Chapter 18. Useful Tips

18.1. Migrating From Pegasus 4.5.X to Pegasus current version

Most of the migrations from one version to another are related to database upgrades, that is addressed by running the tool pegasus-db-admin.

18.1.1. Database Upgrades From Pegasus 4.5.X to Pegasus current version

Since Pegasus 4.5 all databases are managed by a single tool: pegasus-db-admin. Databases will be automatically updated when pegasus-plan is invoked, but WORKFLOW databases from past runs may not be updated accordingly. Since Pegasus 4.6.0, the pegasus-db-admin tool provides an option to automatically update all databases from completed workflows in the MASTER database. To enable this option, run the following command:

$ pegasus-db-admin update -a
Your database has been updated.
Your database is compatible with Pegasus version: 4.7.0

Verifying and updating workflow databases:
21/21

Summary:
Verified/Updated: 21/21
Failed: 0/21
Unable to connect: 0/21
Unable to update (active workflows): 0/21

Log files:
20161006T134415-dbadmin.out (Succeeded operations)
20161006T134415-dbadmin.err (Failed operations)
      

This option generates a log file for succeeded operations, and a log file for failed operations. Each file contains the list of URLs of the succeeded/failed databases.

Note that, if no URL is provided, the tool will create/use a SQLite database in the user's home directory: ${HOME}/.pegasus/workflow.db.

For complete description of pegasus-db-admin, see the man page.

18.1.2. Migration from Pegasus 4.6 to 4.7

In addition to the database changes, in Pegasus 4.7 the default submit directory layout was changed from a flat structure where all submit files independent of the number of jobs in the workflow appeared in a single directory. For 4.7, the default is a hierarchal directory structure two levels deep. To use the earlier layout, set the following property

pegasus.dir.submit.mapper     Flat