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Every once in a while, NetBeans starts a new Tomcat instance even if Tomcat is already running. There is only one open project, and it is using the bundled Tomcat server. In order to reproduce this issue, try creating a Web application with some custom classes, servlets and JSPs and keep clicking on the "Run" button until Tomcat fails to start. This is especially important on low-end machines because starting a new Tomcat instance can cause excessive swapping.
Stepane, is it possible that tomcat is started if there is no response from the http "ping" in isRunning?
Yes, I guess this could happen if Tomcat's respond was slower then 1000 ms. In NetBeans 4.1 it should be possible to overwrite the default timeout value? It would be great, if you could confirm that this workaround is working. Go to: <NB_USERDIR>/config/.nbattrs and add the following line <attr name="J2EE\InstalledServers\Tomcat_instance\runningCheckTimeout" stringvalue="5000"/> under: <attributes version="1.0"> <fileobject name=""> 5000 is the timeout in ms. Please note that this won't work in NB 4.0!
Closing as WORKSFORME since I can't reproduce this issue and there is no farther response from the user.