Hi

I can't promise, this is the solution for your specific problem, but you will always run into "database is locked" issue, when using SQLite.

Hence, I strongly recommend to switch to a PostgreSQL database as the back-end for Galaxy (see also: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server )

Hans-Rudolf


On 02/05/2015 02:44 PM, Roberto Alonso CIPF wrote:
Hello,

I am using the galaxy built-in database,  SQLAlchemy on top of sql lite?
May I swith to postgress?

Regards

On 5 February 2015 at 14:41, Hans-Rudolf Hotz <h...@fmi.ch
<mailto:h...@fmi.ch>> wrote:

    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>
        <http://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>
        <http://history_dataset___association.name
        <http://history_dataset_association.name>> AS
        history_dataset_association___name,
        history_dataset_association.__info
        <http://history_dataset_association.info>
        <http://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>
        <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>
        <http://dataset_1.id> =
        history_dataset_association.__dataset_id \nWHERE
        history_dataset_association.id
        <http://history_dataset_association.id>
        <http://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 <tel:%2B34%20963289680%20Ext.%201021>
        Fax: +34 963289574 <tel:%2B34%20963289574>
        E-Mail: ralo...@cipf.es <mailto:ralo...@cipf.es>
        <mailto:ralo...@cipf.es <mailto:ralo...@cipf.es>>


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--
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>
___________________________________________________________
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