Diff for "EMAN2/COMPILE_EMAN2_MAC_OS_X"

Differences between revisions 2 and 14 (spanning 12 versions)

conda PYTHON ZLIB_L

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 th_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.
PLEASE report any problems or update the page!
1. Install current Python2.x Anaconda from https://www.continuum.io/downloads (remember EMAN is Python2 not Python3). When installing put anaconda in your home directory and name it 'anaconda2'.
2. Obviously you will need to have XCode installed on your Mac as well
3. 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'
```
4. 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
```
5. 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=$HOME/anaconda2/lib/libpython2.7.dylib IBRARY=$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 2 as of 2017-02-08 15:51:40 → 
  Size: 5115
  Editor: SteveLudtke
  Comment:
+   ← Revision 14 as of 2017-02-12 19:32:31 → ⇥
  Size: 3899
  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 7:
-. Install current Python2.x Anaconda from https://www.continuum.io/downloads  (remember EMAN is Python2 not Python3)
+. Install current Python2.x Anaconda from https://www.continuum.io/downloads  (remember EMAN is Python2 not Python3). When installing put anaconda in your home directory and name it 'anaconda2'.
 Line 9:
-. 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:
-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:$HOME/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Developer/usr/bin:/Applications/Chimera.app/Contents/MacOS'
 Line 13:
-. Install FFTW from source. Compile both normal (double) and --enable-single. This requires running ''configure'' and ''make install'' twice. While there are a dozen different versions available from anaconda, I didn't want to try and find one that had the necessary versions, so I just built it. If someone figures out one that works, let me know. You will also need --enable-shared and I used --prefix=$HOME (so you don't have to deal with the Mac's annoying security subsystem).
-Line 15:
+Line 14:
-. 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 20:
-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 28:
+. 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 42:
+fftw                      3.3.5                         0    conda-forge
-Line 28:
+Line 44:
+cmake                     3.6.3                         0
-Line 47:
+Line 64:
-. 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.