Re: [galaxy-dev] job runner error
Hi All, I have moved my database from sqlite to postgresql in my local instance of Galaxy .But I want my old history in new database.How It's possible ? Regards shashi On Wed, Jul 27, 2011 at 7:19 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar meshash...@gmail.com Hi all, I have added separate job runner in my galaxy instance. So far it was running successfully from many months. Now its giving error as below and i am unable to trace it. Please suggest. Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked None None Thanks Shashi On Wed, Jul 27, 2011 at 7:00 PM, Peter Cock p.j.a.c...@googlemail.com You're not using SQLite as the database are you? I've seen that kind of error message from locking problems (e.g. when the SQLite DB was on a CIFS mapped drive), and it wouldn't surprise me that with a separate thread for the job runner you get contention over the SQLite DB. If you are using PostgreSQL (or MySQL) as recommended for a production Galaxy server, then I'm not sure what could be wrong. On Wed, Jul 27, 2011 at 2:42 PM, shashi shekhar meshash...@gmail.com wrote: I am using sqlite database . I think that to avoid this database problem you will have to move to PostgreSQL (which is what the Galaxy team recommend), or possibly MySQL (not sure what the downsides are). This might be hard if you already have a number of users and datafiles. I've CC'd the list again so hopefully Nate or one of the other Galaxy Devs can confirm this. Peter ___ 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/
Re: [galaxy-dev] job runner error
On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar meshash...@gmail.com wrote: Hi all, I have added separate job runner in my galaxy instance. So far it was running successfully from many months. Now its giving error as below and i am unable to trace it. Please suggest. Traceback (most recent call last): File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py, line 202, in __monitor_step self.dispatcher.put( JobWrapper( job, self ) ) ... File /home/gwadmin/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.4.egg/sqlalchemy/engine/base.py, line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) database is locked None None Thanks Shashi You're not using SQLite as the database are you? I've seen that kind of error message from locking problems (e.g. when the SQLite DB was on a CIFS mapped drive), and it wouldn't surprise me that with a separate thread for the job runner you get contention over the SQLite DB. If you are using PostgreSQL (or MySQL) as recommended for a production Galaxy server, then I'm not sure what could be wrong. Peter ___ 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/
Re: [galaxy-dev] job runner error
On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar meshash...@gmail.com Hi all, I have added separate job runner in my galaxy instance. So far it was running successfully from many months. Now its giving error as below and i am unable to trace it. Please suggest. Traceback (most recent call last): ... OperationalError: (OperationalError) database is locked None None Thanks Shashi On Wed, Jul 27, 2011 at 7:00 PM, Peter Cock p.j.a.c...@googlemail.com You're not using SQLite as the database are you? I've seen that kind of error message from locking problems (e.g. when the SQLite DB was on a CIFS mapped drive), and it wouldn't surprise me that with a separate thread for the job runner you get contention over the SQLite DB. If you are using PostgreSQL (or MySQL) as recommended for a production Galaxy server, then I'm not sure what could be wrong. On Wed, Jul 27, 2011 at 2:42 PM, shashi shekhar meshash...@gmail.com wrote: I am using sqlite database . I think that to avoid this database problem you will have to move to PostgreSQL (which is what the Galaxy team recommend), or possibly MySQL (not sure what the downsides are). This might be hard if you already have a number of users and datafiles. I've CC'd the list again so hopefully Nate or one of the other Galaxy Devs can confirm this. Peter ___ 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/
