If you have your data in Theano shared variables though, you give Theano the possibility to copy the entire data on the GPU in a single call when the shared variables are constructed. Brew install python pip install Theano pip install nose. This means that if the website uses some sort of installed player or.Install on mac. However, if you want to get the latest development version, or edit the code, you should follow the instructions in Bleeding-edge installation.Installing EMAN2.2 on OSX from source with AnacondaSHAREit Download is available for Android devices, but Windows/Mac users too can. The easiest way is to install the latest released version (see Basic user installation). Installing Theano Once the dependencies are installed, you can download and install Theano.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. MCMC with multiprocessing seems to work fine on mac, and even Ubuntu when run from the.This approach uses a Python distribution called Anaconda for all of the messy dependencies EMAN2 requires, including the Python interpreter itself. Theano setup is documented in the theano toolbox documentation.Yann is built with theanoo 0.8 but should be forward compatible unless theano makes a drastic release.PyMC3 is built on Theano which is a completely dead framework. Once theano and its pre-requisites are setup you may setup and run this toolbox.
Theano Mac Users TooIt includes the command-line C++ compiler for the Mac. XCode is free and available from the App Store. If you use a different location, you will need to update that in all of the subsequent instructions.If you can successfully run g++ -version from the command line, you should be all set and can skip to the next step. Download the command-line installer, not the graphical installer, since this gives you a choice of where to put the installed folder. If you clone from GitHub into your home folder then $HOME/eman2 will also become the installation folder, and things will be hopelessly confused!Install current Python2.x Anaconda from (remember EMAN is Python2 not Python3). EMAN2 is normally installed in $HOME/EMAN2. Ios emulator for mac december 2017I don't recall how many of these were already installed and how many I had to do. This includes specific versions for a few. Install other necessary Anaconda modules. I have a "useconda2" alias which does this (I just reset the entire PATH to avoid building up redundancies): useconda2='export PYTHONPATH=$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' configure account to use this anaconda. Press g to generate all of the makefilesAgain, ignore warnings for now, then from the command line: make -j4 (you can replace 4 with the number of cores on your machine)If everything works, do a make install and you're doneIf you get errors in compilation, you may want to run make again without the -j4 to more easily see the error messages. See troubleshooting below for tips.Once the options are set as you like them. If you put anaconda somewhere else, you will need to manually configure a bunch of locations. CMake should find everything automatically, as long as you put a directory called anaconda2 in your home directory or in $HOME/EMAN2. You can probably ignore any warnings you see at this point. Once all of this is done you're ready to start building: cd (wherever you checked out the eman2 source) Clearly you will need to adjust these for your own account name: EMAN_INSTALL_PREFIX:PATH=/Users/stevel/EMAN2BOOST_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeBOOST_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libboost_python.dylibFFTW3_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeFFTW3_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libfftw3f.dylibFFTW3d_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeFFTW3d_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libfftw3.dylibFREETYPE_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/freetype2FREETYPE_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libfreetype.dylibFTGL_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeFTGL_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libftgl.dylibGSL_CBLAS_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeGSL_CBLAS_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libgslcblas.dylibGSL_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeGSL_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libgsl.dylibHDF5_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeHDF5_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libhdf5.dylibJPEG_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeJPEG_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libjpeg.dylibNUMPY_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/lib/python2.7/site-packages/numpy/core/includePNG_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includePNG_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libpng.dylibPYTHON_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/include/python2.7PYTHON_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libpython2.7.dylibTIFF_INCLUDE_PATH:PATH=/Users/stevel/anaconda2/includeTIFF_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libtiff.dylibZLIB_LIBRARY:FILEPATH=/Users/stevel/anaconda2/lib/libz. If you are having problems, you can do a conda list and check for these: boost 1.63.0 py27_4 conda-forgeIf you are having ccmake configuration issues, here is the list of the relevant options from my configuration. While I haven't tested absolutely everything, I did go through a lot of the tutorial and everything seemed fine.Here is the list of anaconda packages (installed above) with versions known to work in Feb, 2017.
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