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):

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

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

        % ./configure
                % make

1. 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

2. 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
    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 $EMAN2DIR/lib setenv PYTHONPATH .:$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

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(AMD64): ENABLE_OPTERON - Mac G5: ENABLE_G5

4.2 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 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

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:
   • 1) linux-x86: % bjam 2) SGI Irix: % bjam "-sTOOLS=mipspro" 3) 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