To close this loop -  Ilya Sytchev was experiencing this problem as well
and did a bunch of tests at the recent GCC Hackathon that pretty clearly
demonstrated that this problem occurs when all of the following three
conditions hold - 1) Galaxy targets MySQL 2) MyISAM tables are used and 3)
Galaxy runs separate web and handler processes (even with 1 and 1).

Ilya's work has been documented here: https://trello.com/c/uVYR3IHc and he
kindly updated the wiki to reflect these problems. The Galaxy team already
strongly recommends Postgres over MySQL - but if you have to use MySQL
please use InnoDB tables (the new default) instead of MyISAM.

-John



On Sat, Dec 7, 2013 at 9:36 AM, John Chilton <chil...@msi.umn.edu> wrote:

> Hello Yves,
>
> "duplicates the history the same amount of times as the number of
> threadpool_workers we have configured for the job handlers"
>
> Well that shouldn't be happening. Do each of these multiple histories have
> all of the datasets for the workflow run populated as well?
>
> I assume then that "Send results to a new history" are checked when
> running the workflow. Does this problem happen when that is not checked?
>
> I have couple of related questions - but perhaps if you could send a
> version of your universe_wsgi.ini to galaxy-b...@bx.psu.edu
> with sensitive information redacted (database passwords, id_secret,
> admin_users) it would answer all of them.
>
> It would be great to rule out tool related problems (though they are
> seeming more and more unlikely as you describe the symptoms) - can you
> recreate this with a big workflow that just uses standard Galaxy tools
> bundled with the distribution? Eitherway, if you could send us a workflow
> example that demonstrates the issue along with tool xml files for any
> custom tools that would help. Again - you can send that to
> galaxy-b...@bx.psu.edu if it is sensitive.
>
> Also, this workflow is being run through the GUI right - I want to rule
> out this being an API related problem.
>
> ... as you can probably tell I am still flummoxed. Sorry I don't have
> answers and thanks for your patience :(.
>
> -John
>
>
>
> On Wed, Dec 4, 2013 at 10:09 AM, Yves Gagnon <yves.gag...@dnalandmarks.ca>
> wrote:
>
>> Dear Galaxy mailing list,
>>
>> I will be taking over this issue here now.
>>
>> Here is an update on this issue and our observations.  I would like to
>> know your insight on the matter if you can think of anything!
>>
>> We tried to revert back to a Galaxy instance running only one job
>> handler.  With that configuration, we observed that the out of order
>> execution problem still occured, but MUCH less frequently than when using
>> three handlers.  On multiple workflow runs, only one job started while its
>> input was not ready in only one run of the workflow.  When using three job
>> handlers, it occured on all workflow runs and on multiple jobs inside each
>> workflow run.
>>
>> Our poweruser also noticed that his workflow, when taking too much time
>> to prepare (which is always the case I think since it's a huge workflow),
>> duplicates the history the same amount of times as the number of
>> threadpool_workers we have configured for the job handlers.  Now I am not
>> sure both are related at all since I do not know much what is the effect of
>> running a handler on multiple thread_workers.
>>
>> In any case, as of now we are staying with a single handler configuration
>> since it in part fix the out of order execution problems, but since we have
>> many regular users and some powerusers, that is not the ideal solution.
>>
>> Hope somebody can shed some light on this!
>>
>> Cheers!
>>
>> *Yves Gagnon*
>> LIMS/ELN Developer
>>
>> Phone: +1 450 357-3370 Fax: +1 450 358-1154 E-Mail:
>> yves.gag...@dnalandmarks.ca
>> Postal Address: DNA LandMarks Inc., 84 Rue Richelieu,
>> Saint-Jean-Sur-Richelieu, Quebec, CANADA, J3B 6X3
>>
>> * DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant
>> Science company*
>>
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>>
>> From:        Jean-Francois Payotte <jean-francois.payo...@dnalandmarks.ca
>> >
>> To:        galaxy-dev@lists.bx.psu.edu
>> Date:        13/11/2013 11:12 AM
>> Subject:        Re: [galaxy-dev] Job execution order mixed-up
>> Sent by:        galaxy-dev-boun...@lists.bx.psu.edu
>> ------------------------------
>>
>>
>>
>> Hi John,
>>
>> Thank you for your answer and for trying to help. This is greatly
>> appreciated!
>> I didn't really made any progress in tracking down this error, and
>> hopefully this weird behaviour will not happen anymore with the November
>> 4th, distribution.
>>
>> But here are my answers to your questions, in case it would ring a bell:
>> 1.        Has this behaviour been reported with any other workflow?
>>
>> It has been reported with 2 different workflows as of now. These 2
>> workflows doesn't have anything in common, except that they are huge (one
>> of them has 37 steps, producing a total of about 110 datasets).
>>
>> 2.        Are you running Galaxy as a single process or multiple
>> processes? If multiple processes, how many web, handler and manager
>> processes do you have and are they all on the same machine?
>>
>> We are running Galaxy in multiple processes with 5 web servers, 3 job
>> handlers and no manager (I believe the manager was rendered obsolete in one
>> of the latest Galaxy distributions). All these processes are run on the
>> same machine.
>>
>> 3.        Have you made any modifications to Galaxy that could result in
>> this behaviour?
>> No.
>>
>> 4.        What is the value of track_jobs_in_database in your
>> universe_wsgi.ini configuration file?
>>
>> We never touched this part of the configuration file and the line still
>> reads: "#track_jobs_in_database = None".
>> After reading your answer, I've decided to modify this line to:
>> "track_jobs_in_database = True"
>> Unfortunately, running one of the faulty workflows several times (5x), I
>> noticed that one of them was still showing this strange behaviour where
>> some jobs were executed before their inputs were ready.
>>
>> Do you think this issue could be related to the fact that we are using
>> Galaxy with the multiple processes configuration? We implemented this
>> configuration some time ago because some of our users were complaining
>> about the slow responsiveness of the web interface.
>>
>> Would you recommend using Galaxy without the multiple processes
>> configuration? (Lets say if updating to November 4th distribution doesn't
>> fix this issue)
>> I guess you are probably using the multiple processes configuration as
>> well on Galaxy main?
>>
>>
>> Thanks again for your help!
>>
>> Jean-François
>>
>>
>>
>>
>> -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>
>>
>> Posted by *John Chilton* on *Nov 09, 2013; 2:50pm*
>>
>> Hello Jean-François,
>>
>>  Have you made any progress tracking down this error? This appears very
>> serious, but to tell you the truth I have no clue what could cause it. The
>> distribution you are using is pretty old at this point I feel like if it
>> was a bug the exhibited under relatively standard parameter combinations
>> someone else would have reported it by now.
>>
>>  Can you tell me some things: has this been reported with any other
>> workflows? Is there anything special about this workflow? Can you rebuild
>> the workflow and see if the error occurs again?
>>
>>  Additional questions if the problem is not restricted to the workflow:
>> are you running Galaxy as a single process or multiple processes? If
>> multiple processes, how many web, handler, and manager processes do you
>> have? Are they all on the same machine? Have you made any modifications to
>> Galaxy that could result in this behavior? What is the value of
>> track_jobs_in_database in your universe_wsgi.ini configuration file?
>>
>> -John
>>
>>
>> On Thu, Nov 7, 2013 at 10:34 AM, Jean-Francois Payotte <*[hidden email]*
>> <http://dev.list.galaxyproject.org/user/SendEmail.jtp?type=node&node=4662520&i=0>>
>> wrote:
>> Dear Galaxy mailing-list,
>>
>> Once again I come seeking for your help. I hope someone already had this
>> issue or will have an idea on where to look to solve it. :)
>>
>> One of our users reported having workflows failing because some steps
>> were executed before all their inputs where ready.
>> You can find a screenshot attached, where we can see that step (42) "Sort
>> on data 39" has been executed while step (39) is still waiting to run (gray
>> box).
>>
>> This behaviour has been reproduced with at least two different Galaxy
>> tools (one custom, and the sort tool which comes standard with Galaxy).
>> This behaviour seems to be a little bit random, as running two times a
>> workflow where this issue occurs, only one time did some steps were
>> executed in the wrong order.
>>
>> I could be wrong, but I don't think this issue is grid-related as, from
>> my understanding, Galaxy is not using SGE job dependencies functionality.
>> I believe all jobs stays in some internal queues (within Galaxy) until
>> all input files are ready, and only then the job is submitted to the
>> cluster.
>>
>> Any help or any hint on what to look at to solve this issue would be
>> greatly appreciated.
>> We have updated our Galaxy instance to August 12th distribution on
>> October 1st, and I believe we never experienced this issue before the
>> update.
>>
>> Many thanks for your help,
>> Jean-François
>>
>>
>> ___________________________________________________________
>>
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>
>
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