this point on, everything you type is a Python
command.  Python interprets what you type, operates on your data, and
produces output or error messages, just as if you were typing in
response to Python's interactive prompt ">>>".

You can also type special commands that have been added to the Python
interpreter by Pizza.py or commands that invoke Pizza.py tools.  More
details about these options are explained in "this
section"_Section_basics.html of the documentation.

As with Python, type Ctrl-D to exit Pizza.py at any time.

:line

Setting up the DEFAULTS.py file :h4,link(2_3)

When Pizza.py starts it reads 3 values from the src/DEFAULTS.py file:

PIZZA_TOOLS: directories that contain additional Pizza.py tools
PIZZA_SCRIPTS: directories that contain additional Pizza.py scripts
PIZZA_EXCLUDE: Python files that are not loaded, since they are not tools :tb(s=:)

These are designed to allow users to augment Pizza.py with their own
tools and scripts, which need not be stored in the directories of the
Pizza.py pacakge.  Follow the instructions in the DEFAULTS.py file for
using these options.

The DEFAULTS.py files also contains various variables that specify the
name and path of programs that Pizza.py tools will execute on your
system.  In some cases the variables contain settings that are used by
these programs.  Read the comments in the DEFAULTS.py file for more
information.

The following table lists the keywords in the DEFAULTS.py, the program
or setting that will be used by default if the keyword line is
commented out, and the Pizza.py tools that use the keyword.  If the
program is not in your path or you wish to use an alternate program or
setting, you must edit the DEFAULTS.py file accordingly.  If you don't
plan to use any tool that needs the keyword, you can ignore its
setting.

Keyword: Default Value: Purpose: Tools that Use it
DISPLAY: display: display image files (ImageMagick): rasmol, raster, svg
CONVERT: convert: convert image files (ImageMagick): image
MONTAGE: montage: montage image files (ImageMagick): image
GNUPLOT: gnuplot: Gnu Plotting package: gnu
GNUTERM: x11: GnuPlot terminal: gnu
GUNZIP: gunzip: unzip a compressed *.gz file: dump, log
LABEL3D: label3d: put a label on a Raster3D image: raster
MATLAB: matlab: MatLab numerical analysis & plotting package: matlab
RASMOL: rasmol: RasMol molecular vizualization package: rasmol
RENDER: render: Raster3D vizualization rendering engine: raster 
VMDNAME: vmd: VMD visualization package: vmd
VMDDIR: /usr/local/lib/vmd: VMD visualization package: vmd
VMDDEV: win: VMD visualization package: vmd
VMDARCH: LINUX: VMD visualization package: vmd :tb(s=:)

:line

Installing additional Python packages :h4,link(2_4)

This is the list of extra Python packages various Pizza.py tools
require.  If a tool is not listed it requires no extra packages.
Instructions on where to find the Python extensions and how to install
them are listed below.

Package : Tools that Use it
Numeric or Numpy : dump, mdump, bdump, ldump, tdump
pexpect : vmd
PIL     : animate, gl, image
Pmw     : image
PyOpenGL: gl, vcr
readline: Pizza.py itself
Tkinter and Togl : animate, image, plotview, vcr :tb(s=:)

:line

Numeric or Numpy :h4

"Numeric"_numeric and its follow-on "NumPy"_numpy enables Python to
process vectors and arrays of numbers efficiently, both in terms of
memory and CPU speed.  It's an extremely useful extension to have in
your Python if you do any numerical work on large data sets.  Pizza.py
can use either Numeric or NumPy.

If Numeric or NumPy is already installed in your Python, you should be
able to type one of the following without getting an error:

>>> import Numeric
>>> import numpy :pre

Numeric can be downloaded from "this site"_numdown on SourceForge and
NumPy from "this site"_numeric.  Numeric version 24.2 is fine for
Pizza.py as is a current version of NumPy.  Once unpacked, you can
type the following from the Numeric or NumPy directories to install it
in your Python.

sudo python setup.py install :pre

Note: on my Linux box, when Numeric installed itself under the Python
lib in /usr/local, it did not set all file permsissions correctly to
allow a user to import it.  So I also needed to do this:

sudo chmod -R 755 /usr/local/lib/python2.5/site-packages/Numeric :pre

:link(numeric,http://numeric.scipy.org)
:link(numdown,http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=1351)

:line

pexpect :h4

"Pexpect"_http://pypi.python.org/pypi/pexpect in a pure Python
implementation of the Expect capability of the Tcl language.  It
allows Python to send commands to another program, and handshake the
interaction between them, one command at a time.

If pexpect is already installed in your Python, you should be able to
type the following without getting an error:

>>> import pexpect :pre

Pexpect can be downloaded from "this
site"_http://pypi.python.org/pypi/pexpect.  As of Nov 2010, Version
2.4 is fine.  On my Linux box, this command installed it:

sudo python setup.py install :pre

:line

PIL :h4

The PIL ("Python Imaging Library"_pil) allows Python to read image
files, manipulate them, and convert between several common image
formats.

:link(pil,http://www.pythonware.com/products/pil)
:link(pildown,http://effbot.org/zone/pil-index.htm)

If PIL is already installed in your Python, you should be able to type
the following without getting an error:

>>> import Image,ImageTk :pre

PIL can be downloaded from "this site"_pildown.  As of July 2007,
Version 1.1.6 is fine.  On my Linux box, this command installed it:

sudo python setup.py install :pre

with a notice that Tkinter and ZLIB (PNG) support were enabled.  If
you want the Pizza.py tools to recognize other image formats
(e.g. JPEG), then look at the README for further details, if the PIL
build did not find the correct libraries.

:line

Pmw :h4

Pmw ("Python mega-widgets"_pmw) is a common Tkinter extension that
provides a host of more powerful GUI widgets.

:link(pmw,http://pmw.sourceforge.net)

If Pmw is already installed in your Python, you should be able to type
the following without getting an error:

>>> import Pmw :pre

Pmw can be downloaded from "this site"_pmw.  As of July 2007, Version
1.2 is fine.  On my Linux box, these commands installed it:

cd Pmw.1.3.2/src
sudo python setup.py install :pre

:line

PyOpenGL :h4

The "PyOpenGL"_pyopengl package is a wrapper on the ubiquitous OpenGL
graphics library and allows a Python program to make graphics calls in
standard OpenGL syntax.  It also includes Togl support for opening a
Tk OpenGL widget, assuming your Python has Tkinter intstalled and that
Tkinter was built with Togl.  The Pizza.py tools that use PyOpenGL
require this capability.

:link(pyopengl,http://pyopengl.sourceforge.net)

If PyOpenGL is already installed in your Python, you should be able to
type the following without getting an error:

>>> import OpenGL :pre

If your PyOpenGL supports Togl, you should be able to type the
following without getting an error:

>>> from OpenGL.Tk import *
>>> from OpenGL.GLUT import * :pre

PyOpenGL can be downloaded from "this site"_pyopengl on SourceForge.
You want the latest PyOpenGL release (not OpenGLContext).  As of July
2007, Version 3.0.0a6 is what I used.

IMPORTANT NOTE: I had many problems installing earlier versions of
PyOpenGL on various boxes.  But the 3.0 release was much easier to
install on my Linux box, as outlined here.  Note that version 3.0
requires Python 2.4 or later.

IMPORTANT NOTE #2: By default, your Python may or may not have Tkinter
installed.  Even if Tkinter is installed, it probably was not built
with Togl.  If this is the case, you should install them first before
installing PyOpenGl, otherwise you may get errors when you try to use
the Pizza.py tools that use PyOpenGL, because they require Tkinter and
Togl.  See the Tkinter section below for instructions on installing
Tkinter and Togl in your Python.

Once Tcl/Tk and Togl were in place, Installing PyOpenGL on my Linux
box was as simple as:

sudo python setup.py install :pre

:line

readline :h4

The "readline"_readline library is part of Python but is not supported
on all systems.  If it works in your Python, then Pizza.py (and
Python) prompts are more shell-like and should support arrow keys,
Emacs-style editing, command history, etc.  If you get an error "No
module named readline" when Pizza.py starts up, you can ignore it, or
comment out the line "import readline" in src/pizza.py.

If readline is already installed in your Python, you should be able to
type the following without getting an error:

>>> import readline :pre

The readline library can be downloaded from "this site"_readdown.
After building the library, I believe you then have to rebuild Python
itself.

:link(readline,http://cnswww.cns.cwru.edu/~chet/readline/rltop.html)
:link(readdown,http://cnswww.cns.cwru.edu/~chet/readline/rltop.html#Availability)

:line

Tkinter and Togl :h4

The Tkinter package is part of Python but is not always enabled when
Python is built, typically due to not finding the Tcl/Tk libraries.
If you can type the following without an error message in your Python,
then Tkinter is operational in your Python:

>>> import Tkinter
>>> Tkinter._test() :pre

If this fails, you need to rebuild Python and either insure it finds
the Tcl/Tk libraries or build those libraries first as described here.
Since I wanted a more current Python then was installed with Linux on
my box, I download the latest Python (Python 2.5.1 as of July 2007)
and installed it under /usr/local.

IMPORTANT NOTE: If you want to use any of the Pizza.py tools that use
PyOpenGL, you also need the Togl library installed in the same
directory as your Tcl/Tk libraries, so that Tcl/Tk can find it when it
runs.  Thus you should also install Togl, after building the Tcl/Tk
libraries, and do both before re-building Python, as outlined in the
following 3 steps.

(1) Building Tcl/Tk libraries

You can download the latest versions of Tcl and Tk here:

:link(tcltk,http://sourceforge.net/project/showfiles.php?group_id=10894)

As of Oct 2011, version 8.5 is fine.  After unpacking the two tarballs
I did the following:

cd tcl8.5.10/unix
./configure; make; sudo make install 
cd tk8.5.10/unix
./configure; make; sudo make install :pre

(2) Installing Togl

To intstall Togl, download it from "this site"_togl on SourceForge.
As of Oct 2011, Version 2.0 is fine.

:link(togl,http://togl.sourceforge.net)

After unpacking the tarball, try typing the following to install it:

./configure

The first time I did this, it complained about not finding the Tcl and
Tk strings it needed to point to Tcl/Tk.  I fixed this by installing
the tcl-devel package via yum.

I then noticed that "configure" was finding the system Tcl/Tk instead
of the one I had installed.  So I typed this instead:

configure --with-tcl=/usr/local/lib/tcl8.5 --with-tk=/usr/local/lib/tk8.5 :pre

You should also make sure that "configure" prints a "prefix" string
that points to the correct directory where you want Togl installed.
For example, in my case, I did not want it installed in /usr/lib to
use with the system Python, but in /usr/local/lib to be loaded by my
own installed Python version.

Using the with Tcl/Tk options on the configure command fixed this
as well.

(3) Rebuilding Python

Now you can re-build Python (as described above) and it should find
the correct Tcl/Tk libraries under /usr/local, so that you have
Tkinter and Togl working with your Python as well.  Note that when you
run ./configure as the first step in building Python, it will tell you
what it found for Tcl/Tk.

:line

Installing other software :h4,link(2_5)

Some Pizza.py tools invoke other software which must be installed on
your system for the tool to work.  This is an alphabetic list of the
needed software.  Except where noted, it is freely available for
download on the WWW.  The Pizza.py tools that use this software are
listed above in "this section"_#2_3.  To see if you already have the
software on your box, type "which command", e.g. "which display".

ImageMagick display, convert, montage commands :h4

Several Pizza.py tools display image files.  The ImageMagick "display"
program can be used for this purpose.  Likewise, the ImageMagick
"convert" and "montage" comands are used by the image tool.  The
ImageMagick toolkit can be downloaded from "this site"_imagemagick and
contains a variety of useful image conversion and manipulation
software.

:link(imagemagick,http://www.imagemagick.org/script/index.php)

GnuPlot :h4

The Pizza.py gnu tool is a wrapper on the open-source GnuPlot program.
GnuPlot can be downloaded from "this site"_gnuplot.

:link(gnuplot,http://www.gnuplot.info)

Gunzip :h4

Gunzip is invoked by Python to read compressed (*.gz) data and dump
files.  It is almost certainly on your Unix system.  If not if can be
downloaded from "this site"_gzip.

:link(gzip,http://www.gnu.org/software/gzip/gzip.html)

Label3d :h4

The Pizza.py tool raster uses the label3d and render programs from the
Raster3d visualization package to produce high-quality ray-traced
images.  See the description of "Render" below for information about
Raster3d.

MatLab :h4

The Pizza.py matlab tool is a wrapper on MatLab which is a widely-used
commercial numerical analysis package that also produces nice plots.
Further information is available at "the MathWorks WWW site"_matlab.
When MatLab is installed on your system and the appropriate
environment variables are set, the command "matlab" should launch the
program.

:link(matlab,http://www.mathworks.com)

RasMol :h4

The Pizza.py rasmol tool invokes the RasMol visualization package to
view molecular systems and produce nice images.  RasMol can be
downloaded from "this site"_rasmol, which is for the original
open-source version of RasMol, not the Protein Explorer derivative
version of RasMol.

:link(rasmol,http://www.openrasmol.org)

Note that when using RasMol on a Mac, you will need to launch X11
first (or run Pizza.py from an X11 xterm) to get RasMol to display
properly.

Render :h4

The Pizza.py tool raster uses the render and label3d programs from the
Raster3d visualization package to produce high-quality ray-traced
images.  Raster3d can be downloaded from "this site"_raster.

:link(raster,http://www.bmsc.washington.edu/raster3d/raster3d.html)

For Macs, Raster3d is available for download via "Fink"_fink as an
"unstable package"_unstable.

:link(fink,http://fink.sourceforge.net/pdb/package.php/raster3d)
:link(unstable,http://fink.sourceforge.net/faq/usage-fink.php?phpLang=en#unstable)

VMD :h4

The Pizza.py vmd tool is a simple wrapper on the "VMD visualization
package"_vmd which is a popular tool for visualizing the output of
molecular dynamics simulations.  VMD can be downloaded from "this
site"_vmd.

:link(vmd,http://www.ks.uiuc.edu/Research/vmd)
