Hi Roberto

just double checking: are you using a PostgreSQL database, or are you relying on the built in SQLite?

Hans-Rudolf


On 02/05/2015 02:26 PM, Roberto Alonso CIPF wrote:

Hello,

I am trying to use parallelism in Galaxy.  I added this entry to the
tool xml config:

<tool id="fa_gc_content_1" name="Compute GC content">
   <description>for each sequence in a file</description>
   <parallelism method="basic" split_size="8"
split_mode="number_of_parts"></parallelism>


But when I run the job, the log shows the next:



Traceback (most recent call last):
   File "/home/ralonso/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 158, in prepare_job
     job_wrapper.prepare()
   File "/home/ralonso/galaxy-dist/lib/galaxy/jobs/__init__.py", line
1607, in prepare
     tool_evaluator.set_compute_environment( compute_environment )
   File "/home/ralonso/galaxy-dist/lib/galaxy/tools/evaluation.py", line
53, in set_compute_environment
     incoming = self.tool.params_from_strings( incoming, self.app )
   File "/home/ralonso/galaxy-dist/lib/galaxy/tools/__init__.py", line
2810, in params_from_strings
     return params_from_strings( self.inputs, params, app, ignore_errors )
   File
"/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/__init__.py",
line 103, in params_from_strings
     value = params[key].value_from_basic( value, app, ignore_errors )
   File
"/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
162, in value_from_basic
     return self.to_python( value, app )
   File
"/home/ralonso/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line
1999, in to_python
     return app.model.context.query( app.model.HistoryDatasetAssociation
).get( int( value ) )
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 775, in get
     return self._load_on_ident(key)
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 2512, in _load_on_ident
     return q.one()
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 2184, in one
     ret = list(self)
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 2227, in __iter__
     return self._execute_and_instances(context)
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py",
line 2242, in _execute_and_instances
     result = conn.execute(querycontext.statement, self._params)
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1449, in execute
     params)
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1584, in _execute_clauseelement
     compiled_sql, distilled_params
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context
     context)
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context
     context)
   File
"/home/ralonso/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 331, in do_execute
     cursor.execute(statement, parameters)
OperationalError: (OperationalError) database is locked u'SELECT
history_dataset_association.id <http://history_dataset_association.id>
AS history_dataset_association_id,
history_dataset_association.history_id AS
history_dataset_association_history_id,
history_dataset_association.dataset_id AS
history_dataset_association_dataset_id,
history_dataset_association.create_time AS
history_dataset_association_create_time,
history_dataset_association.update_time AS
history_dataset_association_update_time,
history_dataset_association.state AS history_dataset_association_state,
history_dataset_association.copied_from_history_dataset_association_id
AS
history_dataset_association_copied_from_history_dataset_association_id,
history_dataset_association.copied_from_library_dataset_dataset_association_id
AS
history_dataset_association_copied_from_library_dataset_dataset_association_id,
history_dataset_association.hid AS history_dataset_association_hid,
history_dataset_association.name
<http://history_dataset_association.name> AS
history_dataset_association_name, history_dataset_association.info
<http://history_dataset_association.info> AS
history_dataset_association_info, history_dataset_association.blurb AS
history_dataset_association_blurb, history_dataset_association.peek AS
history_dataset_association_peek,
history_dataset_association.tool_version AS
history_dataset_association_tool_version,
history_dataset_association.extension AS
history_dataset_association_extension,
history_dataset_association.metadata AS
history_dataset_association_metadata,
history_dataset_association.parent_id AS
history_dataset_association_parent_id,
history_dataset_association.designation AS
history_dataset_association_designation,
history_dataset_association.deleted AS
history_dataset_association_deleted, history_dataset_association.purged
AS history_dataset_association_purged,
history_dataset_association.visible AS
history_dataset_association_visible,
history_dataset_association.hidden_beneath_collection_instance_id AS
history_dataset_association_hidden_beneath_collection_instance_id,
history_dataset_association.extended_metadata_id AS
history_dataset_association_extended_metadata_id, dataset_1.id
<http://dataset_1.id> AS dataset_1_id, dataset_1.create_time AS
dataset_1_create_time, dataset_1.update_time AS dataset_1_update_time,
dataset_1.state AS dataset_1_state, dataset_1.deleted AS
dataset_1_deleted, dataset_1.purged AS dataset_1_purged,
dataset_1.purgable AS dataset_1_purgable, dataset_1.object_store_id AS
dataset_1_object_store_id, dataset_1.external_filename AS
dataset_1_external_filename, dataset_1._extra_files_path AS
dataset_1__extra_files_path, dataset_1.file_size AS dataset_1_file_size,
dataset_1.total_size AS dataset_1_total_size, dataset_1.uuid AS
dataset_1_uuid \nFROM history_dataset_association LEFT OUTER JOIN
dataset AS dataset_1 ON dataset_1.id <http://dataset_1.id> =
history_dataset_association.dataset_id \nWHERE
history_dataset_association.id <http://history_dataset_association.id> =
?' (1,)
galaxy.jobs.runners ERROR 2015-02-05 12:58:11,431 (89_486) Failure
preparing job

So when one task tries to run it fails, it seems that the database is
locked by other task. When I run with 4 splits it never happen, but with
5 it begins to happen. Indeed with 5 splits sometimes it doesn't happen,
but since 6 it always occurs.

Could you please help me?



Regards

--
Roberto Alonso
Functional Genomics Unit
Bioinformatics and Genomics Department
Prince Felipe Research Center (CIPF)
C./Eduardo Primo Yúfera (Científic), nº 3
(junto Oceanografico)
46012 Valencia, Spain
Tel: +34 963289680 Ext. 1021
Fax: +34 963289574
E-Mail: ralo...@cipf.es <mailto:ralo...@cipf.es>


___________________________________________________________
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:
   https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/

___________________________________________________________
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:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

Reply via email to