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  1. Pegasus
  2. PM-580

pegasus-analyzer has problems querying MySQL stampede db

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      pegasus-analyzer $PWD
      pegasus-analyzer: initializing...

      ************************************Summary*************************************

       Total jobs : 13 (100.00%)
       # jobs succeeded : 5 (38.46%)
       # jobs failed : 3 (23.08%)
       # jobs unsubmitted : 5 (38.46%)

      ******************************Failed jobs' details******************************
      Traceback (most recent call last):
        File "/opt/pegasus/default/bin/pegasus-analyzer", line 1301, in ?
          analyze_db(options.config_properties)
        File "/opt/pegasus/default/bin/pegasus-analyzer", line 919, in analyze_db
          my_info = workflow_stats.get_job_instance_info(my_job[0])[0]
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/python/netlogger/analysis/workflow/stampede_statistics.py", line 921, in get_job_instance_info
          return q.all()
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/orm/query.py", line 1492, in all
          return list(self)
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/orm/query.py", line 1604, in __iter__
          return self._execute_and_instances(context)
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/orm/query.py", line 1609, in _execute_and_instances
          mapper=self._mapper_zero_or_none())
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/orm/session.py", line 700, in execute
          return self._connection_for_bind(engine, close_with_result=True).execute(
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/engine/base.py", line 1194, in execute
          params)
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/engine/base.py", line 1274, in _execute_clauseelement
          return self.__execute_context(context)
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/engine/base.py", line 1305, in __execute_context
          context.parameters[0], context=context)
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/engine/base.py", line 1404, in _cursor_execute
          context)
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/engine/base.py", line 1397, in _cursor_execute
          context)
        File "/opt/pegasus/pegasus-4.0.0/lib/pegasus/externals/python/sqlalchemy/engine/default.py", line 299, in do_execute
          cursor.execute(statement, parameters)
        File "/usr/lib/python2.4/site-packages/MySQLdb/cursors.py", line 163, in execute
          self.errorhandler(self, exc, value)
        File "/usr/lib/python2.4/site-packages/MySQLdb/connections.py", line 35, in defaulterrorhandler
          raise errorclass, errorvalue
      sqlalchemy.exc.OperationalError: (OperationalError) (1054, "Unknown column 'job_instance.job_instance_id' in 'where clause'") 'SELECT job_instance.job_instance_id AS job_instance_job_instance_id, job_instance.site AS job_instance_site, job_instance.stdout_file AS job_instance_stdout_file, job_instance.stderr_file AS job_instance_stderr_file, job_instance.stdout_text AS job_instance_stdout_text, job_instance.stderr_text AS job_instance_stderr_text, job_instance.work_dir AS job_instance_work_dir, (SELECT workflow.submit_dir \nFROM workflow \nWHERE workflow.wf_id = job_instance.subwf_id) AS subwf_dir, (SELECT job.exec_job_id \nFROM job \nWHERE job.job_id = job_instance.job_id) AS job_name, (SELECT job.submit_file \nFROM job \nWHERE job.job_id = job_instance.job_id) AS submit_file, (SELECT job.executable \nFROM job \nWHERE job.job_id = job_instance.job_id) AS executable, (SELECT job.argv \nFROM job \nWHERE job.job_id = job_instance.job_id) AS argv, (SELECT workflow.submit_dir \nFROM workflow \nWHERE workflow.wf_id = %s) AS submit_dir, (SELECT jobstate.state \nFROM jobstate, (SELECT max(jobstate.jobstate_submit_seq) AS max_job_submit_seq \nFROM jobstate \nWHERE jobstate.job_instance_id = job_instance.job_instance_id) AS anon_1 \nWHERE jobstate.job_instance_id = job_instance.job_instance_id AND jobstate.jobstate_submit_seq = anon_1.max_job_submit_seq) AS state, (SELECT invocation.executable \nFROM invocation \nWHERE invocation.job_instance_id = job_instance.job_instance_id AND invocation.task_submit_seq = %s) AS pre_executable, (SELECT invocation.argv \nFROM invocation \nWHERE invocation.job_instance_id = job_instance.job_instance_id AND invocation.task_submit_seq = %s) AS pre_argv, (SELECT host.hostname \nFROM host \nWHERE host.host_id = job_instance.host_id) AS hostname \nFROM job_instance \nWHERE job_instance.job_instance_id = %s' (2L, -1, -1, 19L)


      However, the column _does_ exist in the database:

      mysql> describe job_instance;
      +-------------------+---------------+------+-----+---------+----------------+
      | Field | Type | Null | Key | Default | Extra |
      +-------------------+---------------+------+-----+---------+----------------+
      | job_instance_id | bigint(20) | NO | PRI | NULL | auto_increment |
      | job_id | bigint(20) | NO | MUL | NULL | |
      | host_id | bigint(20) | YES | MUL | NULL | |
      | job_submit_seq | int(11) | NO | | NULL | |
      | sched_id | varchar(255) | YES | | NULL | |
      | site | varchar(255) | YES | | NULL | |
      | user | varchar(255) | YES | | NULL | |
      | work_dir | text | YES | | NULL | |
      | cluster_start | decimal(16,6) | YES | | NULL | |
      | cluster_duration | decimal(10,3) | YES | | NULL | |
      | local_duration | decimal(10,3) | YES | | NULL | |
      | subwf_id | bigint(20) | YES | MUL | NULL | |
      | stdout_file | varchar(255) | YES | | NULL | |
      | stdout_text | text | YES | | NULL | |
      | stderr_file | varchar(255) | YES | | NULL | |
      | stderr_text | text | YES | | NULL | |
      | stdin_file | varchar(255) | YES | | NULL | |
      | multiplier_factor | int(11) | NO | | NULL | |
      | exitcode | int(11) | YES | | NULL | |
      +-------------------+---------------+------+-----+---------+----------------+
      19 rows in set (0.00 sec)

      I'll attach the submit dir next.

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            • Assignee:
              mmgoode Monte Goode
              Reporter:
              voeckler Jens Voeckler
            • Watchers:
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              • Created:
                Updated:
                Resolved: