Running a new installation of Galaxy on a high performance computer cluster
Hi, We are getting ready to run a local setup of Galaxy here at bristol university on our HPC cluster, BlueCrystal. We have got a mini test setup running fine and now we want to install it properly on the main cluster and have the galaxy instance run in the queue along with all the other HOC jobs that are submitted to BlueCrystal from around the university. The guy doing the install has just sent me this message: When I add the following line: database_connection = postgres://galaxy:@web1.acrc.bris.ac.uk/galaxy to universe_wsgi.ini Galaxy fails to start with the following error message: snip ---------------------- galaxy.model.migrate.check DEBUG 2011-09-16 15:00:47,385 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/app.py", line 33, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 105, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '76' but this code expects version '81'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. postgres on the web server is 8.4 so it should be fine. It looks like python is reporting the wrong version number. Any help from the developers would be much appreciated. Do you know what the problem is he is seeing? Would he be better off emailing you directly? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews@bristol.ac.uk
On Fri, Sep 16, 2011 at 4:44 PM, David Matthews <D.A.Matthews@bristol.ac.uk> wrote:
Hi, We are getting ready to run a local setup of Galaxy here at bristol university on our HPC cluster, BlueCrystal. We have got a mini test setup running fine and now we want to install it properly on the main cluster and have the galaxy instance run in the queue along with all the other HOC jobs that are submitted to BlueCrystal from around the university. The guy doing the install has just sent me this message:
When I add the following line:
database_connection = postgres://galaxy:@web1.acrc.bris.ac.uk/galaxy
to
universe_wsgi.ini
Galaxy fails to start with the following error message:
snip ---------------------- galaxy.model.migrate.check DEBUG 2011-09-16 15:00:47,385 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/app.py", line 33, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 105, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '76' but this code expects version '81'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'.
postgres on the web server is 8.4 so it should be fine. It looks like python is reporting the wrong version number.
That isn't reporting the postgres version number, but the Galaxy schema number.
Any help from the developers would be much appreciated.
The error message tells you what to do, sh manage_db.sh upgrade
Do you know what the problem is he is seeing? Would he be better off emailing you directly?
This is normal when you update the Galaxy code - every so often the Galaxy team make changes to the database tables, e.g. to add new columns to record user disk quotas. Peter
The database 'version' in question is our internal migration number, not the version of your postgres install. What has happened is that since you've last updated galaxy, the database schema has changed, and you need to kick off the migration scripts by running 'sh manage_db.sh upgrade' in your galaxy install directory prior to running galaxy. -Dannon On Sep 16, 2011, at 11:44 AM, David Matthews wrote:
Hi,
We are getting ready to run a local setup of Galaxy here at bristol university on our HPC cluster, BlueCrystal. We have got a mini test setup running fine and now we want to install it properly on the main cluster and have the galaxy instance run in the queue along with all the other HOC jobs that are submitted to BlueCrystal from around the university.
The guy doing the install has just sent me this message:
When I add the following line:
database_connection = postgres://galaxy:@web1.acrc.bris.ac.uk/galaxy
to
universe_wsgi.ini
Galaxy fails to start with the following error message:
snip ---------------------- galaxy.model.migrate.check DEBUG 2011-09-16 15:00:47,385 psycopg2 egg successfully loaded for postgres dialect Traceback (most recent call last): File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/app.py", line 33, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/gpfs/cluster/isys/galaxy/Galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 105, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '76' but this code expects version '81'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'.
postgres on the web server is 8.4 so it should be fine. It looks like python is reporting the wrong version number.
Any help from the developers would be much appreciated.
Do you know what the problem is he is seeing? Would he be better off emailing you directly?
Best Wishes, David.
__________________________________ Dr David A. Matthews
Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K.
Tel. +44 117 3312058 Fax. +44 117 3312091
D.A.Matthews@bristol.ac.uk
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participants (3)
-
Dannon Baker -
David Matthews -
Peter Cock