Diff for "EMAN2/COMPILE_EMAN2_MAC_OS_X"

Differences between revisions 1 and 18 (spanning 17 versions)

conda PYTHON_ ZLIB_LI

Troubleshooting

boost-cpp fftw bsddb cmake freetype ftgl gsl hdf5 ipython ipython_genutils jpeg libpng libtiff matplotlib numpy pyopengl pyqt qt scikit-learn scipy theano tk h_Anaconda">Installing EMAN2.2 on OSX from source with Anaconda class="anchor" id="line-3">
These instructions worked for me on Sierra (10.12). I expect they would also work on versions back several years, but cannot guarantee it.
This approach uses a Python distribution called Anaconda for all of the messy dependencies EMAN2 requires, including the Python interpreter itself. In addition, this means that if you want to use EMAN2 from Python with other Python libraries, you have a rich Anaconda environment where you can install any additional packages you like. Anaconda is cross-platform and we have found it to be a MUCH better choice than Mac-specific package managers like MacPorts.
PLEASE report any problems or update the page!
1. Completely remove any previous eman2 source folders, and check out a fresh copy of the source from GitHub:
```
git clone https://github.com/cryoem/eman2.git
```
2. Install current Python2.x Anaconda from https://www.continuum.io/downloads (remember EMAN is Python2 not Python3).
  - Download the command-line installer, not the graphical installer, since this gives you a choice of where to put the installed folder.
  - Install Anaconda to $HOME/anaconda2
  - If you use a different location, you will need to update that in all of the subsequent instructions.
3. Obviously you will need to have XCode installed on your Mac as well
4. configure account to use this anaconda. I have a "useconda2" alias which does this (I just reset the entire PATH to avoid building up redundancies):
```
useconda2='export PYTHONPATH=$HOME/EMAN2/lib:$HOME/EMAN2/bin; export EMAN2DIR=$HOME/EMAN2; export PATH=.:$HOME/anaconda2/bin:$HOME/EMAN2/bin:$HOME/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Developer/usr/bin:/Applications/Chimera.app/Contents/MacOS'
```
5. Install other necessary Anaconda modules. This includes specific versions for a few. I don't recall how many of these were already installed and how many I had to do. Note that some need a specific version, eg:
```
conda install qt=4 pyqt=4
```
  and a couple are from other channels, eg:
```
conda install -c conda-forge boost boost-cpp fftw install -c jmbell ftgl
```
  The rest:
```
conda install bsddb freetype gsl hdf5 ipython jpeg libpng libtiff matplotlib numpy=1.11 pyopengl scikit-learn scipy theano tk cmake
```
6. Once all of this is done, all you have to do is get your CMake configuration to point at all of the right files. CMake should find everything automatically with 3 exceptions, as long as you put a directory called anaconda2 in your home directory. Replace $HOME below with your actual home directory:
```
PYTHON_INCLUDE_PATH=$HOME/anaconda2/include/python2.7 LIBRARY=$HOME/anaconda2/lib/libpython2.7.dylib BRARY=$HOME/anaconda2/lib/libz.dylib
```
Once this was done (it really didn't take very long to do), everything works for me, including the GUI. While I haven't tested absolutely everything, I did go through a lot of the tutorial and everything seemed fine.
style="list-style-type:none">
Here is the list of packages (installed above) with versions known to work in Feb, 2017. You shouldn't need to do anything with this, if you installed above. If you are having problems, you can do a conda list and check for these:
```
boost                     1.63.0                   py27_4    conda-forge 1.63.0                        1    conda-forge 3.3.5                         0    conda-forge 1.0                      py27_1 3.6.3                         0 2.5.5                         2 2.1.3                         2    jmbell 2.2.1                         0 1.8.17                        1 5.1.0                    py27_0 0.1.0                    py27_0 9b                            0 1.6.27                        0 4.0.6                         3 1.5.3               np111py27_0 1.11.1                   py27_0 3.0.2                    py27_0 4.11.4                   py27_4 4.8.7                         4 0.17.1              np111py27_2 0.18.1              np111py27_0 0.8.2                    py27_0 8.5.18                        0  
```

-  ⇤ ← Revision 1 as of 2017-02-08 15:49:27 → 
  Size: 4994
  Editor: SteveLudtke
  Comment:
+   ← Revision 18 as of 2017-02-12 20:39:51 → ⇥
  Size: 4747
  Editor: SteveLudtke
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-== Installing EMAN2.2 on OSX with Anaconda ==
+== Installing EMAN2.2 on OSX from source with Anaconda ==
 Line 3:
-Note that EMAN2.2 is a Python2 package, not Python3, so please download the corresponding version of Anaconda:
+These instructions worked for me on Sierra (10.12). I expect they would also work on versions back several years, but cannot guarantee it.
 Line 5:
-https://www.continuum.io/downloads
+This approach uses a Python distribution called Anaconda for all of the messy dependencies EMAN2 requires, including the Python interpreter itself. In addition, this means that if you want to use EMAN2 from Python with other Python libraries, you have a rich Anaconda environment where you can install any additional packages you like. Anaconda is cross-platform and we have found it to be a MUCH better choice than Mac-specific package managers like MacPorts.
 Line 7:
-. Install current Python2.x Anaconda
+PLEASE report any problems or update the page!

 1. Completely remove any previous eman2 source folders, and check out a fresh copy of the source from GitHub: 
 {{{
git clone https://github.com/cryoem/eman2.git
}}}
 1. Install current Python2.x Anaconda from https://www.continuum.io/downloads  (remember EMAN is Python2 not Python3). 
  * Download the command-line installer, not the graphical installer, since this gives you a choice of where to put the installed folder. 
  * Install Anaconda to $HOME/anaconda2   
  * If you use a different location, you will need to update that in all of the subsequent instructions.
-Line 9:
+Line 18:
-. configure account to use this anaconda. I have a "useconda2" command which does this (I just reset the entire PATH to avoid building up redundancies):
+. configure account to use this anaconda. I have a "useconda2" alias which does this (I just reset the entire PATH to avoid building up redundancies):
-Line 11:
+Line 20:
-useconda2='export PYTHONPATH=$HOME/EMAN2/lib:$HOME/EMAN2/bin; export PATH=$HOME/anaconda2/bin:$HOME/EMAN2/bin:.:$HOME/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Developer/usr/bin:/Applications/Chimera.app/Contents/MacOS'
+useconda2='export PYTHONPATH=$HOME/EMAN2/lib:$HOME/EMAN2/bin; export EMAN2DIR=$HOME/EMAN2; export PATH=.:$HOME/anaconda2/bin:$HOME/EMAN2/bin:$HOME/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Developer/usr/bin:/Applications/Chimera.app/Contents/MacOS'
-Line 13:
+Line 22:
-. Install FFTW from source. Compile both normal (double) and --enable-single. This requires running ''configure'' and ''make install'' twice. While there are a dozen different versions available from anaconda, I didn't want to try and find one that had the necessary versions, so I just built it. If someone figures out one that works, let me know. You will also need --enable-shared and I used --prefix=$HOME (so you don't have to deal with the Mac's annoying security subsystem).
-Line 15:
+Line 23:
-. Install other necessary Anaconda modules (conda install). This includes specific versions for a few. I don't recall how many of these were already installed and how many I had to do. Note that some need a specific version, eg:
+. Install other necessary Anaconda modules. This includes specific versions for a few. I don't recall how many of these were already installed and how many I had to do. Note that some need a specific version, eg:
-Line 21:
+Line 29:
-conda install -c conda-forge boost boost-cpp
+conda install -c conda-forge boost boost-cpp fftw
conda install -c jmbell ftgl
}}}
 The rest:
 {{{
conda install bsddb freetype gsl hdf5 ipython jpeg libpng libtiff matplotlib numpy=1.11 pyopengl scikit-learn scipy theano tk cmake
-Line 24:
+Line 37:
+. Once all of this is done, all you have to do is get your CMake configuration to point at all of the right files. CMake should find everything automatically with 3 exceptions, as long as you put a directory called anaconda2 in your home directory. Replace $HOME below with your actual home directory:
 {{{
PYTHON_INCLUDE_PATH=$HOME/anaconda2/include/python2.7
PYTHON_LIBRARY=$HOME/anaconda2/lib/libpython2.7.dylib
ZLIB_LIBRARY=$HOME/anaconda2/lib/libz.dylib
}}}

Once this was done (it really didn't take very long to do), everything works for me, including the GUI. While I haven't tested absolutely everything, I did go through a lot of the tutorial and everything seemed fine.

=== Troubleshooting ===
 Here is the list of packages (installed above) with versions known to work in Feb, 2017. You shouldn't need to do anything with this, if you installed above. If you are having problems, you can do a ''conda list'' and check for these:
-Line 27:
+Line 51:
+fftw                      3.3.5                         0    conda-forge
-Line 28:
+Line 53:
+cmake                     3.6.3                         0
-Line 47:
+Line 73:
-. Once all of this is done, all you have to do is get your CMake configuration to point at all of the right files. Unfortunately, since the current CMakeLists file doesn't search anaconda at the moment, this is a manual process:
 {{{
BOOST_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/boost
BOOST_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libboost_python.dylib
FREETYPE_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/freetype2
FREETYPE_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libfreetype.dylib
FTGL_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include
FTGL_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libftgl.2.dylib
GSL_CBLAS_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include
GSL_CBLAS_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libgslcblas.dylib
GSL_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include
GSL_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libgsl.dylib
HDF5_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include
HDF5_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libhdf5.dylib
JPEG_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include
JPEG_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libjpeg.dylib
NUMPY_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/lib/python2.7/site-packages/numpy/core/include
PNG_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include
PNG_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libpng.dylib
PYTHON_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/python2.7
PYTHON_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libpython2.7.dylib
TIFF_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include
TIFF_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libtiff.dylib
ZLIB_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libz.dylib

FFTW3_INCLUDE_PATH:PATH=/Users/stevel/include
FFTW3_LIBRARY:FILEPATH=/Users/stevel/lib/libfftw3f.dylib
FFTW3d_INCLUDE_PATH:PATH=/Users/stevel/include
FFTW3d_LIBRARY:FILEPATH=/Users/stevel/lib/libfftw3.dylib
}}}

Once this was done (it really didn't take very long to do), everything works for me, including the GUI. While I haven't tested absolutely everything, I did go through a lot of the tutorial and everything seemed fine.