CSC

Chipster

Software for DNA high-throughput data analysis

FAQ

Please find below answers to some technical issues regarding the Chipster client software. For questions regarding Chipster server installation, please see the FAQ at the SourceForge site.

Java Web Start Launcher complains: "Could not create the Java virtual machine"

Java Runtime Environment fails to start for some reason. To see what the actual error message is, you need to enable the Java console. For instructions, see http://www.java.com/en/download/help/javaconsole.xml. It can be disabled again after the issue is solved.

Typically these issues are because of memory settings. Some new Java Runtime Environments have become picky about them and refuse to start. You can try the alternative startup link that has no memory requirements: http://chipster.csc.fi/chipster-nomem.jnlp. The negative effect of the alternative link is that the application is limited to only small memory usage and can be slow especially when visualising.

Client application fails to start with "could not connect to message broker at... Connection timed out".

First you should check that there is no service break. Check the Chipster front page for that information.

If you still can't connect to Chipster, the reason is likely to be the the local firewall of your institution. Especially hospitals often have strict firewall configurations, blocking all application use. The easiest solution is to use Chipster elsewhere, such as the local university network.

If you don't have access to a network with normal firewall settings, you have to contact your network administrators and ask for a change to firewall configuration. See the firewall section for more information.

Also make sure that Java is not configured to use a non-compliant proxy server for HTTP. Many proxies do not support HTTP/1.1 properly, so disabling HTTP proxy in Java Runtime configuration is recommended.

Chipster and firewalls

To access the Chipster service running at CSC, you need to be able to make outbound connections to certain CSC servers. Usually most firewalls allow all outbound connections so there is no need for changing the firewall configuration. However some organizations, for example hospitals, may have strict firewalls, which also block outbound connections. In such cases, the firewall needs to be configured like this:

Allow outbound connections to:

Chipster 2.x
chipster.csc.fi:61617
chipster-filebroker.csc.fi:8080

Chipster 1.x
chipster.csc.fi:61616
chipster-filebroker.csc.fi:8060

Embster
chipster.csc.fi:61619
chipster-filebroker.csc.fi:8090
Client application shows splash screen (loading screen), but gives an error before starting up. The error dialog reports "java.lang.NullPointerException" in details box.

Your local firewall is blocking Chipster file server. See firewall section for instructions.

Client application fails to start with SSLException "RSA premaster secret error".

Your local Java installation is missing some security files needed for secure network connections. Please contact your local system administrator or follow these instructions for installing them.

Due to US export restrictions some Java Runtime Environments are not bundled with strong security policy files. You can download the package "Java Cryptography Extension (JCE) Unlimited Strength Jurisdiction Policy Files" from http://java.sun.com/javase/downloads/ or through your system's package manager (if available there). If you are using OpenJDK, we are not aware of a method for installing the policy files there and for that reason recommend using regular Sun JDK or JRE.

When clicking on the start-up link, the browser asks if the file "chipster.jnlp" should be saved or opened with an application

Choose application "Java WebStart" (or "javaws").

Java Webstart is not among the applications in the browser's prompt.

You don't have Java Web Start properly installed. You can either contact your administrator or use the following tips to fix the problem yourself.

1) Check that you have Java Runtime Environment (JRE) properly installed. You can do it by entering "java -version" at the command line. It should output installed Java version. If not, install JRE (preferrably 1.6 or newer). JRE can be found from Java download page.

2) If you have properly functioning JRE, then Java Web Start is not properly configured to your browser (during the JRE installation Java Web Start is configured automatically to Internet Explorer, Mozilla and other Netscape family browsers). Please see Java Web Start installation guide for configuration help.

I have clicked the Launch Chipster -link on the front page, and during the automatic Java WebStart installation I am asked if Chipster should be given permissions of a normal application. What should I answer?

You have to answer "yes" in order for Chipster to start.

Java Web Start tries to update Java runtime environment (JRE), but fails.

In some systems the automatical JRE update does not work. For example, the working directory for the JRE installation might be the browser's directory, where the user is not allowed to install anything. Installing JRE 1.6 or newer manually solves the problem.

Application crashes when selecting "yes" to "create shortcut(s)" (on Mac OS X)

Due to some issue with Java and/or Mac OS X, creating shortcuts fails on some environments. Choosing "no" should allow you to start Chipster normally. As this happens before our application starts, we unfortunately cannot do anything about it.

Client application fails to start with FailedDownloadException/SocketException.

When starting the client you get "com.sun.deploy.net.FailedDownloadException: Unable to load resource: http://chipster.csc.fi/...", with wrapped "java.net.SocketException: Permission denied: connect". Try first to empty Java Web Start cache.

If emptying cache does not help, then your local configuration does not allow loading of Java Web Start startup file. This can be because there is a strict proxy on your local network or because your local security package is configured to block JNLP files. Contact your system administrator, or try using a different workstation.

Client application fails to start with UnknownHostException.

Your own hostname cannot be resolved. This can happen on Linux environments. Add your hostname (e.g, "127.0.0.1 localhost foobar") to you /etc/hosts or contact system administrator to find out why your hostname cannot be resolved.

See technical FAQ for details.

How to empty Java Web Start cache if client application still does not start.

When Chipster configuration changes, some environments can keep old cached copies that cause problems. It is a good idea to empty the Java Web Start cache if the client refuses to start.

To empty the cache, open Java Control Panel ("Java" in Windows Control Panel, or "ControlPanel" at Linux command line). Go to General -> Temporary Internet Files -> View. Select all Chipster files and click Remove selected items (red cross). Then try to restart the application.

How to change proxy settings if application starts, but none of the tools can be run.

If application is otherwise functioning properly but all attempts to run analysis tools result in an immediate error being shown, it is because your local proxy server is messing up file transfers. Best solution is to configure Java proxy settings.

Proxy settings can be accessed using Java Control Panel ("Java" in Windows Control Panel, or "ControlPanel" at Linux command line) and going to Edit -> Preferences -> General -> Network settings. Change selection to "Direct connection". On Mac OS X you have to use Apple -> System Preferences -> Network. Restart Chipster for the change to take effect.

See technical FAQ for details.

If you are still having troubles, please contact the Chipster team.