Troubleshoot Server Installation and Configuration


In case of errors or other problems when installing and running LabKey Server, first review installation basics and options linked on the Install LabKey page.

Developer Mode

Running a server in "devmode" provides enhanced logging and enables the MiniProfiler. To run the server in devmode (using Tomcat 7):

  • Open a command prompt.
  • Go to the %CATALINA_HOME%\bin directory, for example:
C:\Program Files (x86)\LabKey Server\apache-tomcat-7.0.xx\bin
  • Execute the tomcat7w.exe program:
tomcat7w.exe //ES//LabKeyTomcat7
  • The command will open a program window. Click the Java tab.
  • In the Java Option box, scroll to the bottom of the properties. Add the following property at the bottom of the list:
  • Close the program window and restart the server.
  • To confirm that the server is running in devmode:
    • Go to (Admin) > Site > Admin Console.
    • Click Admin Console Links.
    • Under Diagnostics, click System Properties.
    • Locate the devmode property, and confirm that its value is 'true'.

Diagnostic Information

Which Version of LabKey Server Is Running?

  • Find your version number at (Admin) > Site > Admin Console.
  • Click Module Information.
  • Click the (Expand) icon for the Core module. The Version is the version number for your installation of LabKey Server.

Common Issues

Conflicting Applications

Before installing LabKey Server, you should shut down all other running applications. If you have problems during the installation, try additionally shutting down any virus scanning application, internet security applications, or other applications that run in the background.

Compatible Component Versions

Confirm that you are using the supported versions of the required components, as detailed in the Supported Technologies Roadmap. It is possible to have multiple versions of some software, like Java, installed at the same time. Check that other applications, such as Tomcat, are configured to use the correct versions.

PostgreSQL Installation

You may need to remove references to Cygwin from your Windows system path before installing LabKey, due to conflicts with the PostgreSQL installer. The PostgreSQL installer also conflicts with some antivirus or firewall software programs. (see for more information).

Non-English Versions of Windows

If you are running a non-English version of Windows, please use the manual install process, not the Windows Graphical Installer.

Tomcat Failure to Start

If installation fails to start tomcat (such as with an error like "The specified service already exists."), you may need to manually stop or delete a failing Tomcat service.

To stop the service on Windows, open Control Panel > Administrative Tools > Services. Select the relevant service, such as LabKey Server Apache Tomcat 7.0 and click Stop.

To delete, from the command line (may need to run as administrator):

sc delete LabKeyTomcat7

Java 8 Upgrade Note

When you upgrade to Java 8, be sure to remove the setting of MaxPermSize. If your CATALINA_OPTS or other configuration files include something like "-XX:MaxPermSize=256M" you may have errors when starting your server.

Connection Pool Size

If your server becomes unresponsive, it could be due to the depletion of available connections to the database. Watch for a Connection Pool Size of 8, which is the Tomcat connection pool default size and insufficient for a production server. To see the connection pool size for the LabKey data source, select (Admin) > Site > Admin Console and check the setting of Connection Pool Size on the Server Information panel. The connection pool size for every data source is also logged at server startup.

To set the connection pool size, edit your labkey.xml configuration file and change the appropriate setting for your LabKey data source to at least 20. Depending on the number of simultaneous users and the complexity of their requests, your deployment may require a larger connection pool size. The setting name depends on your Tomcat version:

  • Tomcat 7: the setting to change is called "maxActive".
  • Tomcat 8 and 9: the setting to change is called "maxTotal".
You should also consider changing this setting for external data sources to match the usage you expect.

The Tomcat data source connection pool settings changed significantly in Tomcat 8, so you must change your data source settings when you upgrade from Tomcat 7 to Tomcat 8/9. The most important change is to replace your "maxActive" setting (used with Tomcat 7) with "maxTotal" (Tomcat 8/9). Review the Database Connection Pooling section of the Tomcat Migration Guide for more information. See External Schemas and Data Sources for details and data source configuration examples.

Restart Installation from Scratch

If you have encountered prior failed installations, don't have any stored data you need to keep, and want to clean up and start completely from scratch, the following process may be useful:

  • Delete the Tomcat service (if it seems to be causing the failure):
    • From the command line (may need to run as administrator):
sc delete LabKeyTomcat7
  • Uninstall PostgresSQL using their installer.
    • Control Panel > Programs and Features
    • Select PostgreSQL program (PostgreSQL9.2 or similar).
    • Click Uninstall.
  • Delete the entire LabKey installation directory:
C:\Program Files\LabKey Server
  • Run the LabKey Installer again.

Installation Forum

You can search for problems resolved through community support in the LabKey Installation Forum.

If you don't see your issue listed there, you can post a new question. If the install seems successful, it is often helpful to submit debugging logs for diagnosis.

If the install failed to complete, please include the install.log and install-debug.log from your selected LabKey install directory (Note: you may wish to sanitize the logs of any database login information you provided to the installer). PostgreSQL logs its installation process separately. If the installer indicates that PostgreSQL installation/upgrage failed, please locate and include the PostgreSQL install logs as well.

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