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-*- rst -*-\n\n..  image:: https://raw.githubusercontent.com/neurokernel/neurokernel/master/docs/source/_static/logo.png\n    :alt: Neurokernel\n\nPackage Description\n-------------------\n\n`Project Website \u003chttps://neurokernel.github.io\u003e`_ |\n`GitHub Repository \u003chttps://github.com/neurokernel/neurokernel\u003e`_ |\n`Online Documentation \u003chttps://neurokernel.readthedocs.io\u003e`_ |\n`Mailing List \u003chttps://lists.columbia.edu/mailman/listinfo/neurokernel-dev\u003e`_ |\n`Forum \u003chttp://neurokernel.67426.x6.nabble.com/\u003e`_\n\nNeurokernel is a Python framework for developing models of\nthe fruit fly brain and executing them on multiple NVIDIA GPUs.\n\n.. image:: http://prime4commit.com/projects/98.svg\n    :target: http://prime4commit.com/projects/98\n    :alt: Support the project\n\nPrerequisites\n-------------\nNeurokernel requires\n\n* Linux (other operating systems may work, but have not been tested);\n* Python;\n* at least one NVIDIA GPU with `Fermi\n  \u003chttp://www.nvidia.com/content/pdf/fermi_white_papers/nvidia_fermi_compute_architecture_whitepaper.pdf\u003e`_\n  architecture or later;\n* NVIDIA's `GPU drivers \u003chttp://www.nvidia.com/content/drivers/\u003e`_;\n* `CUDA \u003chttp://www.nvidia.com/object/cuda_home_new.html\u003e`_ 5.0 or later;\n* `OpenMPI \u003chttp://www.open-mpi.org\u003e`_ 1.8.4 or later compiled with CUDA support.\n\nTo check what GPUs are in your system, you can use the `inxi\n\u003chttps://code.google.com/p/inxi/\u003e`_ command available on most Linux\ndistributions::\n\n  inxi -G\n\nYou can verify that the drivers are loaded as follows::\n\n  lsmod | grep nvidia\n\nIf no drivers are present, you may have to manually load them by running\nsomething like::\n\n  modprobe nvidia\n\nas root.\n\nAlthough some Linux distributions do include CUDA in their stock package\nrepositories, you are encouraged to use those distributed by NVIDIA because they\noften are more up-to-date and include more recent releases of the GPU drivers.\nSee `this page \u003chttps://developer.nvidia.com/cuda-downloads\u003e`_ for download\ninformation.\n\nIf you install Neurokernel in a virtualenv environment, you will need to\ninstall OpenMPI. See `this page\n\u003chttps://www.open-mpi.org/faq/?category=building#easy-build\u003e`_\nfor OpenMPI installation information. *Note that OpenMPI 1.8* |openmpi_no_windows|_.\n\n.. _openmpi_no_windows: https://www.open-mpi.org/software/ompi/v1.6/ms-windows.php\n.. |openmpi_no_windows| replace:: *cannot run on Windows*\n\nSome of Neurokernel's demos require either `ffmpeg \u003chttp://www.fmpeg.org\u003e`_ or `libav\n\u003chttp://libav.org\u003e`_ installed to generate visualizations (see `Examples`_).\n\nInstallation\n------------\n\nConda\n^^^^^\nThe easiest way to get neurokernel is to install it in a conda environment: ::\n\n  conda create -n nk python=3.7 c-compiler compilers cxx-compiler openmpi -c conda-forge -y\n  conda activate nk\n  python -m pip install neurokernel\n\nMake sure to enable CUDA support in the installed OpenMPI by setting: ::\n\n  export OMPI_MCA_opal_cuda_support=true\n\nExamples\n--------\nIntroductory examples of how to use Neurokernel to build and integrate models of different\nparts of the fly brain are available in the `Neurodriver\n\u003chttps://github.com/neurokernel/neurodriver\u003e`_ package. To install it run the\nfollowing: ::\n\n  git clone https://github.com/neurokernel/neurodriver\n  cd ~/neurodriver\n  python setup.py develop\n\nOther models built using Neurokernel are available on\n`GitHub \u003chttps://github.com/neurokernel/\u003e`_.\n\nBuilding the Documentation\n--------------------------\nTo build Neurokernel's HTML documentation locally, you will need to install\n\n* `mock \u003chttp://www.voidspace.org.uk/python/mock/\u003e`_ 1.0 or later.\n* `sphinx \u003chttp://sphinx-doc.org\u003e`_ 1.3 or later.\n* `sphinx_rtd_theme \u003chttps://github.com/snide/sphinx_rtd_theme\u003e`_ 0.1.6 or\n  later.\n\nOnce these are installed, run the following: ::\n\n  cd ~/neurokernel/docs\n  make html\n\nAuthors \u0026 Acknowledgements\n--------------------------\nSee the included `AUTHORS`_ file for more information.\n\n.. _AUTHORS: AUTHORS.rst\n\nLicense\n-------\nThis software is licensed under the `BSD License\n\u003chttp://www.opensource.org/licenses/bsd-license.php\u003e`_.\nSee the included `LICENSE`_ file for more information.\n\n.. _LICENSE: LICENSE.rst\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurokernel%2Fneurokernel","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fneurokernel%2Fneurokernel","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fneurokernel%2Fneurokernel/lists"}