Harvard CS 205 Final Project, Spring 2015.

Andy Shi, Ding Zhou, Kevin Schmid

To run, first ensure that GraphLab module is installed. This can be found at https://dato.com/download/

Download Dato GraphLab SDK by following the instructions at https://github.com/dato-code/GraphLab-Create-SDK

In the code directory, compile our C++ GraphLab extention hmm.cpp file by following the instructions in compile.txt. Remember to change the /path/to/graphlab-sdk to the path where the GraphLab SDK is installed.

Finally, our Python code to generate synthetic HMM data and run both the parallel and serial implementations (runhmm.py) can be run by using python runhmm.py:

usage: runhmm.py [-h] [--NUM_STATES NUM_STATES]
                 [--NUM_OBSERVATIONS NUM_OBSERVATIONS]
                 [--OBSERVATION_LENGTH OBSERVATION_LENGTH] [--niters niters]

optional arguments:
  -h, --help            show this help message and exit
--NUM_STATES NUM_STATES
		num states
  --NUM_OBSERVATIONS NUM_OBSERVATIONS
		num observations
--OBSERVATION_LENGTH OBSERVATION_LENGTH
		observation length
--niters niters
		Number of iterations to run

(Command-line argument usage instructions obtained from Python argparse default "help" output.)

The default values for these are 4, 4, 16, and 5, respectively.

Please follow the instructions in odyssey-setup.txt for installation instructions, and submit.sh for the job submission script (note that this calls submit.sbatch).

Both the data and the code to analyze the data are found in the analysis folder.

• data.csv: runtime data from Odyssey. Rows with 1 column only correspond to jobs which failed because of time constraints
• drawPlots.R: R code to generate the figures for our paper
• fullout.csv: full data, including the Odyssey output files from which each row of data came from
• gather.sh: Shell script to organize data from Odyssey output files into csv files.

Please find the files for our paper and its associated figures in the paper and figure folders, respectively.

• A prior attempt with a different graph architecture can be found in the attempt folder.