Dear Galaxy Developers,I'm running galaxy local on ubuntu and trying to run a workflow on multiple datasets (separately). Occasionally when I try to run workflow on input dataset I get "Unable to finish job" error in some steps, in most time the problem will be solved when I run the workflow again, but this going to happen more frequently. I attached the error message here. I suspect it may be related to increase in number of datasets of the current history (1757 datasets with ~350GB size).I will appreciate your helpTraceback (most recent call last): File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1068, in finish self.sa_session.flush() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1804, in _flush transaction.commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 365, in commit t[1].commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2045, in commit self._do_commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2075, in _do_commit self.connection._commit_impl() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1280, in _commit_impl self._handle_dbapi_exception(e, None, None, None, None) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1277, in _commit_impl self.engine.dialect.do_commit(self.connection) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 307, in do_commit connection.commit() OperationalError: (OperationalError) database is locked None None
Hi Milad The error message: "database is locked" might be a hint. Are you using a PostgreSQL database or just SQLite ? If the latter, you will often run in troubles when running more than one job at a time, due to file locking. Regards, Hans-Rudolf On 03/11/2014 07:41 PM, Milad Bastami wrote:
Dear Galaxy Developers, I'm running galaxy local on ubuntu and trying to run a workflow on multiple datasets (separately). Occasionally when I try to run workflow on input dataset I get "Unable to finish job" error in some steps, in most time the problem will be solved when I run the workflow again, but this going to happen more frequently. I attached the error message here. I suspect it may be related to increase in number of datasets of the current history (1757 datasets with ~350GB size). I will appreciate your help
Traceback (most recent call last): File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1068, in finish self.sa_session.flush() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1804, in _flush transaction.commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 365, in commit t[1].commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2045, in commit self._do_commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2075, in _do_commit self.connection._commit_impl() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1280, in _commit_impl self._handle_dbapi_exception(e, None, None, None, None) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1277, in _commit_impl self.engine.dialect.do_commit(self.connection) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 307, in do_commit connection.commit() OperationalError: (OperationalError) database is locked None None
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Many thanks for your help. Your are right about database (I'm using SQLite). I've found a tutorial at GMOD (http://gmod.org/wiki/Galaxy_Tutorial_2012) on how to make galaxy work with PostgreSQL, but can I change the current database to PostgreSQL without missing my datasets? I am running a single-user galaxy instance. Cheers, Milad
Date: Wed, 12 Mar 2014 09:07:00 +0100 From: hrh@fmi.ch To: mi.bastami@live.com CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] error in workflow
Hi Milad
The error message: "database is locked" might be a hint.
Are you using a PostgreSQL database or just SQLite ? If the latter, you will often run in troubles when running more than one job at a time, due to file locking.
Regards, Hans-Rudolf
On 03/11/2014 07:41 PM, Milad Bastami wrote:
Dear Galaxy Developers, I'm running galaxy local on ubuntu and trying to run a workflow on multiple datasets (separately). Occasionally when I try to run workflow on input dataset I get "Unable to finish job" error in some steps, in most time the problem will be solved when I run the workflow again, but this going to happen more frequently. I attached the error message here. I suspect it may be related to increase in number of datasets of the current history (1757 datasets with ~350GB size). I will appreciate your help
Traceback (most recent call last): File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 116, in queue_job job_wrapper.finish( stdout, stderr, exit_code ) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1068, in finish self.sa_session.flush() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1804, in _flush transaction.commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 365, in commit t[1].commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2045, in commit self._do_commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2075, in _do_commit self.connection._commit_impl() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1280, in _commit_impl self._handle_dbapi_exception(e, None, None, None, None) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1277, in _commit_impl self.engine.dialect.do_commit(self.connection) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 307, in do_commit connection.commit() OperationalError: (OperationalError) database is locked None None
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Have a look at https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Swi... on how to set up the PostgreSQL database for Galaxy. I am not aware of any tools to port the contents of the SQLite file to a PostgreSQL database, except for setting up an all new Galaxy server (running with PostgreSQL) and exporting the important histories from your old server followed by importing them into your new server - though looking at the size of your history, this might not work. Hans-Rudolf On 03/12/2014 09:57 AM, Milad Bastami wrote:
Many thanks for your help. Your are right about database (I'm using SQLite). I've found a tutorial at GMOD (http://gmod.org/wiki/Galaxy_Tutorial_2012) on how to make galaxy work with PostgreSQL, but can I change the current database to PostgreSQL without missing my datasets? I am running a single-user galaxy instance.
Cheers, Milad
Date: Wed, 12 Mar 2014 09:07:00 +0100 From: hrh@fmi.ch To: mi.bastami@live.com CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] error in workflow
Hi Milad
The error message: "database is locked" might be a hint.
Are you using a PostgreSQL database or just SQLite ? If the latter, you will often run in troubles when running more than one job at a time, due to file locking.
Regards, Hans-Rudolf PostgreSQL
Dear Galaxy Developers, I'm running galaxy local on ubuntu and trying to run a workflow on multiple datasets (separately). Occasionally when I try to run workflow on input dataset I get "Unable to finish job" error in some steps, in most time the problem will be solved when I run the workflow again, but this going to happen more frequently. I attached the error message here. I suspect it may be related to increase in number of datasets of the current history (1757 datasets with ~350GB size). I will appreciate your help
Traceback (most recent call last): File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/runners/local.py",
job_wrapper.finish( stdout, stderr, exit_code ) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/lib/galaxy/jobs/__init__.py",
self.sa_session.flush() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
return getattr(self.registry(), name)(*args, **kwargs) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
self._flush(objects) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
transaction.commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
t[1].commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
self._do_commit() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
self.connection._commit_impl() File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
self._handle_dbapi_exception(e, None, None, None, None) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
self.engine.dialect.do_commit(self.connection) File "/media/milad/acfed08f-e8e7-43d5-b582-5b5acdba9072/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
On 03/11/2014 07:41 PM, Milad Bastami wrote: line 116, in queue_job line 1068, in finish line 114, in do line 1718, in flush line 1804, in _flush line 365, in commit line 2045, in commit line 2075, in _do_commit line 1280, in _commit_impl line 1277, in _commit_impl line 307, in do_commit
connection.commit() OperationalError: (OperationalError) database is locked None None
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participants (2)
-
Hans-Rudolf Hotz -
Milad Bastami