Hello,

What version of LabKey did you install?

Tomcat 8.0.39 currently isn't guaranteed to work well depending on the version of LabKey you've installed (see our supported technologies page here for more details: https://www.labkey.org/home/Documentation/wiki-page.view?name=supported)

Also, is that version of Tomcat a package version or downloaded direct from Apache's website? We've also found that package versions of Tomcat tend to not work so well with LabKey due to various issues, like the connector pool drivers that are provided.

Regards,

Jon

Hey Jon,

I installed the latest build of LabKey 16.3 available from LabKey's download page. Yes, Apache Tomcat was installed from a tarball downloaded from their website. (http://tomcat.apache.org/download-80.cgi)

Hello,

The error sounds like it might be due to multiple instances of Tomcat running on the server.

Can you run a "ps -ef | grep -i java" and see what you have going on your box right now? If there is more than one setup, I'd recommend killing both services, then deleting the new labkey database that was created, then restarting the process again.

Regards,

Jon

Hi Jon,

Here's the output of that command (I included one looking for Postgres, too). This server is brand new, so it's the first time we've run LabKey on it.

jmikkelsen@********:~$ ps -ef | grep -i java
tomcat 1681 1 85 12:00 pts/0 00:00:18 /home/tomcat/jdk1.8.0_112/bin/java -Djava.util.logging.config.file=/home/tomcat/apache-tomcat-8.0.39/conf/logging.properties -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -Xms128m -Xmx2048m -XX:-HeapDumpOnOutOfMemoryError -Djdk.tls.ephemeralDHKeySize=2048 -Djava.protocol.handler.pkgs=org.apache.catalina.webresources -Djava.endorsed.dirs=/home/tomcat/apache-tomcat-8.0.39/endorsed -classpath /home/tomcat/apache-tomcat-8.0.39/bin/bootstrap.jar:/home/tomcat/apache-tomcat-8.0.39/bin/tomcat-juli.jar -Dcatalina.base=/home/tomcat/apache-tomcat-8.0.39 -Dcatalina.home=/home/tomcat/apache-tomcat-8.0.39 -Djava.io.tmpdir=/home/tomcat/apache-tomcat-8.0.39/temp org.apache.catalina.startup.Bootstrap start
jmikkel+ 1709 1063 0 12:00 pts/0 00:00:00 grep --color=auto -i java


jmikkelsen@*********:~$ ps -ef | grep -i postgres
postgres 878 1 0 Nov25 ? 00:00:03 /usr/lib/postgresql/9.5/bin/postgres -D /var/lib/postgresql/9.5/main -c config_file=/etc/postgresql/9.5/main/postgresql.conf
postgres 880 878 0 Nov25 ? 00:00:00 postgres: checkpointer process
postgres 881 878 0 Nov25 ? 00:00:00 postgres: writer process
postgres 882 878 0 Nov25 ? 00:00:00 postgres: wal writer process
postgres 883 878 0 Nov25 ? 00:00:01 postgres: autovacuum launcher process
postgres 884 878 0 Nov25 ? 00:00:02 postgres: stats collector process
postgres 1720 878 0 12:00 ? 00:00:00 postgres: labkey labkey 127.0.0.1(60646) idle
postgres 1739 878 0 12:00 ? 00:00:00 postgres: labkey labkey 127.0.0.1(60650) idle
postgres 1753 878 0 12:00 ? 00:00:00 postgres: labkey labkey 127.0.0.1(60652) idle
jmikkel+ 1795 1063 0 12:03 pts/0 00:00:00 grep --color=auto -i postgres


I can drop the labkey database, restart Tomcat, and it will go back to the initial LabKey setup, but as soon as I enter credentials for an administrator account it just sends me to a sign-in page and I can't complete the setup.

Hello,

Any chance you can try the 8.0.38 version, drop the DB, and try once more?

http://archive.apache.org/dist/tomcat/tomcat-8/v8.0.38/

The behavior you described is definitely not normal and something that I'm suspecting is being caused by Tomcat.

Regards,

Jon

Hey Jon,

I followed your steps, and I still run into the same exact problem. My Postgres logs show that the user labkey was successfully authorized, and created and accessd a database named labkey, and that's where the log stops. Directories have been created inside /usr/local/labkey (i.e files/ ), so it suggests that it is able to start the setup, but for some reason it cannot complete it. Not sure what else to try..

Jordan

Hi Jon,

The issue is now resolved. It was due to cookies not being accepted on the remote-desktop's browser I had the unfortunate experience of using. Thanks for all your help, regardless!

Jordan

Fantastic! Thanks for letting us know Jordan!