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| '''Option A: Change memory allocation at command line startup''' | |
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If you are opening Cytoscape from the command line using the command {{{java –Xmx512M –jar cytoscape.jar –p plugins}}} |
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. |
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then you can increase the value of –Xmx to the desired amount of memory. For example: {{{java –Xmx800M –jar cytoscape.jar –p plugins}}} |
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'''Option B: Change default memory allocation in 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 A: Command line startup (All operating systems/platforms)''' |
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'''Option C: Change default memory allocation in 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. |
Create a '''Cytoscape.vmoptions''' file in the same directory as the cytoscape.sh or cytoscape.bat files. Make sure to add exactly one JVM option per line and that the last line has a line break at the end. The most popular and important option is "-Xmx" followed immediately (no spaces!) by the amount of heap memory. You can add an "M" for megabytes or a "G" for gigabytes. Other options you may use may depend on the particular JVM that you are running. |
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'''Option D: Change default memory allocation when launching Cytoscape from its icon''' ''(under construction)'' 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: |
'''Option B: Using the Cytoscape icon (Windows and/or Linux systems)''' |
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| {{{ lax.nl.java.option.java.heap.size.max=512000000}}} | Just like with Option A, you can use the Cytoscape.vmoptions file. The problem with Windows is that the lines need to be terminated with a single line feed character (a.k.a. a "newline" character) and must not contain any carriage return characters. This is difficult to accomplish on Windows on which the default is line termination with carriage-return/line-feed pairs. You typically need to use a programmers editor and make sure to set the line-end configuration to line-feeds only! Another option on Windows is to create the Cytoscape.vmoptions file on Mac OS or Linux and then to copy it into the Windows installation directory. N.B.: this is not a problem on Linux! (If you have a 64-bit version of Windows and are running a 64-bit version of Java, you can also try using this Cytoscape.vmoptions file.) |
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| and | '''Option C: Using the Cytoscape icon on Mac OS''' |
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{{{lax.nl.java.option.native.stack.size.max=512000000}}} Do not modify other parts of the file. 3. Save and close the file. 4. Open Cytoscape by double-clicking on the icon. |
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 as per Option A. You may put multiple options separated by spaces here. 4. Save and close the file. 5. Open Cytoscape by double-clicking on the icon. |
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
Number of Objects (nodes + edges) |
Suggested Memory Size |
0 - 70,000 |
512M (default) |
70,000 - 150,000 |
800M |
Suggested Memory Size With View
Number of Objects (nodes + edges) |
Suggested Memory Size |
0 - 20,000 |
512M (default) |
20,000 - 70,000 |
800M |
70,000 - 150,000 |
1G |
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 (All operating systems/platforms)
Create a Cytoscape.vmoptions file in the same directory as the cytoscape.sh or cytoscape.bat files. Make sure to add exactly one JVM option per line and that the last line has a line break at the end. The most popular and important option is "-Xmx" followed immediately (no spaces!) by the amount of heap memory. You can add an "M" for megabytes or a "G" for gigabytes. Other options you may use may depend on the particular JVM that you are running.
Option B: Using the Cytoscape icon (Windows and/or Linux systems)
Just like with Option A, you can use the Cytoscape.vmoptions file. The problem with Windows is that the lines need to be terminated with a single line feed character (a.k.a. a "newline" character) and must not contain any carriage return characters. This is difficult to accomplish on Windows on which the default is line termination with carriage-return/line-feed pairs. You typically need to use a programmers editor and make sure to set the line-end configuration to line-feeds only! Another option on Windows is to create the Cytoscape.vmoptions file on Mac OS or Linux and then to copy it into the Windows installation directory. N.B.: this is not a problem on Linux! (If you have a 64-bit version of Windows and are running a 64-bit version of Java, you can also try using this Cytoscape.vmoptions file.)
Option C: Using the Cytoscape icon on Mac OS
- In the Finder, right-click on the Cytoscape icon and select Show Package Contents.
Go to the Contents folder and open the file info.plist.
- In the Property List Editor, expand the Root directory, then Java, and modify the VMOptions value as per Option A. You may put multiple options separated by spaces here.
- Save and close the file.
- Open Cytoscape by double-clicking on the icon.