Help with starting Cytoscape

[Julie Phillippi]

Hello,

I recently downloaded Cytoscape 3.1.1 but cannot open it. I receive the following error "The JVM could not be started. The maximum heap size may be too large or there may be an antivirus or  firewall tool could block the activation."

 

Thank you,

Julie

 

[srikanth bezawada]

Hi ,

This may help. Stay tuned to this thread if it doesn't.

Try to change the Cytoscape.vmoptions file using any text editor accordingly [1],[2] .This file would be in the same directory as Cytoscape_v3.1.1.

[1] - http://wiki.cytoscape.org/How_to_increase_memory_for_Cytoscape

[2] - http://wiki.cytoscape.org/How_to_increase_memory_for_Cytoscape?action=AttachFile&do=view&target=Cytoscape.vmoptions

--
You received this message because you are subscribed to the Google Groups "cytoscape-helpdesk" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cytoscape-helpd...@googlegroups.com.
To post to this group, send email to cytoscape...@googlegroups.com.
Visit this group at http://groups.google.com/group/cytoscape-helpdesk.
For more options, visit https://groups.google.com/d/optout.

[Tim Hull]

Are you on Windows, and if so is it a 32-bit or 64-bit version? How much memory do you have, and what is in the Cytoscape.vmoptions file? This message is commonly seen when there is a mismatch in the bitness between Java/Cytoscape/Windows - most commonly when 32-bit Java is installed on a 64-bit Windows with 64-bit Cytoscape.

If this is the issue, you may have to manually download the 64-bit Java - Oracle's website automatically uses the 32-bit version if a 32-bit browser is used (and most browsers are 32-bit).

Tim

--

[Greg Hanowski]

Tim,
I have the same problem as Julie.  I am running Win8 which is 64bit but can run 32bit apps [C:\Program Files (x86)] as well.  My Path environment variable is set to C:\Program Files (x86)\Java\jdk1.7.0_25; and I am running the 32bit version of Cytoscape located here: "C:\Program Files (x86)\Cytoscape_v3.1.1\Cytoscape.exe".  My Cytoscape.vmoptions file has the following one line in it:  -Xmx1250m.  I also checked my Windows Firewall and it shows Java(TM) Platform SE binary is an allowed app.
Suggestions?
Greg

[Tim Hull]

Hi,

The ceiling for memory on 32-bit Java seems to be somewhat system-dependent (and hard to correctly predict), which is why you're experiencing problems running 32-bit Cytoscape. For this reason, we're planning on removing 32-bit support from the next major Cytoscape release (3.2).

The best thing to do here is to install 64-bit Java and Cytoscape - without it, Cytoscape can't use much more than 1.2GB of memory. If that is not possible, you can try decreasing the memory allocation in Cytoscape.vmoptions until it runs - however, the memory available to Cytoscape will likely be insufficient to handle large networks.

Hope this helps...

Tim