Compiling EMAN2 on Linux System

Linux Distribution-specific comments

Ubuntu 10.04 (and 9.x for the most part)

This is one of the best EMAN2 development platforms, and what I use now. All of the dependencies can be installed with the package manager and work fine. You will need:

libhdf5-serial libhdf5-serial-dev lipng12 libpng12-dev libjpeg62 libjpeg62-dev libtiff4 libtiff4-dev python-qt4 python-qt4-gl python-opengl python-matplotlib libfftw3 libfftw3-dev libgsl0-dev db4.8-util libdb4.8 python-bsddb3 libboost-python1.40-dev python-dev cmake cmake-curses-gui ipython libgl1-mesa-dev libglu1-mesa-dev

You may also need the following (but these should already be installed):

freeglut3 libgl1-mesa-dri libgl-mesa-glx libglu1-mesa libqt4-opengl mesa-common-dev nvidia-current nvidia-settings python-opengl python-gt4gl

(and all of the dependencies it wants to install as a consequence) Newer versions of any of these packages should also be ok as replacements, with the exception of python, which MUST be 2.x not 3.x.

Mandriva 2009.0 - 2010.0

Unfortunately, a lot of problems, all due to Mandriva using broken versions of various dependencies. Mandriva used to be my platform of choice, but many issues, such as the OpenGL support in PyQt4 being broken, have lead me to stop using this distro. It is possible to make it work by recompiling your own version of many dependencies, but it is a very painful process.

• PyQt4 is broken on Mandriva, and you will get a message Cannot make invalid context current. The only solution we have found is to install PyQt4 yourself on top of the system one.

• No package for bsddb3, install python-setuptools, then you can use easy_install to install bsddb3. Might be a good idea to use a newer version of BerkeleyDB as well, though this may not be strictly required.
• Mandriva uses a broken version of the Boost libraries. You need to install a newer version. You can just put in the default /usr/local location then point to this version in ccmake.

External Libraries

EMAN2 has lots of dependent libraries. To compile EMAN2 from source, you need install development packages for these external libraries. Depends on your Linux distribution, you can either install them by yum(Fedora, CentOS, RedHat), urpmi(Mandriva), yast(SuSE), synaptic/apt-get(Ubuntu). Or compile them form source code.

• We collect all these dependent packages under this link. These may not be the current versions of EMAN2 dependent libraries, but they are versions we have tried to compile from source and proved works for EMAN2.

Required Libraries / Programs

All of these libraries can be installed

The following libraries are required for EMAN2 installation (the libraries should be installed as shared-object libraries where applicable):

1. 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
   % make install

2. gsl (version 1.3+) (http://www.gnu.org/software/gsl/)

   % ./configure
   % make
   % make install

3. 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

4. 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

Once all the dependencies are installed, you can install the source code using cmake. Suppose you have source code eman2.source.tar.gz:

1. % cd $home/username/
   % tar -zxvf eman2.source.tar.gz

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/username/EMAN2
   setenv PATH $EMAN2DIR/bin:${PATH}
   setenv LD_LIBRARY_PATH $EMAN2DIR/lib:${LD_LIBRARY_PATH}
   setenv PYTHONPATH $EMAN2DIR/lib:${PYTHONPATH}

   For bash in .bashrc add:

   export EMAN2DIR=/home/username/EMAN2
   export PATH=$PATH:$EMAN2DIR/bin
   export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EMAN2DIR/lib
   export PYTHONPATH=$PYTHONPATH:$EMAN2DIR/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:

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

4. Type 'c' if it asks about "CMAKE_BACKWARDS_COMPATIBILITY".
5. 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)
6. Then type 'c', and type 'g'.

7. % 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

1. Install doxygen (version 1.4.3+, http://www.doxygen.org)

2. Install graphviz (http://www.graphviz.org/)

3. install latex (http://www.latex-project.org/)

4. After you have a successful EMAN2 install, i.e., you can import EMAN2 in Python,

   cd EMAN2/src/build
   ccmake ../eman2

   set ENABLE_AUTODOC to ON,

   make
   make install

   All documents will be in your EMAN2/doc directory.

Notes For Developers

1. For Emacs users, please add the following line to your $HOME/.emacs:

   (setq default-tab-width 4)

2. Ensure the Boost.Python
3. To generate new boost python wrapper, run

   % cd eman2/libpyEM
   % ./create_boost_python

4. 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

1. Download 'bjam' for your platform.

2. 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.

3. 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

4. cd libs/python/build [didn't do this]

5. Run 'bjam' with your options: a) linux-x86: % bjam b) SGI Irix: % bjam "-sTOOLS=mipspro" c) Mac OS X: % bjam "-sTOOLS=darwin"
6. Login as root

7. 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