Compiling EMAN2 on Linux System FROM SOURCE

Linux Distribution-specific comments

Ubuntu and Kubuntu

This is one of the best EMAN2 development platforms, and what I use now, though I use Kubuntu due to its improved desktop and Qt integration (Gnome has become irritating recently). One of the best things about this distribution is that ALL of the dependencies are available from the package manager. However, with recent ubuntu releases, I suggest installing 'synaptic' and using that in preference to the current default package managers, which don't find development packages very readily.

13.04

Install the following (you can just use apt-get install): libhdf5-7 libhdf5-dev libpng12-0 libpng12-dev libtiff4 libtiff4-dev python-qt4 python-qt4-gl python-opengl python-matplotlib libfftw3-3 libfftw3-dev libgsl0-dev db-util libdb-dev python-bsddb3 libboost-filesystem-dev liboost-python1.49.0 libboost-python1.49-dev python-dev cmake cmake-curses-gui ipython libgl1-mesa-dev libglu1-mesa-dev libftgl2 libftgl-dev libboost-thread-dev

12.10 and earlier

The version numbers in this list are a bit out of date, so you will need to search for the current version of each package. You will need:

libhdf5-serial libhdf5-serial-dev libpng12 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 libftgl2 libftgl-dev

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

freeglut3 libgl1-mesa-dri libgl-mesa-glx libglu1-mesa libqt4-opengl mesa-common-dev

Assuming you have an Nvidia based graphics card (you should):

nvidia-current nvidia-settings

Note that Python MUST be 2.X not 3.X. While you can install packages from the command-line with apt-get, it may be more difficult to find the right version numbers that way.

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 2009.1, 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.

Fedora

All dependent packages can be installed in Fedora system with its package manage system, yum. This is the list of dependent packages I installed for Fedora 14 x86_64 for the default ccmake configuration. What you need install may vary depends on how may libraries pre-exists on you system. There are the compile-time dependent packages.

• yum install fftw-devel.x86_64
• yum install gsl-devel.x86_64
• yum install hdf5-devel.x86_64
• yum install python-devel.x86_64
• yum install numpy.x86_64
• yum install boost-devel.x86_64
• yum install freeglut.x86_64
• yum install ftgl-devel.x86_64 (Optional with ENABLE_FTGL in ccmake)

After compiling and installing EMAN2, we need install some run time dependent packages for EMAN2's GUI part.

• yum install PyQt4.x86_64

• yum install PyOpenGL.noarch
• yum install ipython.noarch
• yum install python-matplotlib.x86_64

CentOS 5

On CentOS system, by default you can find all dependency libraries with yum. You need install EPEL(Extra Packages for Enterprise Linux) first. Follow the instruction on this webpage (http://fedoraproject.org/wiki/EPEL/FAQ#howtouse) to install epel. Then you can do the same thing as in Fedora system to install all dependent packages.

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):

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

gsl

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

• % ./configure
  % make
  % make install

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.

hdf5

Download the source code file hdf5-1.8.7.tar.gz from http://www.hdfgroup.org/ftp/HDF5/current/src/

• % ./configure --disable-dependency-tracking --disable-static --enable-shared
  make
  sudo make install

easy_install

To be able to use easy_install on linux, install the python-setuptools package either via the Synaptic Package Manager or just type

• sudo apt-get install python-setuptools

Optional Libraries / Programs

• 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

This is **STILL** part of installation "from source"

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. % cd EMAN2/src/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
  x86_64(AMD64):                  ENABLE_X86_64
  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. 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

A.4. How to Install bsddb3 (instead of using bsddb come with Python)

Download non-encryption version of Berkeley DB (for example, db-5.1.25.NC.tar.gz) from oracle (http://www.oracle.com/technetwork/database/berkeleydb/downloads/index.html).

• % tar xvzf db-5.1.25.NC.tar.gz
  % cd db-5.1.25.NC/build_unix
  % ../dist/configure --disable-static --prefix="you specify a install directory"
  % make
  % make install

Download Python bsddb binding (for example, bsddb3-5.1.2.tar.gz) from http://www.jcea.es/programacion/pybsddb.htm

• % tar xvzf bsddb3-5.1.2.tar.gz
  % cd bsddb3-5.1.2
  % python setup.py --berkeley-db="the directory you used to install Berkeley DB" build
  % python setup.py --berkeley-db="the directory you used to install Berkeley DB" install