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| Known working versions listed in parentheses. Older versions may or may not work; newer versions (unless noted: iPython, png) are generally fine. Some packages have known issues compiling on Mac OS X, particularly FTGL. Please see the Notes section at the bottom of the page if you encounter errors. __IF you are running on Lion (OSX 10.7) or Mountain Lion (OSX 10.8) you MUST install Xcode 4 from the App store.__ After you do so, try typing "gcc -v", "make" or "import" at the command line. If things aren't working (the previous commands listed are not found), try removing the developer tools (Xcode) "cleanly" and re-installing both Lion and Xcode. To remove Xcode thoroughly, type the following command at the command line: |
For each dependency, a known working versions is listed in parentheses. Older versions may or may not work; newer versions (unless noted: iPython, png) are generally fine. Some packages have known issues compiling on Mac OS X. Please see the Notes section at the bottom of the page if you encounter errors. These instructions have been tested on Mac OS X 10.7 and 10.8, and should also work fine on 10.6. = Required Packages = == Xcode (4.3) == Starting with Mac OS X 10.7 and Xcode 4.3, the developer tools are distributed through the Mac App Store instead of an installer package. If you have upgraded your system from a previous version of Mac OS X and/or a previous version of Xcode, make sure previous versions have been "cleanly" removed. |
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| If after re-installing the commands still aren't found, install the additional "Command Line Tools for Xcode" from Apple: https://developer.apple.com/downloads/index.action __On Mountain Lion, you MUST open Xcode (once you install it), go to PREFERENCES, then DOWNLOADS, and install "Command Line Tools" and "iOS 5.1 Simulator"__ = Required Packages = == Qt4 (4.7) == Qt is a graphics library for cross-platform user interfaces. Suggest installing the Qt SDK binary available here: |
Installing Xcode is a two step process. First, install Xcode from the Mac App Store. Second, open Xcode, and go to "Preferences" then "Downloads". Select "Command Line Tools" and click the "Install" button to the right. Wait for this to complete. == Qt4 (4.8) == Qt is a graphics library for cross-platform user interfaces. I recommend using the binary installer for the Qt libraries here: |
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| Qt4 is much easier to install using their binary package. You will want the "Mac OS X 10.6 or later 64-bit" which includes a GUI-based installer inside the disk image. IF the binary fails to install properly (as it can happen in Lion, OSX 10.7.3), try building from source. First, remove the old or binary version of Qt "cleanly" by typing the following command at the command line: {{{ sudo /Developer/Tools/uninstall-qt.py }}} If this doesn't work to remove Qt, try the following: {{{ 1. sudo QtSDK/SDKMaintenanceTool.app/Contents/MacOS/SDKMaintenanceTool 2. The tool’s dialog window will show up. in the dialog window select “Remove all components”, continue and uninstall the SDK. 3. By comparing the filesystem before and after the uninstall, this uninstallation only removed the QtSDK directory. 4. When reinstall, make sure to check the box “remove the old Qt Creator’s setting” in the installation interface. }}} Then download the source code qt-everywhere-opensource-src-4.8.0.tar.gz, from here: http://qt.nokia.com/downloads/qt-for-open-source-cpp-development-on-mac-os-x/ untar the tar.gz file you just downloaded by typing {{{ tar xvzf qt-everywhere-opensource-src-4.8.0.tar.gz }}} Go to the folder where the source file were uncompressed (it has the same name as the tar.gz file but without the ending) Compile Qt4 by running: {{{ ./configure make sudo make install }}} == boost (1.47) == |
You will want the "Qt libraries 4.8.3 for Mac" which includes a GUI-based installer inside the disk image. '''Note:''' If there is an error that the installer cannot be opened because it is from an "unidentified developer", control-click on the installer package and select "Open" to override the system's security settings. == boost (1.51) == |
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| http://sourceforge.net/projects/boost/files/boost/1.47.0 boost_1_47_0.tar.gz |
http://sourceforge.net/projects/boost/files/boost/1.51.0/ boost_1_51_0.tar.gz |
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| ./configure --disable-dependency-tracking --disable-static --enable-shared | ./configure --disable-static --enable-shared |
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| ./configure --disable-dependency-tracking --enable-shared --enable-float make sudo make install }}} == XQuartz (2.7.3) == To install Berkely DB (following dependency, below), you will need FreeType, which is part of X11. X11 is NOT included in MOUNTAIN LION; therefore, you must get it yourself from here: (Download the .dmg binary). http://xquartz.macosforge.org/landing/ == Berkeley DB (5.2) == |
./configure --enable-shared --enable-float make sudo make install }}} == Berkeley DB (5.3) == |
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| Berkeley DB 5.2.28.NC.tar.gz | Berkeley DB 5.3.21.NC.tar.gz |
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| == Freetype2 (2.4) == On Mac OS X 10.8 and later, X11 and Freetype are no longer included by default. Even if you are using an earlier Mac OS X, I recommend installing your own Freetype. http://download.savannah.gnu.org/releases/freetype/ freetype-2.4.10.tar.gz {{{ ./configure --enable-shared make sudo make install }}} '''Important Note''': There is an issue with the Freetype headers, resulting in errors about a missing "freetype/config/ftheader.h". To correct this, make the following link if you installed your own Freetype: {{{ sudo ln -s /usr/local/include/freetype2/freetype /usr/local/include/freetype }}} If you are using the system's Freetype, make an analogous link in the SDK package, e.g.: {{{ ln -s /Developer/SDKs/MacOSX10.7.sdk/usr/X11/include/freetype2/freetype /Developer/SDKs/MacOSX10.7.sdk/usr/X11/include/freetype }}} |
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| Please see the [[#FreeType2_Issues|compilation notes]] before proceeding. You will need to adjust the FreeType2 configuration. {{{ ./configure --disable-dependency-tracking --enable-shared --enable-float |
{{{ ./configure --enable-shared |
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| If you installed the Qt SDK version 1.2.1 binary, then you will need to use something like this (depending on where you installed the binary, change 'username'): {{{ python ./configure.py --confirm-license -e QtCore -e QtGui -e QtOpenGL -q /Users/username/QtSDK/Desktop/Qt/4.8.1/gcc/bin/qmake make sudo make install }}} |
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| == matplotlib (1.0) == Matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments. ''Note: On Mountain Lion, you should first make sure you have X11 installed on your machine (optional install on 10.8, was included automatically on 10.6 and 10.7). Then (if you don't mind making these links): {{{ ln -s /opt/X11/include/freetype2/freetype /usr/include ln -s /opt/X11/include/libpng15/*.h /usr/include ln -s /opt/X11/lib/libpng.dylib /usr/lib }}}'' You should then be able to: {{{ sudo easy_install matplotlib }}} If that fails, or if you prefer not to make symbolic links into /usr/include, you may need to get the source and install yourself. http://matplotlib.sourceforge.net matplotlib-1.0.0.tar.gz matplotlib is quite obstinate in their build configuration for OS X -- libpng, libz, freetype2, etc. are included in 10.6, but setup.py does not find the freetype2 installation. Set the CFLAGS and LDFLAGS environment variables to use the included freetype2: {{{ export CFLAGS="-I/usr/X11R6/include -I/usr/X11R6/include/freetype2/" export LDFLAGS="-L/usr/X11R6/lib/" }}} Then proceed to build using the standard procedure for distutils-based Python packages: |
If you receive an error about "unable to find qmake" or similar during configure, locate the qmake tool (e.g., /usr/bin/qmake-4.8, $HOME/QtSDK/Desktop/Qt/4.8.1/gcc/bin/qmake, etc) and provide the path using the "-q" option, e.g.: {{{ python ./configure.py --confirm-license -e QtCore -e QtGui -e QtOpenGL -q $HOME/QtSDK/Desktop/Qt/4.8.1/gcc/bin/qmake }}} == bsddb3 (5.3) == bsddb3 provides Python bindings for the Berkeley DB API. http://pypi.python.org/pypi/bsddb3/ bsddb3-5.3.0.tar.gz bsddb3 can be installed using easy_install ("sudo easy_install bsddb3"), or compiled and installed from the source distribution. |
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| == bsddb3 (5.0) == bsddb3 provides Python bindings for the Berkeley DB API. http://pypi.python.org/pypi/bsddb3/ bsddb3-5.2.0.tar.gz bsddb3 can be installed using easy_install ("sudo easy_install bsddb3"), or compiled and installed from the source distribution. {{{ python setup.py build --berkeley-db=/usr/local/BerkeleyDB.5.2 sudo python setup.py install }}} Note: you may encounter similar problem as in matplotlib, follow the same solution in matplotlib. |
'''Note''': You may need need to provide the path to where Berkeley DB is installed, using the --berkeley-db option: {{{ python setup.py build --berkeley-db=/usr/local/BerkeleyDB.5.3 }}} |
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| == readline == Readline is a module that provides command-line editing in iPython. ie - it allows you to use up and down arrows to look at previous commands, and a variety of other useful functions. OSX ships with a readline module. However, this module is not the official readline module, but a ''mostly'' compatible one with more liberal licensing. The ''mostly'' is the problem, and this library causes all sorts of problems with command-line editing in ipython (not just for EMAN2) ! Installing the official readline module is trivial, just 'easy_install readline'. However, what is less obvious is that you also need to disable the OSX provided readline, or it will be used in preference to the one you install. To do this under 10.7, for example: ''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'' |
== matplotlib (1.1) == Matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments. http://matplotlib.sourceforge.net matplotlib-1.1.1.tar.gz '''Note''': Earlier versions of matplotlib have known difficulties compiling easily on Mac OS X; use 1.1 or higher. '''Note''': If you want PNG image format support, make sure to install libpng as described below first. Otherwise, matplotlib installs the same way as other distutils-based packages: {{{ python setup.py build sudo python setup.py install }}} |
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| These packages are optional, and provide support for additional file formats (tiff, hdf5, png, jpeg.) If you skip these packages, you will need to adjust your EMAN2 cmake configuration (see below.) | These packages are optional, and provide support for additional file formats (tiff, hdf5, png, jpeg). If you skip these packages, you will need to adjust your EMAN2 cmake configuration. I recommend installing all of them. |
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| ./configure --disable-dependency-tracking --disable-static --enable-shared | ./configure --enable-shared make sudo make install }}} == jpeg (8c) == Library for writing JPEG image files. JPEG used to be difficult to compile on OS X, but it has been improved recently and should compile without problems. http://www.ijg.org/files jpegsrc.v8c.tar.gz {{{ ./configure --enable-shared make sudo make install }}} '''Note''': if you disable JPEG support in the cmake file you must also disable TIFF support. == tiff (3.8) == Library for reading and writing TIFF image files. http://dl.maptools.org/dl/libtiff tiff-3.8.2.tar.gz {{{ ./configure --enable-shared |
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| ./configure --disable-dependency-tracking --disable-static --enable-shared make sudo make install }}} == jpeg (8c) == Library for writing JPEG image files. JPEG used to be difficult to compile on OS X, but it has been improved recently and should compile without problems. http://www.ijg.org/files jpegsrc.v8c.tar.gz {{{ ./configure --disable-dependency-tracking --disable-static --enable-shared make sudo make install }}} Note: if you disable JPEG support in the cmake file you must also disable TIFF support. == tiff (3.8) == Library for reading and writing TIFF image files. http://dl.maptools.org/dl/libtiff tiff-3.8.2.tar.gz {{{ ./configure --disable-dependency-tracking --disable-static --enable-shared make sudo make install }}} = Build EMAN2 using cmake = First, you have to DOWNLOAD EMAN2's source code. To do so using CVS ("version control system"), a program that should already be on your Mac by default and that lets you easily download, manage and update open source software (free software), you have to set up the CVSROOT environment variable. Do so by adding a line like the following to your .bashrc file (your .bashrc is an invisible text file that should be in your home directory). export CVSROOT=<username_at_server>@<server_address>:<path_to_CVS> For example: export CVSROOT=jgalaz @ grid.blake.bcm.edu:/usr/local/CVS/CVS Then, "source" your .bashrc file by typing the following at the command line: {{{ source .bashrc }}} Create a folder where you will have eman2's source code. For example: {{{ mkdir ~/EMAN2/src/ }}} Go to it, (cd ~/EMAN2/src/), and once you're there download the source code: {{{ cvs co eman2 }}} This should have created an 'eman2' folder inside /EMAN2/src/. Create a separate folder from which you will "build" eman2, and go to it. For example: {{{ mkdir ~/EMAN2/build/ && cd /EMAN2/build/ }}} Once you're in the build directory, run ccmake with the EMAN2 source directory as the argument. {{{ ccmake ../src/eman2 }}} Press "c" to do an initial configuration. For Mac OS X 10.7, Use default options except those below. You may need to enter advanced mode ('t' key) to set some. Note: set EMAN_INSTALL_PREFIX to your home directory, or /usr/local/EMAN, or similar. When done, press "c" again, then "g" to generate Makefiles. {{{ BOOST_INCLUDE_PATH /usr/local/include/boost BOOST_LIBRARY /usr/local/lib/libboost_python.dylib CMAKE_OSX_SYSROOT /Developer/SDKs/MacOSX10.7.sdk CMAKE_VERBOSE_MAKEFILE ON EMAN_INSTALL_PREFIX /Users/irees/EMAN2 ENABLE_LEOPARD ON ENABLE_OPENGL ON FFTW3_INCLUDE_PATH /usr/local/include FFTW3_LIBRARY /usr/local/lib/libfftw3f.dylib FREETYPE_INCLUDE_PATH /usr/X11R6/include FREETYPE_LIBRARY /usr/X11R6/lib/libfreetype.dylib FTGL_INCLUDE_PATH /usr/local/include FTGL_LIBRARY /usr/local/lib/libftgl.dylib GLU_INCLUDE_PATH /Developer/SDKs/MacOSX10.7.sdk/usr/X11/include GLU_LIBRARY /Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib GL_INCLUDE_PATH /Developer/SDKs/MacOSX10.7.sdk/usr/X11/include GL_LIBRARY /Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib GSL_CBLAS_INCLUDE_PATH /usr/local/include GSL_CBLAS_LIBRARY /usr/local/lib/libgslcblas.dylib GSL_INCLUDE_PATH /usr/local/include GSL_LIBRARY /usr/local/lib/libgsl.dylib HDF5_INCLUDE_PATH /usr/local/include HDF5_LIBRARY /usr/local/lib/libhdf5.dylib JPEG_INCLUDE_PATH /usr/local/include JPEG_LIBRARY /usr/local/lib/libjpeg.dylib NUMPY_INCLUDE_PATH /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include PNG_INCLUDE_PATH /usr/local/include PNG_LIBRARY /usr/local/lib/libpng.dylib PYTHON_INCLUDE_PATH /Developer/SDKs/MacOSX10.7.sdk/System/Library/Frameworks/Python.framework/Versions/2.7/Headers PYTHON_LIBRARY /Developer/SDKs/MacOSX10.7.sdk/usr/lib/libpython.dylib TIFF_INCLUDE_PATH /usr/local/include TIFF_LIBRARY /usr/local/lib/libtiff.dylib ZLIB_LIBRARY /Developer/SDKs/MacOSX10.7.sdk/usr/lib/libz.dylib }}} If you are using Mac OS X 10.6, you will use basically the same configuration. Use "MacOSX10.6.sdk" where applicable, and the Python version will be 2.6 instead of 2.7. Additionally, you can link against the SDK-provided libpng instead of your own version. Compile in the build directory and install by typing the following at the command line: |
./configure --enable-shared --prefix=/usr/local make sudo make install }}} '''Note''': Curiously, HDF5 does not use /usr/local as the default installation prefix. Make sure to include the --prefix option above. == readline == Readline is a module that provides command-line editing in iPython. ie - it allows you to use up and down arrows to look at previous commands, and a variety of other useful functions. OSX ships with a readline module. However, this module is not the official readline module, but a ''mostly'' compatible one with more liberal licensing. The ''mostly'' is the problem, and this library causes all sorts of problems with command-line editing in ipython (not just for EMAN2)! Installing the official readline module is trivial, just 'easy_install readline'. However, what is less obvious is that you also need to disable the OSX provided readline, or it will be used in preference to the one you install. To do this under 10.7, for example: ''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'' = Configure EMAN2 = First, create a build directory for EMAN2. I generally keep the EMAN2 source CVS working directory in $HOME/src/eman2, and use $HOME/src/eman2build as my build directory. Go to your build directory, and run ccmake with the EMAN2 source directory as the argument: {{{ ccmake $HOME/src/eman2 }}} Press "c" to do an initial configuration. If you have followed the instructions above, all of the library and include paths should automatically be set correctly. Review the options, including EMAN_INSTALL_PREFIX which is the installation directory. When done, press "c" again, then "g" to generate Makefiles. The following is my configuration on Mac OS X 10.8: {{{ BOOST_INCLUDE_PATH /usr/local/include BOOST_LIBRARY /usr/local/lib/libboost_python.dylib CMAKE_OSX_ARCHITECTURES CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk CMAKE_VERBOSE_MAKEFILE OFF EMAN_INSTALL_PREFIX /Volumes/irees/EMAN2 ENABLE_ATHLON OFF ENABLE_AUTODOC OFF ENABLE_BOUNDS_CHECKING OFF ENABLE_DEBUG OFF ENABLE_EMAN_CUDA OFF ENABLE_FFTW2 OFF ENABLE_FFTW3 ON ENABLE_FFTW_PLAN_CACHING ON ENABLE_FTGL ON ENABLE_HDF5 ON ENABLE_HDFIOCACHE OFF ENABLE_IOCACHE OFF ENABLE_JPEG ON ENABLE_LEOPARD OFF ENABLE_MEMDEBUG OFF ENABLE_MEMDEBUG2 OFF ENABLE_MOUNTAIN_LION ON ENABLE_NATIVE_FFT OFF ENABLE_NFFT2 OFF ENABLE_OPENGL ON ENABLE_OPTPP OFF ENABLE_PNG ON ENABLE_PROFILE OFF ENABLE_RT ON ENABLE_SPARX_CUDA OFF ENABLE_TIFF ON ENABLE_V4L2 OFF ENABLE_WINDOWS_VC OFF ENABLE_X86_64 ON FFTW3_INCLUDE_PATH /usr/local/include FFTW3_LIBRARY /usr/local/lib/libfftw3f.dylib FREETYPE_INCLUDE_PATH /usr/local/include FREETYPE_LIBRARY /usr/local/lib/libfreetype.dylib FTGL_INCLUDE_PATH /usr/local/include FTGL_LIBRARY /usr/local/lib/libftgl.dylib GLU_INCLUDE_PATH /usr/local GLU_LIBRARY /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib GL_INCLUDE_PATH /usr/local GL_LIBRARY /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib GSL_CBLAS_INCLUDE_PATH /usr/local/include GSL_CBLAS_LIBRARY /usr/local/lib/libgslcblas.dylib GSL_INCLUDE_PATH /usr/local/include GSL_LIBRARY /usr/local/lib/libgsl.dylib HDF5_INCLUDE_PATH /usr/local/include HDF5_LIBRARY /usr/local/lib/libhdf5.dylib JPEG_INCLUDE_PATH /usr/local/include JPEG_LIBRARY /usr/local/lib/libjpeg.dylib NUMPY_INCLUDE_PATH /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include PNG_INCLUDE_PATH /usr/local/include PNG_LIBRARY /usr/local/lib/libpng.dylib PYTHON_INCLUDE_PATH /System/Library/Frameworks/Python.framework/Headers PYTHON_LIBRARY /usr/lib/libpython2.7.dylib TIFF_INCLUDE_PATH /usr/local/include TIFF_LIBRARY /usr/local/lib/libtiff.dylib ZLIB_LIBRARY /usr/lib/libz.dylib }}} Configurations for 10.6 and 10.7 will be basically equivalent, except for version-specific options like ENABLE_MOUNTAIN_LION, and the CMAKE_OSX_SYSROOT option: For 10.6, it should be: /Developer/SDKs/MacOSX10.6.sdk For 10.7, it will be either /Developer/SDKs/MacOSX10.7.sdk or /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk if you are using Xcode 4.3 or higher. For convenience, some people like to link /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs to /Developer/SDKs for shorter, more manageable paths. = Build EMAN2 = Compile in the build directory and install: |
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| The default installation directory (EMAN2_INSTALL_PREFIX) is $HOME/EMAN2. |
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| export EMAN2DIR=$HOME/EMAN2 | export EMAN2DIR=${HOME}/EMAN2 |
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| 1. IF you follow these instructions and get a segfault when running some of the GUI programs, you probably did not fully read the section on CCMAKE parameters. Pay special attention to the GL and GLU libraries 2. IF you have EMAN2 binaries installed, move them out of the way BEFORE trying to build from source. Conflicts with library versions might arise otherwise. 3. IF you have attempted to build EMAN2 from source before, SOME of the new builds for some dependencies WILL NOT REPLACE THE OLD LIBRARIES. You might want to DELETE or MOVE the OLD LIBRARIES in the /usr/local/lib/ directory. Alternatively, link to wherever the new .dylib files are generated. == FreeType2 Issues == Most programs will look for FreeType2 in /usr/X11/include; however, they're generally installed in /usr/X11/include/freetype2/freetype on OS X. The simplest way to resolve missing FreeType headers (e.g. ft2build.h) is to use a symlink: {{{ sudo ln -s /usr/X11/include/freetype2/freetype/ /usr/X11/include/freetype }}} FreeType2 also expects the "freetype-config" command to be in your $PATH. To do this, add /usr/X11/bin. {{{ export PATH=$PATH:/usr/X11/bin }}} == Matplotlib Issues == === libpng API === The current release (1.0.1) has the same problem with libpng 1.5 deprecated APIs that EMAN2 does. The fix is available in their source repository. So, instead of the latest release, I downloaded a nightly source archive. === FreeType2 === Again, FreeType2 configuration may need some tweaking. You will need to tweak $CFLAGS and $LDFLAGS. I used the following values on 10.7: {{{ export PATH=$PATH:/usr/X11/bin export CFLAGS="$CFLAGS -I/Developer/SDKs/MacOSX10.7.sdk/usr/X11/include" export LDFLAGS="$LDFLAGS -L/Developer/SDKs/MacOSX10.7.sdk/usr/X11/lib" }}} |
1. If you follow these instructions and get a segfault when running some of the GUI programs, you probably did not fully read the section on ccmake parameters. Pay special attention to the GL and GLU libraries 2. If you have EMAN2 binaries installed, move them out of the way BEFORE trying to build from source. Conflicts with library versions might arise otherwise. 3. If you have attempted to build EMAN2 from source before, SOME of the new builds for some dependencies WILL NOT REPLACE THE OLD LIBRARIES. You might want to DELETE or MOVE the OLD LIBRARIES in the /usr/local/lib/ directory. Alternatively, link to wherever the new .dylib files are generated. |
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| If you see this compilation error: | PowerPC is no longer actively maintained, and might not build. If you see this compilation error: |
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| }}} == Freetype Issues == If a package cannot find the Freetype header files, you will need to make a symlink to the correct locations. Please see the Freetype section in required dependencies. == Qt4 Issues == If the binary fails to install properly, try running the Qt uninstaller. {{{ sudo /Developer/Tools/uninstall-qt.py }}} If this doesn't work to remove Qt, try the following: {{{ 1. sudo QtSDK/SDKMaintenanceTool.app/Contents/MacOS/SDKMaintenanceTool 2. The tool’s dialog window will show up. in the dialog window select “Remove all components”, continue and uninstall the SDK. 3. By comparing the filesystem before and after the uninstall, this uninstallation only removed the QtSDK directory. 4. When reinstall, make sure to check the box “remove the old Qt Creator’s setting” in the installation interface. |
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Compiling EMAN2 on Mac OS X
Contents
- Compiling EMAN2 on Mac OS X
- Required Packages
- Required Packages (Python Modules)
- Optional Dependencies
- Configure EMAN2
- Configure Shell
- Unit Tests
- Common Problems
It is recommended to install or build all dependency packages directly, instead of using a package manager such as Fink or MacPorts. We will also link against the Python environment included with Mac OS X.
For each dependency, a known working versions is listed in parentheses. Older versions may or may not work; newer versions (unless noted: iPython, png) are generally fine.
Some packages have known issues compiling on Mac OS X. Please see the Notes section at the bottom of the page if you encounter errors.
These instructions have been tested on Mac OS X 10.7 and 10.8, and should also work fine on 10.6.
Required Packages
Xcode (4.3)
Starting with Mac OS X 10.7 and Xcode 4.3, the developer tools are distributed through the Mac App Store instead of an installer package.
If you have upgraded your system from a previous version of Mac OS X and/or a previous version of Xcode, make sure previous versions have been "cleanly" removed.
sudo /Developer/Library/uninstall-devtools --mode=all
Installing Xcode is a two step process. First, install Xcode from the Mac App Store. Second, open Xcode, and go to "Preferences" then "Downloads". Select "Command Line Tools" and click the "Install" button to the right. Wait for this to complete.
Qt4 (4.8)
Qt is a graphics library for cross-platform user interfaces. I recommend using the binary installer for the Qt libraries here:
http://qt-project.org/downloads
You will want the "Qt libraries 4.8.3 for Mac" which includes a GUI-based installer inside the disk image.
Note: If there is an error that the installer cannot be opened because it is from an "unidentified developer", control-click on the installer package and select "Open" to override the system's security settings.
boost (1.51)
Boost is a set of useful, standardized libraries for C++. It is used to generate the Python-C++ interface in EMAN2.
http://sourceforge.net/projects/boost/files/boost/1.51.0/
boost_1_51_0.tar.gz
./bootstrap.sh --with-libraries=python ./bjam sudo ./bjam install
gsl (1.15)
The GNU Scientific Library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
http://mirrors.kernel.org/gnu/gsl
gsl-1.15.tar.gz
./configure --disable-static --enable-shared make sudo make install
fftw3 (3.2)
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
http://www.fftw.org/download.html
fftw-3.2.2.tar.gz
./configure --enable-shared --enable-float make sudo make install
Berkeley DB (5.3)
The Oracle Berkeley DB family of open source, embeddable databases provides developers with fast, reliable, local persistence with zero administration. EMAN2 uses Berkeley DB as a mechanism for local storage of project metadata.
http://www.oracle.com/technology/software/products/berkeley-db/index.html
Berkeley DB 5.3.21.NC.tar.gz
cd build_unix ../dist/configure make sudo make install
Freetype2 (2.4)
On Mac OS X 10.8 and later, X11 and Freetype are no longer included by default. Even if you are using an earlier Mac OS X, I recommend installing your own Freetype.
http://download.savannah.gnu.org/releases/freetype/
freetype-2.4.10.tar.gz
./configure --enable-shared make sudo make install
Important Note: There is an issue with the Freetype headers, resulting in errors about a missing "freetype/config/ftheader.h". To correct this, make the following link if you installed your own Freetype:
sudo ln -s /usr/local/include/freetype2/freetype /usr/local/include/freetype
If you are using the system's Freetype, make an analogous link in the SDK package, e.g.:
ln -s /Developer/SDKs/MacOSX10.7.sdk/usr/X11/include/freetype2/freetype /Developer/SDKs/MacOSX10.7.sdk/usr/X11/include/freetype
ftgl (2.1)
FTGL is a free, open source library to enable developers to use arbitrary fonts in their OpenGL applications.
http://sourceforge.net/projects/ftgl
ftgl-2.1.2.tar.gz
./configure --enable-shared make sudo make install
cmake (2.8)
CMake is a family of tools designed to build, test and package software. It is used to generate the Makefiles for compiling EMAN2.
http://www.cmake.org/cmake/resources/software.html
cmake-2.8.5.tar.gz
You may use the CMake binary installer package, or compile from source.
./configure make sudo make install
Required Packages (Python Modules)
sip (4.12)
SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. It was originally developed to create PyQt, the Python bindings for the Qt toolkit, but can be used to create bindings for any C or C++ library.
http://www.riverbankcomputing.co.uk/software/sip/download
sip-4.12.4.tar.gz
python configure.py make sudo make install
PyQt4 (4.8)
PyQt4 provides Python bindings for Qt4.
http://www.riverbankcomputing.co.uk/software/pyqt/download
PyQt-mac-gpl-4.8.5.tar.gz
If you have compiled from source:
python ./configure.py --confirm-license -e QtCore -e QtGui -e QtOpenGL make sudo make install
If you receive an error about "unable to find qmake" or similar during configure, locate the qmake tool (e.g., /usr/bin/qmake-4.8, $HOME/QtSDK/Desktop/Qt/4.8.1/gcc/bin/qmake, etc) and provide the path using the "-q" option, e.g.:
python ./configure.py --confirm-license -e QtCore -e QtGui -e QtOpenGL -q $HOME/QtSDK/Desktop/Qt/4.8.1/gcc/bin/qmake
bsddb3 (5.3)
bsddb3 provides Python bindings for the Berkeley DB API.
http://pypi.python.org/pypi/bsddb3/
bsddb3-5.3.0.tar.gz
bsddb3 can be installed using easy_install ("sudo easy_install bsddb3"), or compiled and installed from the source distribution.
python setup.py build sudo python setup.py install
Note: You may need need to provide the path to where Berkeley DB is installed, using the --berkeley-db option:
python setup.py build --berkeley-db=/usr/local/BerkeleyDB.5.3
PyOpenGL (3.0)
PyOpenGL provides Python bindings for OpenGL.
http://pyopengl.sourceforge.net
PyOpenGL-3.0.1.tar.gz
PyOpenGL can be installed using easy_install ("sudo easy_install PyOpenGL"), or installed from the source distribution.
python setup.py build sudo python setup.py install
iPython (0.10)
IPython provides a rich toolkit to help you make the most out of using Python interactively. EMAN2 uses iPython for the "e2.py" interactive interpreter environment.
Please note that iPython versions 0.11 and NEWER are currently NOT supported. The developers refactored parts of the API without providing any backwards compatibilty. We are currently updating EMAN2 to use the new API, at which point I will remove this warning. In the interim, please use iPython version 0.10. You will need to download it yourself instead of relying on easy_install.
http://archive.ipython.org/release/0.10.2
ipython-0.10.2.tar.gz
python setup.py build sudo python setup.py install
matplotlib (1.1)
Matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments.
http://matplotlib.sourceforge.net
matplotlib-1.1.1.tar.gz
Note: Earlier versions of matplotlib have known difficulties compiling easily on Mac OS X; use 1.1 or higher.
Note: If you want PNG image format support, make sure to install libpng as described below first.
Otherwise, matplotlib installs the same way as other distutils-based packages:
python setup.py build sudo python setup.py install
Optional Dependencies
These packages are optional, and provide support for additional file formats (tiff, hdf5, png, jpeg). If you skip these packages, you will need to adjust your EMAN2 cmake configuration. I recommend installing all of them.
png (1.2)
The PNG (Portal Network Graphics) format provides lossless-compressed image support. Mac OS X 10.7 Lion ships with libpng 1.5, in which some deprecated features in the PNG API were removed. EMAN2 is being updated to use these new methods. For now, use libpng 1.2 if you are compiling on 10.7.
http://sourceforge.net/projects/libpng/files/libpng12/1.2.46/ libpng-1.2.46.tar.gz
./configure --enable-shared make sudo make install
jpeg (8c)
Library for writing JPEG image files. JPEG used to be difficult to compile on OS X, but it has been improved recently and should compile without problems.
jpegsrc.v8c.tar.gz
./configure --enable-shared make sudo make install
Note: if you disable JPEG support in the cmake file you must also disable TIFF support.
tiff (3.8)
Library for reading and writing TIFF image files.
http://dl.maptools.org/dl/libtiff
tiff-3.8.2.tar.gz
./configure --enable-shared make sudo make install
hdf5 (1.8)
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
http://www.hdfgroup.org/ftp/HDF5/current/src/
hdf5-1.8.5.tar.gz
./configure --enable-shared --prefix=/usr/local make sudo make install
Note: Curiously, HDF5 does not use /usr/local as the default installation prefix. Make sure to include the --prefix option above.
readline
Readline is a module that provides command-line editing in iPython. ie - it allows you to use up and down arrows to look at previous commands, and a variety of other useful functions. OSX ships with a readline module. However, this module is not the official readline module, but a mostly compatible one with more liberal licensing. The mostly is the problem, and this library causes all sorts of problems with command-line editing in ipython (not just for EMAN2)!
Installing the official readline module is trivial, just 'easy_install readline'. However, what is less obvious is that you also need to disable the OSX provided readline, or it will be used in preference to the one you install. To do this under 10.7, for example: 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
Configure EMAN2
First, create a build directory for EMAN2. I generally keep the EMAN2 source CVS working directory in $HOME/src/eman2, and use $HOME/src/eman2build as my build directory.
Go to your build directory, and run ccmake with the EMAN2 source directory as the argument:
ccmake $HOME/src/eman2
Press "c" to do an initial configuration. If you have followed the instructions above, all of the library and include paths should automatically be set correctly. Review the options, including EMAN_INSTALL_PREFIX which is the installation directory. When done, press "c" again, then "g" to generate Makefiles.
The following is my configuration on Mac OS X 10.8:
BOOST_INCLUDE_PATH /usr/local/include BOOST_LIBRARY /usr/local/lib/libboost_python.dylib CMAKE_OSX_ARCHITECTURES CMAKE_OSX_SYSROOT /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk CMAKE_VERBOSE_MAKEFILE OFF EMAN_INSTALL_PREFIX /Volumes/irees/EMAN2 ENABLE_ATHLON OFF ENABLE_AUTODOC OFF ENABLE_BOUNDS_CHECKING OFF ENABLE_DEBUG OFF ENABLE_EMAN_CUDA OFF ENABLE_FFTW2 OFF ENABLE_FFTW3 ON ENABLE_FFTW_PLAN_CACHING ON ENABLE_FTGL ON ENABLE_HDF5 ON ENABLE_HDFIOCACHE OFF ENABLE_IOCACHE OFF ENABLE_JPEG ON ENABLE_LEOPARD OFF ENABLE_MEMDEBUG OFF ENABLE_MEMDEBUG2 OFF ENABLE_MOUNTAIN_LION ON ENABLE_NATIVE_FFT OFF ENABLE_NFFT2 OFF ENABLE_OPENGL ON ENABLE_OPTPP OFF ENABLE_PNG ON ENABLE_PROFILE OFF ENABLE_RT ON ENABLE_SPARX_CUDA OFF ENABLE_TIFF ON ENABLE_V4L2 OFF ENABLE_WINDOWS_VC OFF ENABLE_X86_64 ON FFTW3_INCLUDE_PATH /usr/local/include FFTW3_LIBRARY /usr/local/lib/libfftw3f.dylib FREETYPE_INCLUDE_PATH /usr/local/include FREETYPE_LIBRARY /usr/local/lib/libfreetype.dylib FTGL_INCLUDE_PATH /usr/local/include FTGL_LIBRARY /usr/local/lib/libftgl.dylib GLU_INCLUDE_PATH /usr/local GLU_LIBRARY /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib GL_INCLUDE_PATH /usr/local GL_LIBRARY /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib GSL_CBLAS_INCLUDE_PATH /usr/local/include GSL_CBLAS_LIBRARY /usr/local/lib/libgslcblas.dylib GSL_INCLUDE_PATH /usr/local/include GSL_LIBRARY /usr/local/lib/libgsl.dylib HDF5_INCLUDE_PATH /usr/local/include HDF5_LIBRARY /usr/local/lib/libhdf5.dylib JPEG_INCLUDE_PATH /usr/local/include JPEG_LIBRARY /usr/local/lib/libjpeg.dylib NUMPY_INCLUDE_PATH /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include PNG_INCLUDE_PATH /usr/local/include PNG_LIBRARY /usr/local/lib/libpng.dylib PYTHON_INCLUDE_PATH /System/Library/Frameworks/Python.framework/Headers PYTHON_LIBRARY /usr/lib/libpython2.7.dylib TIFF_INCLUDE_PATH /usr/local/include TIFF_LIBRARY /usr/local/lib/libtiff.dylib ZLIB_LIBRARY /usr/lib/libz.dylib
Configurations for 10.6 and 10.7 will be basically equivalent, except for version-specific options like ENABLE_MOUNTAIN_LION, and the CMAKE_OSX_SYSROOT option:
For 10.6, it should be: /Developer/SDKs/MacOSX10.6.sdk
For 10.7, it will be either /Developer/SDKs/MacOSX10.7.sdk or /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk if you are using Xcode 4.3 or higher.
For convenience, some people like to link /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs to /Developer/SDKs for shorter, more manageable paths.
= Build EMAN2 =
Compile in the build directory and install:
make make install
The default installation directory (EMAN2_INSTALL_PREFIX) is $HOME/EMAN2.
Configure Shell
If you are using the bash shell, add the following lines to your .bashrc file
export EMAN2DIR=${HOME}/EMAN2
export PATH=${EMAN2DIR}/bin:${PATH}
export PYTHONPATH=${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}Note: If you installed EMAN2 in someplace other than $HOME/EMAN2 (the EMAN_INSTALl_PREFIX in cmake above), place the correct path in this variable.
Then on the command line type bash or source ~/.bashrc. To test if EMAN2 is working properly, see if you can run e2.py. You should be greeted with some version information, then an ">>>" interactive interpreter prompt.
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
Common Problems
General Issues
1. If you follow these instructions and get a segfault when running some of the GUI programs, you probably did not fully read the section on ccmake parameters. Pay special attention to the GL and GLU libraries
2. If you have EMAN2 binaries installed, move them out of the way BEFORE trying to build from source. Conflicts with library versions might arise otherwise.
3. If you have attempted to build EMAN2 from source before, SOME of the new builds for some dependencies WILL NOT REPLACE THE OLD LIBRARIES. You might want to DELETE or MOVE the OLD LIBRARIES in the /usr/local/lib/ directory. Alternatively, link to wherever the new .dylib files are generated.
Unsupported PowerPC
PowerPC is no longer actively maintained, and might not build. If you see this compilation error:
/usr/libexec/gcc/powerpc-apple-darwin10/4.2.1/as: assembler (/usr/bin/../libexec/gcc/darwin/ppc/as or /usr/bin/../local/libexec/gcc/darwin/ppc/as) for architecture ppc not installed Installed assemblers are: /usr/bin/../libexec/gcc/darwin/x86_64/as for architecture x86_64 /usr/bin/../libexec/gcc/darwin/i386/as for architecture i386 Modules/_bsddb.c:10059: fatal error: error writing to -: Broken pipe
You need set gcc's ARCHFLAGS before compilation:
export ARCHFLAGS="-arch i386 -arch x86_64"
Freetype Issues
If a package cannot find the Freetype header files, you will need to make a symlink to the correct locations. Please see the Freetype section in required dependencies.
Qt4 Issues
If the binary fails to install properly, try running the Qt uninstaller.
sudo /Developer/Tools/uninstall-qt.py
If this doesn't work to remove Qt, try the following:
1. sudo QtSDK/SDKMaintenanceTool.app/Contents/MacOS/SDKMaintenanceTool 2. The tool’s dialog window will show up. in the dialog window select “Remove all components”, continue and uninstall the SDK. 3. By comparing the filesystem before and after the uninstall, this uninstallation only removed the QtSDK directory. 4. When reinstall, make sure to check the box “remove the old Qt Creator’s setting” in the installation interface.
PyQt4 Issues
_sipQtConnect
With some newer versions of PyQt4 (for example, 4.8), but earlier than 4.8.3, this error MIGHT occur:
'ImportError: dlopen(/Library/Python/2.6/site-packages/PyQt4/QtCore.so, 2): Symbol not found: _sipQtConnect'
The way to fix it requires to REMOVE your dysfunctional build of PyQt, untar the clean files again, and modify the configure.py file as follows: Look for these lines:
for a in sipcfg.arch.split():
- if a == 'i386':
- qmake_archs.append('x86')
- qmake_archs.append('x86_64')
- qmake_archs.append('ppc')
And CHANGE the 'x86' in the third line for 'x86_64'. Then REBUILD. This appears to take care of the problem.
Broken Macro
Some people who have compiled Qt themselves have reported an error like this:
/usr/include/c++/4.2.1/bits/localefwd.h:58:34: error: macro "isspace" passed 2 arguments, but takes just 1
I haven't sorted out the cause of the problem, but one workaround that seemed to work was editing the offending C++ file (in our case, qpy/QtOpenGL/qpyopengl_attribute_array.cpp), and adding a #include <Python.h> directive as the first line, so the beginning of the file is:
#include <Python.h> #include <QtGlobal>
RuntimeError unidentifiable C++ exception
Problem: When I try to run an eman2 python program I can get a RuntimeError unidentifiable C++ exception error
Solution: That probably means that the BOOST_LIBRARY in you ccmake file (see above) is set to /usr/local/lib/libboost_python.a and not /usr/local/lib/libboost_python-1_34_1.dylib. Change it, configure again (press c), then press g, then run a make install again. The problem should go away.
Running e2.py gives an ImportError complaining about libraries
For each of the dynamic libraries (*.dylib) in the EMAN2/lib directory make symbolic links to them in the same directory, but make it so the symbolic links have the .so extension (not the .dylib) extension To do this, type: sudo ln <source> <target> Where the source is EACH .dylib file, and the target is THE SAME FILE NAME, with .so ending replacing the .dylib
Linking CXX shared library ../lib/libEM2.dylib ld: cycle in dylib re-exports with /usr/X11R6/lib/libGL.dylib
Turn the ENABLE_LEOPARD flag ON in the ccmake file.
See http://developer.apple.com/qa/qa2007/qa1567.html for the details behind the issue.