from Notes on memory consumption, Cytoscape User Manual
For users interested in loading large networks, the amount of memory needed by Cytoscape will increase. Memory usage depends on both number of network objects (nodes+edges) and the number of attributes. Here are some rough suggestions for memory allocation:
Suggested Memory Size Without View
Table 28.
Number of Objects (nodes + edges) | Suggested Memory Size |
0 - 70,000 | 512M (default) |
70,000 - 150,000 | 800M |
Suggested Memory Size With View
Table 29.
Number of Objects (nodes + edges) | Suggested Memory Size |
0 - 20,000 | 512M (default) |
20,000 - 70,000 | 800M |
70,000 - 150,000 | 1G |
There are a number of ways to change Cytoscape's memory allocation, depending on your preferred method of opening the application. All of them will change Cytoscape's default memory parameters except starting from the command line.
Option A: Command line startup (note: this does not permanently change Cytoscape's default 512M setting)
If you are opening Cytoscape from the command line using the command
java –Xmx512M –jar cytoscape.jar –p plugins
then you can increase the value of –Xmx to the desired amount of memory. For example:
java –Xmx800M –jar cytoscape.jar –p plugins
Option B: Using cytoscape.bat (Windows systems)
Open the file cytoscape.bat
in a text editor (eg. right-click and select Open With Notepad).
Option C: Using cytoscape.sh (UNIX, Linux, and Mac OS X systems)
Open the file cytoscape.sh
in a text editor (eg. right-click and select Open With TextEdit).
Option D: Using the Cytoscape icon (Mac OS X systems)
Go to the Contents folder and open the file info.plist
.
Option E: Using the Cytoscape icon (Windows systems)
Open the file cytoscape.lax
in a text editor.
lax.nl.java.option.java.heap.size.max=838860800 lax.nl.java.option.native.stack.size.max=838860800Do not modify other parts of the file, and be careful not to add any trailing spaces to these lines.