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pegasus-db-admin failure on hpc-pegasus.usc.edu

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    • Type: Icon: Bug Bug
    • Resolution: Fixed
    • Priority: Icon: Major Major
    • master, 4.5.0
    • Affects Version/s: master
    • Component/s: CLI: pegasus-db-admin
    • None
    • Environment:
      hpc-pegasus.usc.edu which has 4.4.3cvs installed

      pegasus-db-admin failed for me on hoc-pegasus.usc.edu

      there i have not run 4.5.0 yet , just set it up.

      2015.04.15 14:39:47.849 PDT: [INFO] event.pegasus.code.generation dax.id mpi-hello-world_0 (0.351 seconds) - FINISHED
      2015.04.15 14:39:49.519 PDT: processing properties file /auto/rcf-40/vahi/tutorial/mpi-hello-world/work/2015-04-15_143945/dags/vahi/pegasus/mpi-hello-world/run0001/pegasus.4545870554415408793.properties...
      2015.04.15 14:39:50.206 PDT: Your database has been updated.
      2015.04.15 14:39:50.315 PDT: [ERROR] Traceback (most recent call last):
      2015.04.15 14:39:50.320 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/bin/pegasus-db-admin", line 37, in <module>
      2015.04.15 14:39:50.326 PDT: [ERROR] main()
      2015.04.15 14:39:50.331 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/python2.6/site-packages/Pegasus/db/admin/commands.py", line 301, in main
      2015.04.15 14:39:50.336 PDT: [ERROR] DBAdminCommand().main()
      2015.04.15 14:39:50.342 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/python2.6/site-packages/Pegasus/command.py", line 105, in main
      2015.04.15 14:39:50.347 PDT: [ERROR] cmd.main(args)
      2015.04.15 14:39:50.353 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/python2.6/site-packages/Pegasus/command.py", line 25, in main
      2015.04.15 14:39:50.358 PDT: [ERROR] self.run()
      2015.04.15 14:39:50.364 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/python2.6/site-packages/Pegasus/db/admin/commands.py", line 95, in run
      2015.04.15 14:39:50.369 PDT: [ERROR] db = _get_connection(dburi, self.options.config_properties, self.options.submit_dir, self.options.db_type, pegasus_version=self.options.pegasus_version, create=True, force=self.options.force)
      2015.04.15 14:39:50.375 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/python2.6/site-packages/Pegasus/db/admin/commands.py", line 244, in _get_connection
      2015.04.15 14:39:50.380 PDT: [ERROR] return connection.connect_by_properties(config_properties, db_type, pegasus_version=pegasus_version, schema_check=schema_check, create=create, force=force)
      2015.04.15 14:39:50.385 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/python2.6/site-packages/Pegasus/db/connection.py", line 72, in connect_by_properties
      2015.04.15 14:39:50.391 PDT: [ERROR] return connect(dburi, echo, schema_check, create=create, pegasus_version=pegasus_version, force=force)
      2015.04.15 14:39:50.396 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/python2.6/site-packages/Pegasus/db/connection.py", line 54, in connect
      2015.04.15 14:39:50.402 PDT: [ERROR] db_create(dburi, engine, db, pegasus_version=pegasus_version, force=force)
      2015.04.15 14:39:50.407 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/python2.6/site-packages/Pegasus/db/admin/admin_loader.py", line 59, in db_create
      2015.04.15 14:39:50.412 PDT: [ERROR] metadata.create_all(engine)
      2015.04.15 14:39:50.418 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/schema.py", line 2784, in create_all
      2015.04.15 14:39:50.423 PDT: [ERROR] tables=tables)
      2015.04.15 14:39:50.428 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/base.py", line 1487, in _run_visitor
      2015.04.15 14:39:50.434 PDT: [ERROR] conn._run_visitor(visitorcallable, element, **kwargs)
      2015.04.15 14:39:50.439 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/base.py", line 1130, in _run_visitor
      2015.04.15 14:39:50.444 PDT: [ERROR] **kwargs).traverse_single(element)
      2015.04.15 14:39:50.450 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/sql/visitors.py", line 111, in traverse_single
      2015.04.15 14:39:50.455 PDT: [ERROR] return meth(obj, **kw)
      2015.04.15 14:39:50.461 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/ddl.py", line 70, in visit_metadata
      2015.04.15 14:39:50.466 PDT: [ERROR] self.traverse_single(table, create_ok=True)
      2015.04.15 14:39:50.471 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/sql/visitors.py", line 111, in traverse_single
      2015.04.15 14:39:50.477 PDT: [ERROR] return meth(obj, **kw)
      2015.04.15 14:39:50.482 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/ddl.py", line 93, in visit_table
      2015.04.15 14:39:50.487 PDT: [ERROR] self.traverse_single(index)
      2015.04.15 14:39:50.493 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/sql/visitors.py", line 111, in traverse_single
      2015.04.15 14:39:50.498 PDT: [ERROR] return meth(obj, **kw)
      2015.04.15 14:39:50.503 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/ddl.py", line 105, in visit_index
      2015.04.15 14:39:50.509 PDT: [ERROR] self.connection.execute(schema.CreateIndex(index))
      2015.04.15 14:39:50.514 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/base.py", line 664, in execute
      2015.04.15 14:39:50.519 PDT: [ERROR] params)
      2015.04.15 14:39:50.525 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/base.py", line 723, in _execute_ddl
      2015.04.15 14:39:50.530 PDT: [ERROR] compiled
      2015.04.15 14:39:50.536 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/base.py", line 878, in _execute_context
      2015.04.15 14:39:50.541 PDT: [ERROR] context)
      2015.04.15 14:39:50.546 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/base.py", line 871, in _execute_context
      2015.04.15 14:39:50.552 PDT: [ERROR] context)
      2015.04.15 14:39:50.557 PDT: [ERROR] File "/auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/lib64/pegasus/externals/python/sqlalchemy/engine/default.py", line 320, in do_execute
      2015.04.15 14:39:50.562 PDT: [ERROR] cursor.execute(statement, parameters)
      2015.04.15 14:39:50.568 PDT: [ERROR] sqlalchemy.exc.OperationalError: (OperationalError) index wf_id_KEY already exists u'CREATE UNIQUE INDEX "wf_id_KEY" ON workflow (wf_id)' ()
      2015.04.15 14:39:50.574 PDT: [FATAL ERROR] java.lang.RuntimeException: pegasus-db-admin failed with non zero exit status /auto/rcf-proj/gmj/pegasus/SOFTWARE/pegasus/pegasus-4.5.0cvs/bin/pegasus-db-admin update -t master -c /auto/rcf-40/vahi/tutorial/mpi-hello-world/work/2015-04-15_143945/dags/vahi/pegasus/mpi-hello-world/run0001/pegasus.4545870554415408793.properties
      at edu.isi.pegasus.planner.common.PegasusDBAdmin.checkDatabase(PegasusDBAdmin.java:188)
      at edu.isi.pegasus.planner.common.PegasusDBAdmin.checkMasterDatabaseForVersionCompatibility(PegasusDBAdmin.java:128)
      at edu.isi.pegasus.planner.client.CPlanner.checkMasterDatabaseForVersionCompatibility(CPlanner.java:1867)
      at edu.isi.pegasus.planner.client.CPlanner.executeCommand(CPlanner.java:683)
      at edu.isi.pegasus.planner.client.CPlanner.executeCommand(CPlanner.java:362)
      at edu.isi.pegasus.planner.client.CPlanner.main(CPlanner.java:243)

            Assignee:
            rafsilva Rafael Ferreira Da Silva (Inactive)
            Reporter:
            vahi Karan Vahi
            Watchers:
            2 Start watching this issue

              Created:
              Updated:
              Resolved: