Hi Andrej,

When you installed LabKey, did you make sure that the Tomcat user had permission to the respective location you installed LabKey in?

Reviewing the errors in the log, the specific error appears to have been trigged after the system tried to send out an email on an invalid email host configuration. But prior to that, it also appeared that the system had no way of creating a heapdump due to invalid permissions for the tomcat user trying to run LabKey.

Regards,

Jon

Hi Jon!

Thank you for your reply. I had the same notion. However, the permissions on most probable locations for audit to access seem to be fine. For example, tomcat8 is the owner of /usr/share/labkey where labkey was installed.

Could it be a postgreSQL error? Is there a simple way to verify that labkey can access the database?

Thank you!

Andrej

HI Andrej,

You should be able to use PSQL to see if you can login and access the database.

For example, if you're using the default port of 5432 for the PostgreSQL server, you can run the psql command like this:

>psql -h localhost -p 5434 -U postgres

This assumes that you're doing this from the server (localhost) and the username being "postgres".

Can you give this a try and provide us with the output?

Regards,

Jon

andrej@merlin:~$ psql -h localhost -p 5432 -U postgres
Password for user postgres:
psql (9.4.6)
SSL connection (protocol: TLSv1.2, cipher: ECDHE-RSA-AES256-GCM-SHA384, bits: 256, compression: off)
Type "help" for help.

postgres=# \l
                                  List of databases
   Name | Owner | Encoding | Collate | Ctype | Access privileges
-----------+----------+----------+-------------+-------------+-----------------------
 labkey | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
 postgres | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 |
 template0 | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =c/postgres +
           | | | | | postgres=CTc/postgres
 template1 | postgres | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =c/postgres +
           | | | | | postgres=CTc/postgres
(4 rows)

As you see I am running under SSL. The labkey database is the one I created by hand . The password is the same as given in the labkey.xml configuration file (Attaching it for reference).

Edit: I restarted postgresql writing to a different location w/o creating a labkey database. Even then, once I tried to modify the Site Settings, the problem persists, even though the labkey database is created via the webapp. During postgresql restart the logging was made more verbose; attaching both labkey.log as well as postgresql-9.4-main.log. The latter definitely shows that labkey does indeed connect to the postgresql driven database. From labkey.log it is also evident that the servlet can access labkey user space as it moves the modules.

Edit2: Got it. I was changing the authorityID portion of the LSID. If I leave that part unchanged, the rest of the configuration can be set. Since the current setting was (I guess) extracted from my mail address, it would be nice to be able to set it somewhere. Clearly, by running Site Settings, one can not do that.

Thank you!

Andrej

Glad things are working for you now Andrej!