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 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 AS history_dataset_association_name,
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 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 = history_dataset_association.dataset_id \nWHERE
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
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