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: ralonso@cipf.es
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: ralonso@cipf.es <mailto:ralonso@cipf.es>
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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 <hrh@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> 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: ralonso@cipf.es <mailto:ralonso@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: ralonso@cipf.es
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#Swi... ) 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 <hrh@fmi.ch <mailto:hrh@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: ralonso@cipf.es <mailto:ralonso@cipf.es> <mailto:ralonso@cipf.es <mailto:ralonso@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: ralonso@cipf.es <mailto:ralonso@cipf.es>
Hi Roberto, Hans-Rudolf, I can confirm from personal testing that enabling the parallelism task-splitting in Galaxy does not work well with SQLite. This caused me problems with development and testing since my development Galaxy instance uses SQLite. As you found, testing with smaller splits is one way round this, to reduce the chances of a database lock. We use PostgreSQL as recommended on our production Galaxy instance with parallelism enabled, and it works nicely. Peter On Thu, Feb 5, 2015 at 1:53 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
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#Swi... )
Hans-Rudolf
Hello, Postgres did it perfectly, but as I would like to enable this option in my production servers I changed two configs in galaxy.ini: # This enables splitting of jobs into tasks, if specified by the particular tool config. # This is a new feature and not recommended for production servers yet. use_tasked_jobs = True local_task_queue_workers = 4 So I have two questions, 1. Why is this not appropriate for productions server yet? 2. What is local_task_queue_workers doing? I think I misunderstand something because I put this parameter in the tool config file: <parallelism method="basic"* split_size="20" * split_mode="number_of_parts"></parallelism> on ther other hand, I don't see any documentation about parallelism tag, is there any? Would you so kind to answer me, please? Regards On 5 February 2015 at 15:14, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Roberto, Hans-Rudolf,
I can confirm from personal testing that enabling the parallelism task-splitting in Galaxy does not work well with SQLite.
This caused me problems with development and testing since my development Galaxy instance uses SQLite. As you found, testing with smaller splits is one way round this, to reduce the chances of a database lock.
We use PostgreSQL as recommended on our production Galaxy instance with parallelism enabled, and it works nicely.
Peter
On Thu, Feb 5, 2015 at 1:53 PM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
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#Swi...
)
Hans-Rudolf
-- 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: ralonso@cipf.es
On Fri, Feb 6, 2015 at 9:59 AM, Roberto Alonso CIPF <ralonso@cipf.es> wrote:
Hello,
Postgres did it perfectly, but as I would like to enable this option in my production servers I changed two configs in galaxy.ini:
# This enables splitting of jobs into tasks, if specified by the particular tool config. # This is a new feature and not recommended for production servers yet. use_tasked_jobs = True local_task_queue_workers = 4
So I have two questions, 1. Why is this not appropriate for productions server yet?
At a practical level, I believe this setting is not used on the main usegalaxy.org instance, and thus has not been stress tested by the Galaxy developers. Also (see below), it has little documentation.
2. What is local_task_queue_workers doing?
I'm not entiruely sure, but I think it is how many task-splitters would be run at once (e.g. several splittable jobs are submitted together). We use local_task_queue_workers = 4 but I forget why exactly.
I think I misunderstand something because I put this parameter in the tool config file: <parallelism method="basic" split_size="20" split_mode="number_of_parts"></parallelism> on ther other hand, I don't see any documentation about parallelism tag, is there any?
I don't think there is anything explicit on the wiki about how to use the parallelism tag :( Peter
Hello, thanks a lot for your answers, and the last one :), is there any plan to keep on working with this feature? Regards On 6 February 2015 at 11:39, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hello,
Postgres did it perfectly, but as I would like to enable this option in my production servers I changed two configs in galaxy.ini:
# This enables splitting of jobs into tasks, if specified by the
On Fri, Feb 6, 2015 at 9:59 AM, Roberto Alonso CIPF <ralonso@cipf.es> wrote: particular
tool config. # This is a new feature and not recommended for production servers yet. use_tasked_jobs = True local_task_queue_workers = 4
So I have two questions, 1. Why is this not appropriate for productions server yet?
At a practical level, I believe this setting is not used on the main usegalaxy.org instance, and thus has not been stress tested by the Galaxy developers.
Also (see below), it has little documentation.
2. What is local_task_queue_workers doing?
I'm not entiruely sure, but I think it is how many task-splitters would be run at once (e.g. several splittable jobs are submitted together). We use local_task_queue_workers = 4 but I forget why exactly.
I think I misunderstand something because I put this parameter in the tool config file: <parallelism method="basic" split_size="20" split_mode="number_of_parts"></parallelism> on ther other hand, I don't see any documentation about parallelism tag, is there any?
I don't think there is anything explicit on the wiki about how to use the parallelism tag :(
Peter
-- 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: ralonso@cipf.es
participants (3)
-
Hans-Rudolf Hotz -
Peter Cock -
Roberto Alonso CIPF