Diff for "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 cytoscape.bat file 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 cytoscape.sh file in a text editor.
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) (under construction) - in the finder, right-click on the icon and select Show Package Contents - Go to the Contents folder and open info.plist - In the Property List, expand the Root directory, then Java, and modify the VMOptions value (originally set as -Xmx512M) as per Option A. - save and exit - open Cytoscape using the icon

Option E: Using the Cytoscape icon (Windows systems)

1. Open the cytoscape.lax file in a text editor.
2. Increase the numerical value (bytes of memory) of the heap size and stack size lines. The original code looks like this:

 lax.nl.java.option.java.heap.size.max=512000000

and

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

Do not modify other parts of the file.

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

- do not add trailing spaces