If you have encountered errors or other problems when installing and starting LabKey Server, first review the topic Troubleshooting: Common Issues. If you're still encountering problems, please review the list below for common errors, messages, and problems.
You can also search the LabKey Community Support Forums for guidance. If you don't already see your issue listed there, please post a new question.
1.
| Error |
Error on startup, "Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections." |
| Problem | Tomcat cannot connect to the database. |
| Likely causes |
|
| Solution | Make sure that database is started and fully operational before starting Tomcat. Check the database connection URL, user name, and password in the <tomcat>/conf/Catalina/localhost/labkey.xml file. |
2.
| Problem | Error when connecting to LabKey server on Linux: Can't connect to X11 window server or Could not initialize class ButtonServlet. |
| Solution |
Run tomcat headless. Edit tomcat's catalina.sh file, and add the following line near the top of the file:
|
3.
| Problem |
Viewing certain pages results in a specific NoSuchMethodError. |
| Error |
java.lang.NoSuchMethodError:
org.apache.jasper.runtime.JspRuntimeLibrary.releaseTag(Ljavax/servlet/jsp/tagext/Tag;Lorg/apache/tomcat/InstanceManager;Z)V
at org.labkey.jsp.compiled.org.labkey.core.admin.maintenance_jsp._jspx_meth_labkey_005ferrors_005f0(maintenance_jsp.java:159)
at org.labkey.jsp.compiled.org.labkey.core.admin.maintenance_jsp._jspService(maintenance_jsp.java:110)
at org.labkey.api.view.JspView.renderView(JspView.java:170)
at org.labkey.api.view.WebPartView.renderInternal(WebPartView.java:372)
|
| Solution |
Upgrade your Apache Tomcat deployment to a supported version. |
4.
| Problem |
After upgrading LabKey Server the following error is shown. |
| Error |
java.lang.NoSuchMethodError: org.labkey.api.settings.HeaderProperties: method 'void <init>()' not found |
| Solution |
This may be the result of a partial upgrade, where some but not all of the binaries get upgraded.
|
5.
| Error |
You receive a message "The requested resource () is not available." OR "500: Unexpected server error" and see something like one of the following in the log file: |
| Problem |
SEVERE: Error deploying configuration descriptor labkey.xml java.lang.IllegalStateException: ContainerBase.addChild: start: LifecycleException: start: : java.lang.UnsupportedClassVersionError: org/labkey/bootstrap/LabkeyServerBootstrapClassLoader : Unsupported ... A failure occurred during LabKey Server startup. java.lang.NoClassDefFoundError: javax/script/ScriptEngineFactory.... A failure occurred during LabKey Server startup. java.lang.UnsupportedClassVersionError: Bad version number in .class file at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:675) ... |
| Solution |
You may need to use a newer version of the JDK. See Install Required Components. Confirm that Tomcat is configured to use the correct version of Java, as it is possible to have multiple versions installed simultaneously. |
6.
| Problem |
Fatal Error in Java Runtime Environment |
| Error |
# A fatal error has been detected by the Java Runtime Environment: |
| Cause |
These are typically bugs in the Java Virtual Machine itself. |
| Solution |
Ensuring that you are on the latest patched release for your preferred Java version is best practice for avoiding these errors. If you have multiple versions of Java installed, be sure that JAVA_HOME and other configuration is pointing at the correct location. If you are running through the debugger in IntelliJ, check the JDK configuration: under Project Structure > SDKs check the JDK home path and confirm it points to the newer version. |
7.
| Problem |
If you see the following error when running complex queries on PostgreSQL: |
| Error |
org.postgresql.util.PSQLException: ERROR: failed to build any 8-way joins |
| Solution |
Increase the join collapse limit. Edit postgresql.conf and change the following line:
to
|
8.
| Problem |
Plots are not rendered as expected, or cannot be exported to formats like PDF or PNG |
| Error |
java.lang.InternalError: java.lang.reflect.InvocationTargetException
at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:312)
at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74)
...
Caused by: java.lang.NullPointerException: Cannot load from short array because "sun.awt.FontConfiguration.head" is null
at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1260)
at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:223)
...
or
java.lang.InternalError: java.lang.reflect.InvocationTargetException at java.desktop/sun.font.FontManagerFactory$1.run(FontManagerFactory.java:86) at java.base/java.security.AccessController.doPrivileged(AccessController.java:312) at java.desktop/sun.font.FontManagerFactory.getInstance(FontManagerFactory.java:74) ... Caused by: java.lang.NullPointerException at java.desktop/sun.awt.FontConfiguration.getVersion(FontConfiguration.java:1262) at java.desktop/sun.awt.FontConfiguration.readFontConfigFile(FontConfiguration.java:225) at java.desktop/sun.awt.FontConfiguration.init(FontConfiguration.java:107) ... |
| Solution |
Install the fonts required to generate plots, most typically missing on some Linux JDK installations |
10.
| Error |
One or more of:
|
| Problem | WebSocket connection errors are preventing a variety of actions from succeeding. Try using browser developer tools and checking the Console tab to see the specific errors. |
| Likely causes | A load balancer or proxy may be blocking websocket connections and needs to have its configuration updated. |
| Solution | Make sure that websockets are available and configured properly. |
11.
| Error |
On Java 16 or later, pipeline jobs and some other operations fail with errors |
| Problem | To be compatible with some libraries, such as Jackson, Java 16 and later need to be configured with a command-line argument to allow for successful serialization and deserialization. Errors may take different forms, but include messages like:
or
|
| Solution |
Add to the Java command line:
|
12.
| Error |
ERROR ModuleLoader 2022-04-07T10:09:07,707 main : Failure occurred during ModuleLoader init. |
| Cause | Beginning in January 2022, you can only upgrade from versions less than a year old. |
| Solution | Following the guidance in this topic, you will need to perform intermediate upgrades of LabKey Server to upgrade from older versions. |
13.
| Problem | Disk filling with Tomcat temporary files. For example, Excel exports might be leaving one file for every export in "temp/poifiles" folder. |
| Error |
...| comment: Exported to Excel | ERROR ExceptionUtil 2022-07-19T11:24:20,609 ps-jsse-nio-8443-exec-25 : Unhandled exception: No space left on device java.io.IOException: No space left on device |
| Likely causes | The Excel export writer is leaving temporary "poi-sxssf-####.xml" files behind. These can be fairly large and may correlate 1:1 with Excel exports. This issue was reported in version 22.3.5 and will be fixed in version 22.11.0 (or sooner). |
| Solution | These temporary "poifiles" may be safely deleted after the export is completed. Administrators can periodically clean these up; when this issue is resolved, they will be automatically cleaned up within 10 minutes of an Excel export |
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