Graphviz

Category

Visualization

Description

Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

Available versions (Euler, old software stack)

Legacy versions	Supported versions	New versions
	2.38

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Environment modules (Euler, old software stack)

Version	Module load command	Additional modules loaded automatically
2.38	module load gcc/4.8.2 python/2.7.6 graphviz/2.38	openblas/0.2.13_seq legacy centos_cruft/6

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

Example

As an example for using Graphviz, we are drawing a flow chart.

[leonhard@euler09 ~]$ ls
test.gv
[leonhard@euler09 ~]$ cat test.gv
digraph {
 label="Getting help with the Euler cluster"

 "Consult the wiki https://scicomp.ethz.ch"[shape="box",style=rounded];
 "Check the FAQ"[shape="box",style=rounded];
 "Use search box"[shape="box",style=rounded];
 "Look at application pages"[shape="box",style=rounded];
 "Problem solved ?"[shape="box",style=rounded];
 "Happy computing"[shape="box",style=rounded];
 "Contact cluster support"[shape="box",style=rounded];

 "Consult the wiki https://scicomp.ethz.ch" -> "Check the FAQ";
 "Consult the wiki https://scicomp.ethz.ch" -> "Use search box";
 "Consult the wiki https://scicomp.ethz.ch" -> "Look at application pages";
 "Check the FAQ" -> "Problem solved ?";
 "Use search box" -> "Problem solved ?";
 "Look at application pages" -> "Problem solved ?";
 "Problem solved ?" -> "Happy computing"[label="yes"];
 "Problem solved ?" -> "Contact cluster support"[label="no"];
}
[leonhard@euler09 ~]$ module load gcc/4.8.2 python/2.7.6 graphviz/2.38
Autoloading openblas/0.2.13_seq
[leonhard@euler09 ~]$ bsub -n 1 -W 0:05 -R "rusage[mem=50]" "dot -Tpng test.gv -o test.png"
Generic job.
Job <34267333> is submitted to queue <normal.4h>.
[leonhard@euler09 ~]$ bjobs
JOBID      USER       STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
34267333   leonhard   PEND  normal.4h  euler09                 * test.png Dec 21 08:16
[leonhard@euler09 ~]$ bjobs
JOBID      USER       STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
34267333   leonhard   RUN   normal.4h  euler09     e1021       * test.png Dec 21 08:16
[leonhard@euler09 ~]$ bjobs
No unfinished job found
[leonhard@euler09 ~]$ ls
lsf.o34267333  test.gv  test.png
[leonhard@euler09 ~]$

You can find the resource usage summary of the job in the LSF log file.

Simple flowchart created with Graphviz

License information

Graphviz license

Links

http://www.graphviz.org

https://en.wikipedia.org/wiki/Graphviz
https://wiki.ubuntuusers.de/Graphviz