Re: [galaxy-dev] job runner error
On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar <meshashi29@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.cock@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 <meshashi29@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
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.cock@googlemail.com>wrote:
On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar <meshashi29@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.cock@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 <meshashi29@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
participants (2)
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Peter Cock -
shashi shekhar