Cortex

Neural networks, regression and feature learning in Clojure.

Cortex has been developed by ThinkTopic in collaboration with Mike Anderson.

Mailing List

https://groups.google.com/forum/#!forum/clojure-cortex

Usage

[thinktopic/cortex 0.9.10]

All libraries are released on clojars. Cortex is not 1.0 yet preliminary and you should expect quite a few things to change over time but it should allow you to train some initial classifiers or regressions. Note that the save format has not stabilized and although we do just save edn data in nippy format it may require some effort to bring versions of saved forward.

Cortex Design

Design is detailed here: Cortex Design Document

Please see the various unit tests and examples for training a model. Specifically see: mnist verification

Also, for an example of using cortex in a more real-world scenario please see: mnist example.

Existing Framework Comparisons

Stanford CS 231 Lecture 12 contains a detailed breakdown of Caffe, Torch, Theano, and TensorFlow.

TODO:

hdf5 import of major keras models (vgg-net). This requires each model along with a single input and per-layer outputs for that input. Please don't ask for anything to be supported unless you can provide the appropriate thorough test.
Recurrence in all forms. There is some work towards that direction in the compute branch and it is specifically designed to match the cudnn API for recurrence. This is less important at this point than running some of the larger pre-trained models.
Speaking of larger nets, multiple GPU support and multiple machine support (which could be helped by the above graph based description layer).
Profiling GPU system to make sure we are using as much GPU as possible in the single-gpu case.
Better data import/visualization support. We have geom and we have a clear definition of the datasets, now we need to put together the pieces and build some great visualizations as examples.

Getting Started:

Get the project and run lein test in both cortex and compute. The various unit tests train various models.

GPU Compute Install Instructions

Ubuntu

Download Cuda and follow the installation commands provided

$ sudo dpkg -i cuda-repo-<distro>_<version>_<architecture>.deb
$ sudo apt-get update
$ sudo apt-get install cuda

Install the Cuda driver and any dependencies. Use driver version specific to device being used (to check on Ubuntu: System Settings -> Software & Updates -> Additional Drivers)

$ sudo apt-get install nvidia-<driver version>

Install cuDNN and copy the cuDNN files to the corresponding folders in the local cuda installation (probably at /usr/local/cuda). For reference, follow the "Installing cuDNN" section here.

Add Cuda to the PATH in ~/.bashrc

# CUDA Toolkit
export CUDA_HOME=/usr/local/cuda
export LD_LIBRARY_PATH=${CUDA_HOME}/lib64:$LD_LIBRARY_PATH
export PATH=${CUDA_HOME}/bin:${PATH}

Run $ nvcc -V to make sure cuda version is as expected.

To check everything is working, run $ nvidia-smi

Depending on which distribution you're on you will either have cuda7.5 or cuda8.0. Current master is 8.0, so if you're running 7.5 you will need to change the javacpp dependency in your project file of the mnist Example.

Mac OS

These instructions follow the gpu setup from Tensor Flow, i.e.:

Install coreutils and cuda:

$ brew install coreutils
$ brew tap caskroom/drivers
$ brew cask install cuda

Add CUDA Tool kit to bash profile

export CUDA_HOME=/usr/local/cuda
export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$CUDA_HOME/lib"
export PATH="$CUDA_HOME/bin:$PATH"

Download the CUDA Deep Neural Network libraries.

Once downloaded and unzipped, moving the files:

$ sudo mv include/cudnn.h /Developer/NVIDIA/CUDA-8.0/include/
$ sudo mv lib/libcudnn* /Developer/NVIDIA/CUDA-8.0/lib
$ sudo ln -s /Developer/NVIDIA/CUDA-8.0/lib/libcudnn* /usr/local/cuda/lib/

Should you see a jni linking error similar to this

Retrieving org/bytedeco/javacpp-presets/cuda/8.0-1.2/cuda-8.0-1.2-macosx-x86_64.jar from central
Exception in thread "main" java.lang.UnsatisfiedLinkError: no jnicudnn in java.library.path, compiling:(think/compute/nn/cuda_backend.c
lj:82:28)
        at clojure.lang.Compiler.analyze(Compiler.java:6688)
        at clojure.lang.Compiler.analyze(Compiler.java:6625)
        at clojure.lang.Compiler$HostExpr$Parser.parse(Compiler.java:1009)

Make sure you have installed the appropriate CUDNN for your version of CUDA.

Windows

Some preliminary information about getting gpu-acceleration working on windows is available here: https://groups.google.com/forum/#!topic/clojure-cortex/hNFW1T_2PZc

owengalenjones/cortex