Hey,
I wanted to know if anyone else has had experience with database deadlock when using dataset collections and running a large number of samples through a workflow.
Traceback (most recent call last): File "/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 565, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1250, in finish self.sa_session.flush() File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1789, in _flush flush_context.execute() File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 331, in execute rec.execute(self) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 475, in execute uow File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 59, in save_obj mapper, table, update) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements execute(statement, params) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context context) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) DBAPIError: (TransactionRollbackError) deadlock detected DETAIL: Process 25859 waits for ShareLock on transaction 144373; blocked by process 25858. Process 25858 waits for ShareLock on transaction 144372; blocked by process 25859. HINT: See server log for query details. 'UPDATE workflow_invocation SET update_time=%(update_time)s WHERE workflow_invocation.id = %(workflow_invocation_id)s' {'update_time': datetime.datetime(2015, 2, 27, 3, 51, 57, 81403), 'workflow_invocation_id': 48}
I saw this post http://dev.list.galaxyproject.org/data-collections-workflow-bug-td4666496.ht... with a similar issue and the solution was to make sure not to use a sqlite database, but I'm using a postgres database and still encountered this issue. This was after running a very large number of samples (~200) using dataset collections. Just wondering if anyone else was running into this issue?
Thanks,
Aaron
Hey Aaron,
Thanks for the bug report - I have added it to Trello here (https://trello.com/c/I0n23JEP). I assume this is the January stable release (15.01)? Any clue if this workflow was being scheduled in a web thread or a background job handler thread? (Did the submission take forever - or was the web page responsive and the server bogged down).
So there is a race condition here it would seem - and I don't have a fix right away - but I do think (hope) the next release due out in a couple of weeks will result in a massive speed up in workflow scheduling - so hopefully we will be less likely to hit these conditions.
-John
On Fri, Feb 27, 2015 at 10:11 AM, Aaron Petkau aaron.petkau@gmail.com wrote:
Hey,
I wanted to know if anyone else has had experience with database deadlock when using dataset collections and running a large number of samples through a workflow.
Traceback (most recent call last): File "/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 565, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1250, in finish self.sa_session.flush() File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1718, in flush self._flush(objects) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1789, in _flush flush_context.execute() File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 331, in execute rec.execute(self) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py", line 475, in execute uow File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 59, in save_obj mapper, table, update) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py", line 485, in _emit_update_statements execute(statement, params) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1584, in _execute_clauseelement compiled_sql, distilled_params File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context context) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) DBAPIError: (TransactionRollbackError) deadlock detected DETAIL: Process 25859 waits for ShareLock on transaction 144373; blocked by process 25858. Process 25858 waits for ShareLock on transaction 144372; blocked by process 25859. HINT: See server log for query details. 'UPDATE workflow_invocation SET update_time=%(update_time)s WHERE workflow_invocation.id = %(workflow_invocation_id)s' {'update_time': datetime.datetime(2015, 2, 27, 3, 51, 57, 81403), 'workflow_invocation_id': 48}
I saw this post http://dev.list.galaxyproject.org/data-collections-workflow-bug-td4666496.ht... with a similar issue and the solution was to make sure not to use a sqlite database, but I'm using a postgres database and still encountered this issue. This was after running a very large number of samples (~200) using dataset collections. Just wondering if anyone else was running into this issue?
Thanks,
Aaron
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Hello John,
Awesome, thanks so much for looking into this and all the other work you've been doing on dataset collections. Yes, this is the January stable release, exact commit is https://bitbucket.org/galaxy/galaxy-dist/commits/097bbb3b7d3246faaa5188a1fc2.... I currently have one web worker and one background job handler so it would have been scheduled in the job handler. It is configured like:
[server:handler0] use = egg:Paste#http port = 8079 host = 127.0.0.1 use_threadpool = true threadpool_workers = 5
I can paste the relevant section from the handler log, but I didn't see anything there other then the same exception and stack trace.
Our job handler is submitting to our cluster using DRMAA, from job_conf.xml:
<plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="8"/>
The submission did take forever, over an hour. It was being submitted through the API so I didn't check the web response time but from my experience before I imagine it would be very slow. I've noticed this slowdown before when I get into the 150-200 paired-end samples range.
I'll look forward to the next release though. It would be awesome to have the workflow submission sped up.
Let me know if there's any other info I can provide to help debug,
Aaron
On Fri, Feb 27, 2015 at 9:38 AM, John Chilton jmchilton@gmail.com wrote:
Hey Aaron,
Thanks for the bug report - I have added it to Trello here (https://trello.com/c/I0n23JEP). I assume this is the January stable release (15.01)? Any clue if this workflow was being scheduled in a web thread or a background job handler thread? (Did the submission take forever - or was the web page responsive and the server bogged down).
So there is a race condition here it would seem - and I don't have a fix right away - but I do think (hope) the next release due out in a couple of weeks will result in a massive speed up in workflow scheduling - so hopefully we will be less likely to hit these conditions.
-John
On Fri, Feb 27, 2015 at 10:11 AM, Aaron Petkau aaron.petkau@gmail.com wrote:
Hey,
I wanted to know if anyone else has had experience with database deadlock when using dataset collections and running a large number of samples
through
a workflow.
Traceback (most recent call last): File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 565, in finish_job job_state.job_wrapper.finish( stdout, stderr, exit_code ) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 1250, in finish self.sa_session.flush() File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py",
line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1718, in flush self._flush(objects) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py",
line 1789, in _flush flush_context.execute() File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
line 331, in execute rec.execute(self) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/unitofwork.py",
line 475, in execute uow File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
line 59, in save_obj mapper, table, update) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/persistence.py",
line 485, in _emit_update_statements execute(statement, params) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1449, in execute params) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1584, in _execute_clauseelement compiled_sql, distilled_params File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1698, in _execute_context context) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py",
line 1691, in _execute_context context) File
"/Warehouse/Applications/irida/galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py",
line 331, in do_execute cursor.execute(statement, parameters) DBAPIError: (TransactionRollbackError) deadlock detected DETAIL: Process 25859 waits for ShareLock on transaction 144373;
blocked by
process 25858. Process 25858 waits for ShareLock on transaction 144372; blocked by
process
HINT: See server log for query details. 'UPDATE workflow_invocation SET update_time=%(update_time)s WHERE workflow_invocation.id = %(workflow_invocation_id)s' {'update_time': datetime.datetime(2015, 2, 27, 3, 51, 57, 81403),
'workflow_invocation_id':
48}
I saw this post
http://dev.list.galaxyproject.org/data-collections-workflow-bug-td4666496.ht...
with a similar issue and the solution was to make sure not to use a
sqlite
database, but I'm using a postgres database and still encountered this issue. This was after running a very large number of samples (~200)
using
dataset collections. Just wondering if anyone else was running into this issue?
Thanks,
Aaron
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/
galaxy-dev@lists.galaxyproject.org
-
Aaron Petkau -
John Chilton