Compiling EMAN2 on Linux System
Required libraries / Programs
The following libraries are required for EMAN2 installation (the libraries should be installed as shared-object libraries where applicable):
fftw (version 2.1.3+) (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
OR
% ./configure --enable-shared=yes --enable-float
- Followed by:
% make
gsl (version 1.3+) (http://www.gnu.org/software/gsl/)
% ./configure % make
Boost (version 1.32+) (http://www.boost.org)
- 3.1 Installing Boost requires Boost.Jam. Executables and
- source code for jam can be found at the Boost website.
http://www.boost.org/more/getting_started.html#Tools for a complete listing. % bjam "-sTOOLS=gcc" install Header files from the Boost installation (located in the "boost" subdirectory of the Boost installation (eg. /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
- 3.1 Installing Boost requires Boost.Jam. Executables and
CMake (version 2.0.6+) (http://www.cmake.org)
- Executables for several platforms are available; source code can also be used for custom installations.
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) For development the following libraries/programs are required (see Appendix A for installation help):
- Python (version 2.2+) (http://www.python.org)
- Boost Python (version 1.32+) (http://www.boost.org)
- numpy (http://www.scipy.org)
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
- % cd build
- % make % make install
- 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 $EMAN2DIR/lib setenv PYTHONPATH .:$HOME/EMAN2/lib for bash in .bashrc add: export EMAN2DIR=$HOME/EMAN2
export PATH=$PATH:$EMAN2DIR/bin export LD_LIBRARY_PATH=$EMAN2DIR/lib export PYTHONPATH=$PYTHONPATH:$HOME/EMAN2/lib
- 1) % cd $HOME
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
- - 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)
- - developers will probably want to set BOOST-LIBRARY to a
- % make install
- set up the related environment variables:
- 1) follow the first 2 steps in Quick Installation. 2) If your libraries are not installed at the default places,
4.1 Platform Dependent Optimization
- In CMake Configuration, enable the following option for your platform:
- - Athlon: ENABLE_ATHLON - Opteron(AMD64): ENABLE_OPTERON - Mac G5: ENABLE_G5
4.2 How to Generate Latest Documentation
Install doxygen (version 1.4.3+, http://www.doxygen.org)
Install graphviz (http://www.graphviz.org/)
install latex (http://www.latex-project.org/)
- After you have a successful EMAN2 install, i.e., you can import EMAN2 in Python,
- cd EMAN2/src/build ccmake ../eman2 type 't' toggle to advanced mode, check ENABLE_AUTODOC to ON make make install
- All documents will be in your EMAN2/doc directory.
Notes For Developers
- For Emacs users, please add the following line to your $HOME/.emacs:
- (setq default-tab-width 4)
- Ensure the Boost.Python
- To generate new boost python wrapper, run
- % cd eman2/libpyEM % ./create_boost_python
- 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
- Download 'bjam' for your platform.
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.
- 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
- 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
- cd libs/python/build [didn't do this]
- run 'bjam' with your options:
- 1) linux-x86: % bjam 2) SGI Irix: % bjam "-sTOOLS=mipspro" 3) Mac OS X: % bjam “-sTOOLS=darwinâ€
- login as root
- 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
- % python setup.py install