Exception in thread Thread-73: Traceback (most recent call last): File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: database is locked The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/simulator_service.py", line 104, in async_launch_and_prepare_simulation self.operation_service.store_view_model(operation, project, session_stored_simulator) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/operation_service.py", line 268, in store_view_model dao.store_entity(operation) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/session_maker.py", line 377, in dec result = func(*args, **kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/root_dao.py", line 70, in store_entity self.session.commit() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1042, in commit self.transaction.commit() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 504, in commit self._prepare_impl() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 483, in _prepare_impl self.session.flush() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2536, in flush self._flush(objects) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2678, in _flush transaction.rollback(_capture_exception=True) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__ with_traceback=exc_tb, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2638, in _flush flush_context.execute() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute rec.execute(self) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute uow, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 236, in save_obj update, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 995, in _emit_update_statements statement, multiparams File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1011, in execute return meth(self, multiparams, params) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 298, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1130, in _execute_clauseelement distilled_params, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1317, in _execute_context e, statement, parameters, cursor, context File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1511, in _handle_dbapi_exception sqlalchemy_exception, with_traceback=exc_info[2], from_=e File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1277, in _execute_context cursor, statement, parameters, context File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 593, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) database is locked [SQL: UPDATE "OPERATIONS" SET view_model_disk_size=? WHERE "OPERATIONS".id = ?] [parameters: (7606, 2)] (Background on this error at: http://sqlalche.me/e/13/e3q8) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/burst_service.py", line 96, in mark_burst_finished dao.store_entity(burst_entity) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/session_maker.py", line 377, in dec result = func(*args, **kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/root_dao.py", line 70, in store_entity self.session.commit() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1042, in commit self.transaction.commit() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 504, in commit self._prepare_impl() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 483, in _prepare_impl self.session.flush() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2536, in flush self._flush(objects) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2678, in _flush transaction.rollback(_capture_exception=True) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__ with_traceback=exc_tb, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2638, in _flush flush_context.execute() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute rec.execute(self) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute uow, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 236, in save_obj update, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 1028, in _emit_update_statements % (table.description, len(records), rows) sqlalchemy.orm.exc.StaleDataError: UPDATE statement on table 'BurstConfiguration' expected to update 1 row(s); 0 were matched. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/threading.py", line 926, in _bootstrap_inner self.run() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/simulator_service.py", line 126, in async_launch_and_prepare_simulation self.burst_service.mark_burst_finished(burst_config, error_message=str(excep)) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/burst_service.py", line 103, in mark_burst_finished dao.store_entity(burst_entity) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/session_maker.py", line 377, in dec result = func(*args, **kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/root_dao.py", line 64, in store_entity self.logger.debug("We will store entity of type: %s with id %s" % (entity.__class__.__name__, str(entity.id))) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/attributes.py", line 287, in __get__ return self.impl.get(instance_state(instance), dict_) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/attributes.py", line 718, in get value = state._load_expired(state, passive) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/state.py", line 652, in _load_expired self.manager.deferred_scalar_loader(self, toload) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/loading.py", line 944, in load_scalar_attributes "attribute refresh operation cannot proceed" % (state_str(state)) sqlalchemy.orm.exc.DetachedInstanceError: Instance is not bound to a Session; attribute refresh operation cannot proceed (Background on this error at: http://sqlalche.me/e/13/bhk3) Exception in thread Thread-72: Traceback (most recent call last): File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/simulator_service.py", line 106, in async_launch_and_prepare_simulation session_stored_simulator.gid) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/burst_service.py", line 184, in update_simulation_fields burst.fk_simulation = op_simulation_id AttributeError: 'NoneType' object has no attribute 'fk_simulation' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/burst_service.py", line 96, in mark_burst_finished dao.store_entity(burst_entity) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/session_maker.py", line 377, in dec result = func(*args, **kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/root_dao.py", line 70, in store_entity self.session.commit() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1042, in commit self.transaction.commit() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 504, in commit self._prepare_impl() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 483, in _prepare_impl self.session.flush() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2536, in flush self._flush(objects) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2678, in _flush transaction.rollback(_capture_exception=True) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__ with_traceback=exc_tb, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2638, in _flush flush_context.execute() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute rec.execute(self) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute uow, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 236, in save_obj update, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 1028, in _emit_update_statements % (table.description, len(records), rows) sqlalchemy.orm.exc.StaleDataError: UPDATE statement on table 'BurstConfiguration' expected to update 1 row(s); 0 were matched. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/threading.py", line 926, in _bootstrap_inner self.run() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/simulator_service.py", line 126, in async_launch_and_prepare_simulation self.burst_service.mark_burst_finished(burst_config, error_message=str(excep)) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/burst_service.py", line 103, in mark_burst_finished dao.store_entity(burst_entity) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/session_maker.py", line 377, in dec result = func(*args, **kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/root_dao.py", line 64, in store_entity self.logger.debug("We will store entity of type: %s with id %s" % (entity.__class__.__name__, str(entity.id))) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/attributes.py", line 287, in __get__ return self.impl.get(instance_state(instance), dict_) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/attributes.py", line 718, in get value = state._load_expired(state, passive) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/state.py", line 652, in _load_expired self.manager.deferred_scalar_loader(self, toload) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/loading.py", line 944, in load_scalar_attributes "attribute refresh operation cannot proceed" % (state_str(state)) sqlalchemy.orm.exc.DetachedInstanceError: Instance is not bound to a Session; attribute refresh operation cannot proceed (Background on this error at: http://sqlalche.me/e/13/bhk3) Exception in thread Thread-74: Traceback (most recent call last): File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/simulator_service.py", line 201, in async_launch_and_prepare_pse first_simulator.gid) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/burst_service.py", line 184, in update_simulation_fields burst.fk_simulation = op_simulation_id AttributeError: 'NoneType' object has no attribute 'fk_simulation' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/burst_service.py", line 96, in mark_burst_finished dao.store_entity(burst_entity) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/session_maker.py", line 377, in dec result = func(*args, **kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/root_dao.py", line 70, in store_entity self.session.commit() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1042, in commit self.transaction.commit() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 504, in commit self._prepare_impl() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 483, in _prepare_impl self.session.flush() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2536, in flush self._flush(objects) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2678, in _flush transaction.rollback(_capture_exception=True) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__ with_traceback=exc_tb, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2638, in _flush flush_context.execute() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute rec.execute(self) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute uow, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 236, in save_obj update, File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 1028, in _emit_update_statements % (table.description, len(records), rows) sqlalchemy.orm.exc.StaleDataError: UPDATE statement on table 'BurstConfiguration' expected to update 1 row(s); 0 were matched. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/threading.py", line 926, in _bootstrap_inner self.run() File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/threading.py", line 870, in run self._target(*self._args, **self._kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/simulator_service.py", line 227, in async_launch_and_prepare_pse self.burst_service.mark_burst_finished(burst_config, error_message=str(excep)) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/services/burst_service.py", line 103, in mark_burst_finished dao.store_entity(burst_entity) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/session_maker.py", line 377, in dec result = func(*args, **kwargs) File "/Users/duke/src/tvb-root/framework_tvb/tvb/core/entities/storage/root_dao.py", line 64, in store_entity self.logger.debug("We will store entity of type: %s with id %s" % (entity.__class__.__name__, str(entity.id))) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/attributes.py", line 287, in __get__ return self.impl.get(instance_state(instance), dict_) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/attributes.py", line 718, in get value = state._load_expired(state, passive) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/state.py", line 652, in _load_expired self.manager.deferred_scalar_loader(self, toload) File "/Users/duke/miniconda3/envs/tvb-full-x86/lib/python3.7/site-packages/sqlalchemy/orm/loading.py", line 944, in load_scalar_attributes "attribute refresh operation cannot proceed" % (state_str(state)) sqlalchemy.orm.exc.DetachedInstanceError: Instance is not bound to a Session; attribute refresh operation cannot proceed (Background on this error at: http://sqlalche.me/e/13/bhk3)