So, see the commentary on the bioblend issue you added as well, but in
short -- while you should currently expect to wait while the entire
workflow was queued, bioblend *should not* be blocking waiting for all jobs
to complete and that sounds like a bioblend bug if it is. That's what the
'wait' param is for after all.
On Thu, Aug 21, 2014 at 5:27 PM, Evan Bollig <boll0107(a)umn.edu> wrote:
Thanks Dannon. Looking forward to the resolution. We've got some
long
workflows (100+ steps) that take days to compute. It takes about 2
minutes to finish queuing tasks, and then I found that they continue
to execute even if I interrupt the bioblend thread. I'll add a
signal.alarm interrupt to kill the bioblend thread and continue manual
monitoring.
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
evan(a)msi.umn.edu
boll0107(a)umn.edu
On Thu, Aug 21, 2014 at 4:20 PM, Dannon Baker <dannon.baker(a)gmail.com>
wrote:
> There is no reason workflow invocation *has* to be synchronous, but
that's
> how galaxy works right now as, mostly, a historical artifact. Workflow
> scheduling happens inside the web request, and other than bioblend
issuing
> the request in another thread there won't be an implementation w/
no_wait.
> This is definitely suboptimal, and backgrounded (among other
enhancements to
> scheduling) workflow invocation is something we're working on right now,
and
> it's a high priority.
>
>
> On Thu, Aug 21, 2014 at 4:12 PM, Evan Bollig <boll0107(a)umn.edu> wrote:
>>
>> I'm using bioblend to launch a workflow, but i find that the
>> gi.workflows.run_workflow() command does not provide an option for
>> no_wait.
>>
>> Can anyone provide justification for why this needs to be synchronous?
>>
>> -Evan Bollig
>> Research Associate | Application Developer | User Support Consultant
>> Minnesota Supercomputing Institute
>> 599 Walter Library
>> 612 624 1447
>> evan(a)msi.umn.edu
>> boll0107(a)umn.edu
>> ___________________________________________________________
>> 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:
>>
http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>
http://galaxyproject.org/search/mailinglists/
>
>