Re: [Cytoscape-discuss] error when running cytoscape 3.0

[Jason Montojo]

Hello,

Can you send the error message you saw?  How much RAM do you have installed on your system?  I suspect that might be the cause, but it's hard to confirm without the error message.

Thanks,

Jason

On Tue, Sep 11, 2012 at 11:49 PM, Xuan-Hung <hung...@gmail.com> wrote:

Hi all,
After extracting it and run cytoscape.bat file in Windows 7, 32bit, an following error occurred:

I already installed jdk_7u6.

Please help to fix the Cytoscape 3.0 running problem.

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[girishanem]

Hi Xuan-Hung,

I also faced the same issue. For the first time execute cytoscape.bat. If it fails try to execute karaf.bat( in my app environment its path is Cy_3_1\target\framework\bin\karaf.bat). It will start the Cytoscape. And as Jason said check your available RAM when you are executing Cytoscape.bat.

Regards,

Girish Anem

[Duc-Hau, Le]

Hi All,

Regarding to the Cy 3.0 starting error (particularly, I am using Cy3.0 M6 version), I met another problem about maximum heap memory. That is if I set JAVA_MAX_MEM greater than ~1000M, then it could not start and produced an error about Outofmemory (Even I installed 3GB RAM in my computer, I am now using win7, 32 bit). However, it started perfectly with JAVA_MAX_MEM less than or equal to ~1000M. This will be a big problem if I run some plugins (after Cy 3.0 started) which require larger memory space.

Any help will be appreciated

Thanks,  

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[Jason Montojo]

Hi Duc-Hau,

That's a limitation of the 32-bit Java JVM.  I can't run it with a heap size greater than 1200M on my particular configuration.  If you need access to more memory, running 64-bit Java on a 64-bit OS is probably the best solution.

Hope this helps,

Jason

[Duc-Hau, Le]

Thank you, Jason,

It may be a particular limitation of Cy 3.0? Because it run OK if I set greater than 1200MB for maximum heap size (e.g,. -Xmx1600M) when I run Cy 2.8.x (I am using the same PC and win7, 32bit, 3G RAM for both Cy 3.0 and Cy 2.8.x).

Cheers,

Duc-Hau