Multithreaded Gephi Force Atlas2 Layout in 2 or 3-d

Features

• Parallel Barnes-Hut tree building
• Computes total distance that all points move at each iteration in order to determine when the algorithm has converged
• Parallel force, attraction, and speed computations
• Option to rebuild Barnes-Hut tree every n iterations
• Option to update Barnes-Hut tree centers every n iterations
• Command line interface

Installation

Download gephi-toolkit-0.9.2-all.jar and forceatlas2.jar from https://github.com/klarman-cell-observatory/forceatlas2/releases

Command Line Usage

java -Djava.awt.headless=true -Xmx8g -cp forceatlas2.jar:gephi-toolkit-0.9.2-all.jar kco.forceatlas2.Main flags 

where flags are

Flag	Description	Default Value
–input	Input graph in one of Gephi input file formats https://gephi.org/users/supported-graph-formats/
–output	Output file
–nsteps	Number of iterations. Mutually exclusive with –targetChangePerNode
–targetChangePerNode	Target distance change per node before stop the algorithm. Mutually exclusive with –nsteps
–targetSteps	Maximum number of iterations before stopping the algoritm. This option is together with –targetChangePerNode	10000
–2d	Whether to produce a 2d layout	false
–directed	Whether input graph is directed	false
–nthreads	Number of threads to use.	All cores
–format	Output file format. One of csv, gdf, gexf, gml, graphml, pajek, txt	txt
–coords	Tab separated file containing initial coordinates with headers id, x, y, and, z
–seed	Seed for random number generation for initial node position	timestamp
–barnesHutSplits	Rounds of splits to use for Barnes-Hut tree building. Number of regions after splitting is 4^barnesHutSplits for 2D and 8^barnesHutSplits for 3D
–barnesHutTheta	Theta of the Barnes Hut optimization	1.2
–barnesHutUpdateIter	Update Barnes-Hut tree every barnesHutUpdateIter iterations	1
–updateCenter	Update Barnes-Hut region centers when not rebuilding Barnes-Hut tree	false
–jitterTolerance	How much swinging you allow. Above 1 discouraged. Lower gives less speed and more precision.	1.0
–linLogMode	Switch ForceAtlas’ model from lin-lin to lin-log (tribute to Andreas Noack). Makes clusters more tight.	false
–scalingRatio	How much repulsion you want. More makes a more sparse graph	2.0 if # nodes >= 100, otherwise 10.0
–gravity	Attracts nodes to the center	1.0
–strongGravityMode	A stronger gravity law	false
–outboundAttractionDistribution	Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.	false

Example Datasets

Gephi example datasets