Database Issues

Authors: orcid logoNate Coraor avatar Nate CoraorAdd Contributions!

For slow queries, start with EXPLAIN ANALYZE

However it can be useful to dig into the queries with the Postgres EXPLAIN Visualizer (PEV) to get a more visual and clear representation. (Try it with this demo data)

You can set some options in the Galaxy configuration or database that will help debugging this:

  • database_engine_option_echo (but warning, extremely verbose)
  • slow_query_log_threshold logs to Galaxy log file
  • sentry_sloreq_threshold if using Sentry

Additionally check that your database is running VACUUM regularly enough and look at VACUUM ANALYZE

There are some gxadmin query pg-* commands which can help you monitor and track this information.

Lastly, check your database settings! It might not have enough resources allocated. Check PGTune for some suggestions of optimised parameters.

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Resource PURL: https://gxy.io/GTN:F00195
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