On May 21, 2010, at 4:38 PM, Nate Coraor wrote:
Davide Cittaro wrote:
Mmm...
Do you happen to know how your Postgres was compiled? This can happen if --enable-thread-safety wasn't specified.
Mmm.. I've installed the binary version provided for nexenta (i.e. apt-get install), I'll check for that
Also, if you're scrambling psycopg2 for a platform we don't provide, the bug could be in the way I've instructed the scramble script to compile the static libpq.
Using this psycopg2-2.0.13_8.4.2_static-py2.6-solaris-2.10-i86pc_64-ucs2.egg
I see that you used postgres 8.4 while I have postgres 8.3.... Mmm... the strange fact is that, before trying the multiserver I was able to run some job...
For Main on Solaris I build the egg by hand and dynamically link with the real Postgres install instead of statically linking our auto-compiled version:
PYTHONPATH=/path/to/galaxy/scripts/scramble/lib python setup.py build_ext --rpath=/usr/postgres/8.3/lib/64 egg_info --tag-build=_8.2.6_static bdist_egg
I'll try that
Also, is threadlocal enabled in the config?
database_engine_option_strategy = threadlocal
It is
thanks
d
--nate
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 <mailto:davide.cittaro@ifom-ieo-campus.it>
*/