A query runs for awhile, then an error occurs, well before the 180 second timeout

There are other timeouts that might need to be configured:

1. php timeout (default_socket_timeout in php.ini) too small
2. Apache/IIS timeout too small
3. Wildfly worker thread pool too small
4. IIS PHP Fast CGI Activity Timeout might be set to 30 seconds by default. (Go to IIS --> Fast CGI Settings --> Edit )

The webclient keeps saying "The PM Cell or the address in the properties file is incorrect."

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Tips for Optimizing i2b2 query speed

Postgres

1. Do not use '%' in any concept code. In Postgres, this is known to prevent the database from using indexes.
2. In Postgres, consider using table partitioning

MSSQL

1. Use clustered columnstore indexes for the fact table.

All platforms

1. If your fact table is extremely large, consider splitting it into multiple fact tables.
2. ... more to come...

I can log in, but nothing else works. On the server, I see a lot of "invalid session" errors in the Wildfly log

Your database server and Wildfly server might not have the same system date and time. Make sure they are the same, and that they are in the same time zone.