mpi-network-motif

Network Motif analysis using MPI (Java)

Test Drive

Prerequisites

• Mac/Linux platform
• labelg program compiled for your computer. If you're working through the UWB Linux Lab, the provided executable will suffice. Otherwise you will need to compile and include your own: replace labelg with an identically named executable and change the mode to allow execution (chmod +x labelg). The source is available at http://cs.anu.edu.au/~bdm/nauty/ (to build, bash configure && make all).
• mpiJava (http://www.hpjava.org/mpiJava.html).
• MPI.

Setup

• Configure the mpiJava class path in the run.sh and compile.sh scripts (preconfigured for UWB Linux Lab).
• Create and configure the contents of .mpd.conf to be secretword=your-secret-word, where your-secret-word is a secure key that only you know.
• Create and configure mpd.hosts to be the remotes nodes you wish to add to the MPI network at execution time.

Project structure:

.
├── run.sh               <- configure
├── compile.sh           <- configure
├── .mpd.conf            <- create
├── mpd.hosts            <- create
├── labelg               <- provided for UWB linux lab
├── README.md            (this file)
├── data/                (data files)
├── src/                 (source code)
│   ├── Main.java
│   └── ...
└── ...                  (other files)

Execution

Compile the code, then run the program on the master node:

$ ./compile.sh

$ ./run.sh datafile motif nThreads [--show-results]

# examples:

# motif size of 3, 4 threads per node, print canonical label counts:
$ ./run.sh data/Scere20131031CR.txt 3 4 --show-results

# motif size of 4, 2 threads per node, don't print results
$ ./run.sh data/test05 4 2

Measuring Performance

For convenience, this program includes a script to automate testing program performance for a variety of scenarios. measure.sh assumes that the run.sh script is properly configured (as explained above). This script runs the program in the following scenarios: 1, 2, 4, 8, and 16 nodes, each at 1, 2, and 4 threads per node, for a total of 15 different combinations. This script is designed for the UWB Linux Lab.

Execution

$ ./measure.sh datafile motif

# example:
# run all scenarios on test04 file, with motif size 6
$ ./measure.sh data/test04 6

Data File Format

Text file, with each line containing a "from" node and a "to" node, as indicated by the string. These are interpreted to be undirected connections, so the ordering does not actually matter.

Example:

a b
b c
b d
d e

This represents the following graph:

 ___        ___        ___
| a | ---- | b | ---- | c |
 ---        ---        ---
             |
             |
            ___        ___
           | d | ---- | e |
            ---        ---