Error when running Cytoscape 3.0

[Duc-Hau, Le]

Hi All,

I have downloaded  cytoscape-windows-3.0.0-M4.zip  at:  http://chianti.ucsd.edu/cytoscape-3.0.0-M4/ 

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

Error: missing `server' JVM at `C:\Program Files\Java\jre7\bin\server\jvm.dll'.
Please install or use the JRE or JDK that contains these missing components.

I already installed JRE 7 (and also reinstalled it), but I could not find "server\jvm.dll" in the "C:\Program Files\Java\jre7\bin" of installed folder of  JRE7.

I also tried to copy "server\jvm.dll" from "C:\Program Files\Java\jdk1.7.0_03\bin" to "C:\Program Files\Java\jre7\bin" and run cytoscape.bat file again. But, following error message appeared:

"The procedure entry point _JVM_SetNativeThreadName@1 could not be located in the dynamic link library jvm.dll".

Please help to fix the Cytoscape 3.0 running problem.

Thanks.

--
Duc-Hau Le, Ph.D (Vietnamese: Lê Đức Hậu)
Cell phone: (82)10-6869-2999 (Republic of Korea), (84) 912-324564 (Vietnam)
Email: haul...@mail.ulsan.ac.kr, haul...@wru.edu.vn, haul...@gmail.com
Website: https://sites.google.com/site/duchaule2011/
School of Computer Electrical Engineering, University of Ulsan.
San 29, Mugeo 2-dong, Nam-gu, Ulsan 680-749, Republic of Korea

[Jason Montojo]

Hi Duc-Hau,

You can work around this by editing the file framework/bin/karaf.bat.  Look for the following line:

set DEFAULT_JAVA_OPTS=-server -Xms%JAVA_MIN_MEM% -Xmx%JAVA_MAX_MEM% -XX:PermSize=%JAVA_PERM_MEM% -XX:MaxPermSize=%JAVA_MAX_PERM_MEM% -Dderby.system.home="%KARAF_DATA%\derby" -Dderby.storage.fileSyncTransactionLog=true -Dcom.sun.management.jmxremote

...and change it to remove "-server", like this:

set DEFAULT_JAVA_OPTS=-Xms%JAVA_MIN_MEM% -Xmx%JAVA_MAX_MEM% -XX:PermSize=%JAVA_PERM_MEM% -XX:MaxPermSize=%JAVA_MAX_PERM_MEM% -Dderby.system.home="%KARAF_DATA%\derby" -Dderby.storage.fileSyncTransactionLog=true -Dcom.sun.management.jmxremote

Please let me know if this fixes the issue.  Some people have reported it before but I haven't been able to reproduce it myself.

Thanks,

Jason

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[Duc-Hau, Le]

Hi Jason,

Thanks for your reply,

The previous error is fixed. But, following error occurred:

"Error: Could not find or load main class Tools\Cytoscape"

How can I fix it?

Thanks,

[Jason Montojo]

Hi Duc-Hau,

I'll need some more information to diagnose that error.  Can you edit your cytoscape.bat and framework\bin\karaf.bat files and look for this line at the top:

@echo off

...and change it in both files to this:

rem @echo off

The next time you run cytoscape.bat, it should give you lots more output in the console.  Can you send that to me off-list?  We haven't tested Cytoscape 3 on Java 7 on Windows that much.  We usually run it on Java 6.  We'll probably have to fix some things to make it work on Java 7.

Thanks,

Jason

[Duc-Hau, Le]

I have  just  sent you the errors off-list.

I am now trying with Java 6.

Thanks,

[Duc-Hau, Le]

Hi Jason,

I have tested with JDK 6-u33 and got similar error:

Exception in thread "main" java.lang.NoClassDefFoundError: Tools\Cytoscape

Caused by: java.lang.ClassNotFoundException: Tools\Cytoscape

        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)

        at java.security.AccessController.doPrivileged(Native Method)

        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:306)

        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)

        at java.lang.ClassLoader.loadClass(ClassLoader.java:247)

Could not find the main class: Tools\Cytoscape.  Program will exit.

Please let me know the exact version of JDK on which you tested Cytoscape 3.0 successfully.

Thanks,

[Jason Montojo]

Hi Duc-Hau,

The problem is because Cytoscape is installed in a directory that has a space in it "i.e. Bioinformatics Tools".  I'm trying to figure out how to fix this in the startup scripts, but the usual fixes are making the JVM complain.  For now, you can work around it by keeping Cytoscape in a directory that has no spaces in its name.  I'll continue searching for a proper fix.

Thanks,

Jason

[Duc-Hau, Le]

Hi Jason,

It gets done for both Java 6 and 7 now.

Thank you very much.

[Barry Demchak]

Hi, Gess –

 

Can you tell us which operating system (e.g., Windows XP, Windows 7, Ubuntu 12.10, etc), how much RAM is in the machine, and whether you’re running on a 64 bit or 32 bit Java VM?

 

(To determine the Java VM, start a command window, enter “java –version”, and see whether it mentions 64-bit in the report.)

 

Thanks!

 

From: cytoscap...@googlegroups.com [mailto:cytoscap...@googlegroups.com] On Behalf Of Gess
Sent: Thursday, February 21, 2013 10:25 PM
To: cytoscap...@googlegroups.com
Subject: Re: [Cytoscape-discuss] Error when running Cytoscape 3.0

 

Hi Im new to cytoscape, Installed jre7 and cytoscape no issues while installing but while launching Im getting this error "java.lang.OutOfMemoryError: unable to create new native thread" i hope u guys can provide me a fix

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[Mark Messer]

I had this problem too. I am using 64 bit Windows 7 with 8G RAM, JDK 7.
I was setting up Eclipse as in http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper/SettingUpAnIDE/Eclipse
It directs me to build the App Developer's template, and try to run it.
It would not start if I tried to run it from a cmd window using cytoscape.bat. Nor would ordinary Cytoscape 2.8.2 or 3.0.0 start from the cmd window.
All was well if I started up things by clicking on files in Windows Explorer.

Eventually I found a configuration problem that meant I wasn't running the JDK I thought I was.
This environmental variable was set (I need 32 bit JDK 6 for another app).
    JAVA_HOME=C:\Program Files (x86)\Java\jdk1.6.0_38

I could start from the cmd window after I changed it to
    C:\Program Files\Java\jdk1.7.0_11

Java is supposed to be platform independent. In Windows 64, you should be able to start a 32 or 64 bit JDK or JRE and run any of those apps.
The difference might have been that a 32 bit JDK cannot use as much memory as a 64 bit JDK.
Fiddling with the -Xmx settings in Cytoscape.vmoptions made a difference, but not enough that I could start the App Developer template project.
Still, I shouldn't need all 8 G to just to start up Cytoscape.

So I don't know what was going on. But I suspect the problem is configuration, not a bug.


Gess,

Try checking if you have JAVA_HOME or your path set to a JDK or JRE. If so, make sure it is the one you expect.


P.S.

Just in case the original problem for this post comes back (the missing jvm.dll from last June), check this link. http://java.com/en/download/help/error_mainclass.xml

[Gess Thoms Xavier]

Im using Windows 8 64 bit, 3GB RAM, Java 64bit version - 1.7.0 

[Gess Thoms Xavier]

I checked my path for:

JAVA_HOME - C:\Program Files\Java\jdk1.7.0

JRE_HOME -  C:\Program Files\Java\jre7

i think the path is set correctly but still im getting the same error while trying to load the GalFiltered.sif file.