A guide how to install source code of SPARX and EMAN2 in your home directory.

Preparation work for Mac OS

Mac OS X does not come with the C++ compiler and GNU make installed. You need to install them by yourself. Please Install Xcode which is the collection of development tools (g++, make, etc).

Download and install xcode. It will require registration as Mac developer!

You will also need cvs command, which for some reason is gone in Mavericks.

  1. Download http://ftp.gnu.org/non-gnu/cvs/source/feature/1.12.13

  2. untar the file
  3. ./configure
  4. make all
  5. sudo make install

Install some 3rd party libraries(fftw, etc.)

EMAN2 employs the following 3rd party libraries: fftw, gsl, boost, hdf5, jpeglib (optional), tifflib (optional). Below is a detail description of the installation process.

Please refer to the installation instruction from the NCMI lab. (http://blake.grid.bcm.edu/emanwiki/EMAN2/COMPILE_EMAN2_MAC_OS_X). Note that the download links and the installation procedures of 3rd party libraries may be changed.

This is the link to a detail version of installation. (sourcecodeinstallationsparxversion)Please note that it may not as up to date as the NCMI version.

Compiling EMAN2 on a Mac

NOTE: on multi-CPU machines all make commands can be replaced to make -j 4 where 4 is the number of CPUs available. It will significantly reduce the time of compilation.

Prerequisites

  1. Install most recent system

  2. Install all system updates ((apple)->Software update…)

  3. Install Xcode from Apple Store
  4. Install Command line tools from Xcode
    • run Xcode
    • install all updates Xcode ask for
    • old Xcode (from previous OS version) may be moved to trash (Xcode may ask for that)

    • from upper menu open Xcode->Preferences…->Downloads->Components and click button "Install" for option "Command line tools"

  5. If you are upgrading from previous version, you should also remove the old libraries to avoid strange errors:
    • Remove old EMAN2 binaries (or change the directory name)
    • Remove boost 
      sudo rm -rf /usr/local/include/boost /usr/local/lib/libboost*

Required Packages

  1. Install X11 (XQuartz-2.7.5.dmg)
  2. Install Qt4 (qt-opensource-mac-1.6.0-8-olnline.dmg)
  3. Install Boost (boost_1_56_0.tar.gz) 
    ./bootstrap.sh --with-libraries=python
./bjam
sudo ./bjam install
  4. Install GSL (gsl-1.15.tar.gz) 
    ./configure
make
sudo make install
  5. Install FFTW (fftw-3.3.2.tar.gz) 
    ./configure --enable-shared  --enable-float
make
sudo make install
  6. Install Oracle Berkeley DB (db-5.3.21.NC.tar.gz) 
    cd build_unix
../dist/configure
make
sudo make install
  7. Freetype freetype-2.4.10.tar.gz) 
    ./configure  --enable-shared
make
sudo make install
  8. Install FTGL (ftgl-2.1.3-rc5.tar.gz) 
    ./configure
make
sudo make install
  9. Install CMake (cmake-2.8.9-Darwin64-universal.dmg)

  1. Create symlinks to png library (it allows to use png library installed along with X11) 
    sudo ln -s /opt/X11/include/libpng15/*.h /usr/include
sudo ln -s /opt/X11/lib/libpng.dylib /usr/lib

Required Python Modules

  1. Install SIP (sip-4.16.5.tar.gz) 
    python configure.py
make
sudo make install

  2. Install PyQt4 (PyQt-mac-gpl-4.11.3.tar.gz) 

    python ./configure.py --confirm-license -e QtCore -e QtGui -e QtOpenGL -q $HOME/Qt/5.4/clang_64/bin/qmake --verbose
make
sudo make install
  3. Install matplotlib (matplotlib-1.1.1.tar.gz) 
    export CFLAGS="-I/usr/X11R6/include" (it is a bash command)
export LDFLAGS="-L/usr/X11R6/lib/"   (it is a bash command)
python setup.py build
sudo python setup.py install
  4. Install bsddb3 (bsddb3-5.3.0.tar.gz) 
    python setup.py build
sudo python setup.py install
  5. Install PyOpenGL (PyOpenGL-3.0.2b2.tar.gz) 
    python setup.py build
sudo python setup.py install
  6. Install iPython (ipython-1.2.1.tar.gz) 
    python setup.py build
sudo python setup.py install
  7. Replace readline (readline-6.2.2-py2.7-macosx-10.7-intel.egg) 
    sudo easy_install readline-6.2.2-py2.7-macosx-10.7-intel.egg
sudo mv /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/readline.so  /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/readline_disable.so

Optional Dependencies

  1. Install HDF5 (hdf5-1.8.9.tar.gz) 
    ./configure --prefix=/usr/local/
make
sudo make install
  2. Install jpeg (jpegsrc.v8d.tar.gz) 
    ./configure
make
sudo make install
  3. Install tiff (tiff-3.8.2.tar.gz) 
    ./configure
make
sudo make install

Build EMAN2 using CMake

  1. Download and unpack EMAN2 and sparx source code.

    The source code can be found at web page http://ncmi.bcm.edu/ncmi/software/counter_222/software_86, although you might need fill out a registration form. After you get the file (eman2.daily.source.tar.gz), move it to home directory and unpack it: 

    tar -zxvf eman2.daily.source.tar.gz
    which would create directory EMAN2 under your home directory,
  2. Instead of downloading sources, CVS working copy may be used. In this case EMAN2 directory with subdirectories build and src must be created by hand: 
    mkdir ~/EMAN2
mkdir ~/EMAN2/build
mkdir ~/EMAN2/src
    Next, create CVS working copy at ~/EMAN2/src/eman2.
  3. Run CMake in ~/EMAN2/build directory 
    cd ~/EMAN2/build
ccmake ../src/eman2
  4. In ccmake menu do the following steps:
    • press 'c' to configure (some parameters should appear)
    • press 't' to toggle advance mode
    • set parameters: 
      CMAKE_CXX_COMPILER  /usr/bin/g++ 
CMAKE_C_COMPILER      /usr/bin/gcc
    • press 'c' to configure (ccmake will close menu with parameters)
    • the press 'e' to return to menu with parameters
    • set the following parameters: 
      BOOST_INCLUDE_PATH  /usr/local/include/boost 
CMAKE_OSX_ARCHITECTURES  x86_64
CMAKE_OSX_SYSROOT  /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
ENABLE_MOUNTAIN_LION  ON
ENABLE_OPTIMIZE_MACHINE ON
    • press 'c' to configure
    • press 'g' to generate Makefiles
    • press 'q' to exit ccmake
  5. Build EMAN2 
    make
make install

Configure Shell

If you are using the bash shell, add the following lines to your .bash_profile or .bashrc file 

export EMAN2DIR=$HOME/EMAN2
export PATH=${EMAN2DIR}/bin:${PATH}
export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

You have to restart tour terminal after that (or set these variables by hand)

Unit Tests

EMAN2 includes a unit test suite. It will help verify that all components are working correctly. 

cd $EMAN2DIR/test/rt
chmod +x *.py
python ./rt.py

On my Mac 4 unit tests failed, both on Lion and Mountain Lion OS.

SourceCodeInstallation (last edited 2023-07-28 21:31:02 by penczek)