How_to_increase_memory_for_Cytoscape

How to increase memory for Cytoscape

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

Suggested Memory Size With View

Changing memory allocations on Windows, Mac, and Linux machines

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)

1. Open the file cytoscape.bat in a text editor (eg. right-click and select Open With Notepad).

2. Increase the value of the –Xmx tag (found in the last line of the file), as per Option A. Do not modify other parts of the file.
3. Save and close the file.
4. Open Cytoscape by double-clicking on cytoscape.bat.

Option C: Using cytoscape.sh (UNIX, Linux, and Mac OS X systems)

1. Open the file cytoscape.sh in a text editor (eg. right-click and select Open With TextEdit).

2. Increase the value of the –Xmx tag (found in the last line of the file), as per Option A. Do not modify other parts of the file.
3. Save and close the file.
4. Open Cytoscape by running cytoscape.sh from the command line.

Option D: Using the Cytoscape icon (Mac OS X systems)

1. In the Finder, right-click on the Cytoscape icon and select Show Package Contents.

2. Go to the Contents folder and open the file info.plist.

3. In the Property List Editor, expand the Root directory, then Java, and modify the VMOptions value (originally set as -Xmx512M) as per Option A. Do not modify other parts of the file.
4. Save and close the file.
5. Open Cytoscape by double-clicking on the icon.

Option E: Using the Cytoscape icon (Windows systems)

1. Open the file cytoscape.lax in a text editor.

2. Increase the numerical value (bytes of memory) of the heap size and stack size lines, shown below:
   • {{{lax.nl.java.option.java.heap.size.max=512000000

lax.nl.java.option.native.stack.size.max=512000000}}}

• Do not modify other parts of the file, and be careful not to add any trailing spaces to these lines.

1. Save and close the file.
2. Open Cytoscape by double-clicking on the icon.