biohadoop-algorithms

Example algorithms for the Biohadoop framework. The following algorithms are implemented

Dedicated: Show the example usage of a dedicated queue, master and worker endpoint
Echo: Simple example, that sends a string Hello World to a waiting worker endpoint. The string is enclosed with the string Worker adds this string to result () and returned to the caller
GA: Implementation of a genetic algorithm, that tries to solve the Traveling salesman problem
MOEAD: Implementation of MOEAD, that tries to solve multi-objective optimization problems
NSGA-II: Implementation of NSGA-II, that tries to solve multi-objective optimization problems
Sleep: An algorithm that can be used to simulate workloads
Sum: Simple example, that sums the values of an integer value
Tiled matrix multiplication: Find optimal tile sizes for tiled matrix multiplication
TypeTest: Sending and receiving different Java types

Installation

$ git clone https://github.com/gappc/biohadoop-algorithms

Build and copy the examples to the Hadoop environment. The configuration for the copy process can be found and altered in the script file. Currently, the destination user is root, and the destination IP address is 172.17.0.100. Please adjust them to your system.

$ ./biohadoop/scripts/copy-algorithms.sh

Usage

To start Biohadoop in a Hadoop environment, provide the full path to the Biohadoop JAR file, set at.ac.uibk.dps.biohadoop.hadoop.BiohadoopClient as the class to start, and provide a valid location to a configuration file. The example builds on the Quickstart tutorial, where all libraries and configration files are placed in the right position. This example uses biohadoop-0.5.2-SNAPSHOT.jar:

yarn jar $PATH_TO_BIOHADOOP/biohadoop-0.5.2-SNAPSHOT.jar at.ac.uibk.dps.biohadoop.hadoop.BiohadoopClient /biohadoop/conf/biohadoop-echo.json