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 */