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.
Installing Boost requires the user to identify a particular toolset to use during compilation. Most UNIX systems will probably use the "gcc" toolset; visit 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
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
% cd $HOME % mkdir -p EMAN2/src % cd EMAN2/src % gunzip eman2.tar.gz % tar xf eman2.tar
% mkdir build % cd build
% cmake ../eman2 % make % make install
- Set up login shell for csh/tcsh, put the following to your .cshrc or .tcshrc file:
setenv EMAN2DIR $home/username/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/username/EMAN2 export PATH=$PATH:$EMAN2DIR/bin export LD_LIBRARY_PATH=$EMAN2DIR/lib export PYTHONPATH=$PYTHONPATH:$HOME/EMAN2/lib
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:
- Follow the first 2 steps in Quick Installation.
- 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
% 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'.
-
% make % make install
Platform Dependent Optimization
In CMake Configuration, enable the following option for your platform:
Athlon: ENABLE_ATHLON Opteron(AMD64): ENABLE_OPTERON Mac G5: ENABLE_G5
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
- cd libs/python/build [didn't do this]
- run 'bjam' with your options:
- a) linux-x86: % bjam b) SGI Irix: % bjam "-sTOOLS=mipspro" c) Mac OS X: % bjam "-sTOOLS=darwin"
- login as root
cp -df bin-stage/libboost_python.so* /usr/local/lib cd ../../..; cp -rf boost /usr/local/include
- a) Check your shell:
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