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INSTALL
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EMAN 2
------
Table of Contents:
Sec. 1 Required Libraries / Programs
Sec. 2 Optional Libraries / Programs
Sec. 3 Quick Installation
Sec. 4 Advanced Installation
Sec. 5 Notes for Developers
App. A Help for Optional Progam Installation
1. Required libraries / Programs
--------------------------------
The following libraries are required for EMAN2 installation (the
libraries should be installed as shared-object libraries where applicable):
1. fftw2 (version 2.1.3+) or fftw3 (http://www.fftw.org/)
To install fftw from source use either configure option:
% ./configure --enable-static=no --enable-shared=yes --enable-float --enable-type-prefix
% make
2. gsl (version 1.6+) (http://www.gnu.org/software/gsl/)
% ./configure
% make
3. Python (version 2.3+) (http://www.python.org)
4. numpy
(http://www.scipy.org)
5. Boost Python (version 1.32 or upper) (http://www.boost.org)
3.1 Installing Boost requires Boost.Jam. Executables and
source code for jam can be found at the Boost website.
Installing Boost requires the user to identify a particular
toolset to use during compliation. Most UNIX systems will
probably use the "gcc" toolset; visit
http://www.boost.org/more/getting_started.html#Tools for a
complete listing. go to boost/libs/python/build:
% bjam "-sTOOLS=gcc" install
Header files from the Boost installation (located in the
"boost" subdirectory of the Boost installation
(ex. /boost_1_32_0/boost)) must now either be added to the
compilers path or copied into an existing location on the path
in a subdirectory /boost.
One possibility for this might be:
% cp -r boost /usr/include/boost
6. CMake (version 2.0.5+) (http://www.cmake.org)
Executables for several platforms are available; source code
can also be used for custom installations.
7. PyQT4 - Involves several subpackages:
* Qt 4.1+
http://www.trolltech.com/developer/downloads/qt/x11
Suggest:
./configure -no-xrender
* SIP
http://www.riverbankcomputing.co.uk/sip/download.php
* PyQt4
http://www.riverbankcomputing.co.uk/pyqt/download.php
* PyOpenGL
http://sourceforge.net/project/showfiles.php?group_id=5988
8. IPython (version 0.7.3) (http://ipython.scipy.org/moin/)
2. Optional Libraries / Programs
----------------------------------
- To read/write HDF5 image, use hdf5 (http://hdf.ncsa.uiuc.edu/HDF5).
- To read TIFF image, use libtiff (http://www.libtiff.org)
- To read PNG image, use PNG (http://www.libpng.org)
- To create code based auto-generated documentation, see section 4.2.
3. Quick Installation
----------------------
Suppose you have source code eman2.tar.gz
1) % cd $HOME
% mkdir -p EMAN2/src
% cd EMAN2/src
% gunzip eman2.tar.gz
% tar xf eman2.tar
2) % mkdir build
% cd build
3) % cmake ../eman2
% make
% make install
4) set up login shell
for csh/tcsh, put the following to your .cshrc or .tcshrc file:
setenv EMAN2DIR ${HOME}/EMAN2
setenv PATH ${EMAN2DIR}/bin:${PATH}
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
setenv PYTHONPATH .:${HOME}/EMAN2/lib:${PYTHONPATH}
for bash in .bashrc add:
export EMAN2DIR=${HOME}/EMAN2
export PATH=${PATH}:${EMAN2DIR}/bin
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${EMAN2DIR}/lib
export PYTHONPATH=${PYTHONPATH}:${HOME}/EMAN2/lib
4. Advanced Installation
------------------------
If your libraries (fftw, gsl, hdf, etc) are not found by Quick
Installation, or if you want to change the compilation options,
the following steps help:
1) follow the first 2 steps in Quick Installation.
2) If your libraries are not installed at the default places,
set up the related environment variables:
- fftw -> FFTWDIR
- gsl -> GSLDIR
- tiff -> TIFFDIR
- png -> PNGDIR
- hdf5 -> HDF5DIR
- python -> PYTHON_ROOT and PYTHON_VERSION
3) % ccmake ../eman2
- type 'c' if it asks about "CMAKE_BACKWARDS_COMPATIBILITY".
- make necessary changes for compilation flags.
- developers will probably want to set BOOST-LIBRARY to a
Boost.Python object file (ex. libboost_python-gcc-1_32.so)
- Then type 'c', and type 'g'.
4) % make
% make install
4.1 Platform Dependent Optimization
------------------------------------
In CMake Configuration, enable the following option for your platform:
- Athlon: ENABLE_ATHLON
- Opteron(Athlon 64): ENABLE_OPTERON
- Mac G5: ENABLE_G5
4.2 How to Generate Latest Documentation
-----------------------------------------
in EMAN2/doc directory, except some hand-coded html and text files,
we have three groups of auto-generated documents:
1. Latex documents generated from tex files, same content can be viewed
in four formats: dvi, ps, pdf and html.
2. Doxygen html files.
3. two html files describe processor and processor group.
To create these files in EMAN2 building process, you need:
1. Install doxygen (version 1.4.3+, http://www.doxygen.org)
2. Install latex2html (http://www.latex2html.org/)
3. Install Graphviz(dot) (http://www.graphviz.org/)
4. compile and install EMAN2 with "ENABLE_AUTODOC" set to off
5. Choose "ENABLE_AUTODOC" in the CMake configuration, compile and install EMAN2 again
5. Notes For Developers
-----------------------
0. For Emacs users, please add the following line to your $HOME/.emacs:
(setq default-tab-width 4)
1. Ensure the Boost.Python
2. To generate new boost python wrapper, run
% cd eman2/libpyEM
% ./create_boost_python
3. Windows Installer
EMAN uses "Nullsoft Scriptable Install System" (http://nsis.sourceforge.net/)
to generate the windows installer.
It also uses "HM NIS Edit" (http://hmne.sourceforge.net/) as the editor.
Appendix A.
-----------
A.1. How to Install Boost Python
--------------------------------
0. Download 'bjam' for your platform.
1. Download boost source from http://www.boost.org. Assume the
version is boost_1_32_0.
% cd /usr/local/src; tar zxf boost_1_32_0.tar.gz; cd boost_1_32_0.
2. Set up environment variables "PYTHON_ROOT" and "PYTHON_VERSION".
For example, if your python is at /usr/bin/python then PYTHON_ROOT is
"/usr". If your python version is 2.2.X, PYTHON_VERSION is '2.2'.
a) check your shell: % echo $SHELL
b) if you are using bash/zsh, do
% export PYTHON_VERSION=2.2
% export PYTHON_ROOT=/usr
if you are using csh/tcsh, do
% setenv PYTHON_VERSION 2.2
% setenv PYTHON_ROOT /usr
3. cd libs/python/build [didn't do this]
4. run 'bjam' with your options:
1) linux-x86: % bjam
2) SGI Irix: % bjam "-sTOOLS=mipspro"
5. login as root
6. cp -df bin-stage/libboost_python.so* /usr/local/lib
cd ../../..; cp -rf boost /usr/local/include
A.2. How to use your own python version
---------------------------------------
If the python you want to use in your computer is not found by CMake,
you may set up environment variables "PYTHON_ROOT" and "PYTHON_VERSION".
For example, if your python is at /usr/local/python2.4/bin/python.
PYTHON_ROOT is "/usr/local/python2.4". if your python is 2.4.X,
PYTHON_VERSION is '2.4'.
A.3. How to Install numpy
----------------------------------
From the website http://sourceforge.net/projects/numpy download source package.
For windows, run the binary installer and the installation is
complete. Other users must download the source code and install
manually as follows:
- get source code numpy-1.0.1.tar.gz
- % gunzip numpy-1.0.1.tar.gz
% tar xf numpy-1.0.1.tar
- login as root
- % cd numpy-1.0.1;
% python setup.py install