Building

Dependencies

1. Cuda 7.5
2. MPI
3. OpenMp

Project estructure

The bin folder contains all script and executable used in the project. After compiling the project the following executables will be create in this folder:

1. cuda-kmodes The CUDA version of the k-modes algorithm, the fasted version so far.
2. mpi-kmodes The hybrid version of the k-modes algorithm that use MPI and OpenCV.
3. kmodes The sequencial version of the k-modes algorithm.

Input handle

1. binToRNA.py This script reads an binary code input

Install dependencies on OS X

• Download and install Cuda 7.5.
  • After the installation you must define the CUDA_HOME environment variable, on OS X is usually locale at /Developer/NVIDIA/CUDA-[CUDA-Version]
    export CUDA_HOME=/Developer/NVIDIA/CUDA-7-5
• For other dependencies the easiest way to install them is using Homebrew
  1. First install homebrew using the following command:

     /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
     

  2. Then, install all the required formulas:
     • brew install open-mpi
     • brew install clang-omp

Compiling the code

• After the all dependencies are installed , clone the repository. This may take several minutes, the repository is large due the size of the mRNA databases.
  git clone git@github.com:guitcastro/CudaPredTIS.git
• Then, just type make to build the project