On May 21, 2010, at 3:20 PM, Nate Coraor wrote:

Davide Cittaro wrote:
Hi all, after successful configuration of multiple server instances (web and runner) I've placed everything behind apache proxy (actually I'm trying to).
I can see the welcome page and navigate through my history (still I have to delegate the authentication to apache), nevertheless I'm not able to perform any job...
getting data from UCSC is waiting for run after a couple of hours, uploading files is stuck...
Hence I've tried to disable the proxy thing and still have the same issues. I've then checked at the log files for the five runners and two of them report this:
[runner0]

...

[runner1]

This is most likely the problem.  At present we only support a single job runner.  Try only starting runner0 and see if it works.


Mmm...

galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,681 RoundRobin queue: inserted new job for user/session = 6
galaxy.jobs DEBUG 2010-05-21 15:53:48,681 job 24 put in policy queue
galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 15:53:48,682 RoundRobin queue: retrieving job from job queue for session = 6
galaxy.jobs DEBUG 2010-05-21 15:53:48,682 dispatching job 24 to local runner
galaxy.jobs DEBUG 2010-05-21 15:53:48,773 job 24 dispatched
galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,018 executing: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ         71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat   
galaxy.jobs.runners.local DEBUG 2010-05-21 15:53:49,495 execution finished: python /data/galaxy_dist/tools/data_source/upload.py /tmp/tmphIrPuJ         71:/data/galaxy_dist/database/job_working_directory/24/dataset_71_files:/data/galaxy_dist/database/files/000/dataset_71.dat   
galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,689 Job wrapper finish method failed
Traceback (most recent call last):
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 122, in run_job
    job_wrapper.finish( stdout, stderr )
  File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 569, in finish
    self.sa_session.flush()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush
    self._flush(objects)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1443, in _flush
    flush_context.finalize_flush_changes()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 288, in finalize_flush_changes
    self.session._register_newly_persistent(elem.state)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1015, in _register_newly_persistent
    instance_key = mapper._identity_key_from_state(state)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1085, in _identity_key_from_state
    return self.identity_key_from_primary_key(self._primary_key_from_state(state))
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1096, in _primary_key_from_state
    return [self._get_state_attr_by_column(state, column) for column in self.primary_key]
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1110, in _get_state_attr_by_column
    return self._get_col_to_prop(column).getattr(state, column)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/properties.py", line 99, in getattr
    return state.get_impl(self.key).get(state, state.dict)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/attributes.py", line 377, in get
    value = callable_()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/state.py", line 185, in __call__
    attr.impl.key in unmodified
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1878, in _load_scalar_attributes
    result = session.query(mapper)._get(identity_key, refresh_state=state, only_load_props=attribute_names)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get
    return q.all()[0]
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
    return self.__execute_context(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context
    return context.get_result_proxy()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy
    return base.BufferedRowResultProxy(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__
    self._init_metadata()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata
    self.__buffer_rows()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows
    self.__rowbuffer = self.cursor.fetchmany(size)
  File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__
    m = _parser(value.strip())
OperationalError: could not receive data from server: Error 0

galaxy.jobs.runners.local ERROR 2010-05-21 15:53:49,740 Uncaught exception running job
Traceback (most recent call last):
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next
    self.run_job( job_wrapper )
  File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 125, in run_job
    job_wrapper.fail("Unable to finish job", exception=True)
  File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail
    self.sa_session.refresh( job )
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/scoping.py", line 127, in do
    return getattr(self.registry(), name)(*args, **kwargs)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 929, in refresh
    only_load_props=attribute_names) is None:
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1500, in _get
    return q.all()[0]
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1267, in all
    return list(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1361, in __iter__
    return self._execute_and_instances(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances
    result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none())
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 755, in execute
    clause, params or {})
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute
    return Connection.executors[c](self, object, multiparams, params)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement
    return self.__execute_context(context)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 901, in __execute_context
    return context.get_result_proxy()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy
    return base.BufferedRowResultProxy(self)
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1415, in __init__
    self._init_metadata()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata
    self.__buffer_rows()
  File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows
    self.__rowbuffer = self.cursor.fetchmany(size)
  File "/usr/local/lib/python2.6/decimal.py", line 540, in __new__
    m = _parser(value.strip())
OperationalError: could not receive data from server: Error 0

d

/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro@ifom-ieo-campus.it
*/