I have created a Trello card for this (https://trello.com/c/m2x1CXmi)
and I have attached a more flushed out IRC conversation for additional
public comment/posterity. I think this is exciting stuff - though I
need to get my head around mesos and how it would interact with Galaxy
more fully. I think some important (perhaps obvious) concerns are:

- Integration at framework level must be optional - this shouldn't be
a required dependency.
- Existing runners and talk parallelism stuff must continue to
function with or without mesos.

Other thoughts?


16:55 < jmchilton> kellrott: Liked the mesos e-mail. Trying to come up
with something intelligent to say before responding :). Do you any
have specific use cases/tools in
16:56 < kellrott> Starting to move our tools to spark
16:56 < kellrott> That's the big draw for me
16:57 < kellrott> And honestly, it seems better to keep hacking away
with things like

16:57 < mrscribe> Title: galaxy / galaxy-central / Pull request #175:
Parameter Based Bam file parallelization Bitbucket (at bitbucket.org)
17:04 < jmchilton> kellrott: Did you mean "it seems better to keep
hacking away with things like" or did you mean it seems better not
17:04 < kellrott> missed a 'than'
17:05 < kellrott> but yes, pull #175 is a bit of a hack and wouldn't
be needed if there was a really parallelization system
17:06 < kellrott> One of the most relevant usages is any tool that
uses a random sampling for statistics, ie consensus clustering
17:06 < jmchilton> Ahh, thought so. Yeah, I think the current task
splitting framework stuff is suppose to be pretty transparent to the
tool wrapper/application. For
                   applications that depend on something like spark,
you idea sounds pretty good to me.
17:07 < kellrott> no real way to support parallel computation of a
background model in current system
17:08 < kellrott> When talking to different people, the lack of robust
parallelization tends to be the biggest complaint
17:10 < kellrott> I think Mesos is a pretty robust solution, I just
wanted to see if anybody had technical complaints
17:11 < jmchilton> hmm.... interesting. I must admit I had never
really thought of that as being a problem. I will have to chew on what
you said though.
17:11 < jmchilton> All of that said, I have no technical complaints
and I am eager to help in any way I reasonably can with the mesos
stuff. It seems pretty exciting.
17:11 < kellrott> Sorry, if my explanations are a bit choppy
17:12 < kellrott> I think the biggest complaint would be 'yet another
17:13 < jmchilton> We could do it in a way that it is optional though right?
17:13 < kellrott> Exactly
17:13 < jmchilton> ... though maybe specific tools would require it.
17:14 < jmchilton> I will create a Trello card, if anyone has
objections they can note them there.
17:14 < kellrott> Its not hard to support single CPU calculations
(Spark has a built in single CPU mode)
17:15 < kellrott> But tools that require it would probably not be very
fast running on a single machine ;-)
17:15 < kellrott> I'll probably start working on the implementation, I
just wanted to make sure people are open to merging the work into
17:17 < jmchilton> Reserve the right to reject specific
implementations :), but overall I (at least personally) like the idea.
17:18 < pvh_sa> kellrott, agreed 100%
17:18 < kellrott> Obviously I'm open to peoples critiques
17:19 < pvh_sa> the Galaxy execution engine is going to need
replacing, its just a question of with what, and how can it be done in
the least disruptive way
17:19 < kellrott> This has become the thing that it the 'rate limiter'
for adoption by tool writers around here
17:20 < kellrott> are calculations demand robust parallel programming platforms
17:22 < jmchilton> huh... I see the need to support things other than
MPI, but would you say there are problems with our current MPI support
(essentially delegated external
                   resource manager).
17:23 < kellrott> well, MPI is supported under mesos ;-)
17:23 < dannon> THe main problem here is that we wanted something that
supports parallelization for tools that don't natively do it.
17:24 < dannon> new runners for different execution models, totally fine.
17:25 < pvh_sa> dannon, that's something that needs to cooperation of
the execution engine and the type system, right? that's kind of how it
works at the moment - tools
                state that certain inputs are splittable (i.e. are
actually collections)
17:26 < dannon> Right.  I could imagine the parallelization
description langugae being fleshed out more to say "if mesos, do this,
else do naieve file chunking, etc."
17:26 < pvh_sa> of course that needs extending so that collections of
parameters can be provided as inputs, so that tools can explore a
parameter space
17:27 < dannon> But at the core, it needs to be abstract
17:27 < kellrott> I think strait file chunking will only cover a
fraction of parallalization needs
17:27 < dannon> kellrott: Absolutely, file chunking is designed for
embarassingly parallel problems without shared memory/etc
17:27 < dannon> It just won't work for some things.
17:28 < pvh_sa> kellrott, is mesos also scheduling work parcels? or
does it not do scheduling?
17:29 < jmchilton> My understanding is its a framework that you can
plugin scheduling into...
17:30 < kellrott> you write a small 'executor' that the system starts
offering resources to
17:31 < kellrott> then you can accept them, and you scripts are run on
the remote machines
17:31 < pvh_sa> kellrott, ok... so the scheduling is external
17:31 < kellrott> like a queue system, but a two-way dialog rather
then a single sided converation
17:32 < pvh_sa> your "executor" must handle what to do with resource
offers, right? so it matches the resource offers to work that needs
17:32 < kellrott> I believe so
17:33 < pvh_sa> not sure what other people's sense is...
17:34 < kellrott> Sorry, flipped the lingo, you write a scheduler that
then has the system launch executors based on resource offers
17:34 < kellrott>
17:34 < mrscribe> Title: mesos/docs/App-Framework-Development-Guide.md
at master · apache/mesos · GitHub (at github.com)
17:34 < pvh_sa> ok dokey. so conceivably you could use celery with a
mesos backend or something
17:35 < kellrott> Exactly, there is already a Torque framework
17:35 < pvh_sa> one of my bugbears with galaxy's execution engine at
the moment is that it schedules tasks, not workflows... workflows
simply become a set of tasks at
                execution time
17:37 < jmchilton> pvh_sa: What should Galaxy be doing instead?
17:38 < jmchilton> i.e. how does one "schedule a workflow" if not by
individual tasks?
17:38 < pvh_sa> jmchilton, workflows should exist as objects in the
execution environment so that you can e.g. pause and restart them
17:38 < pvh_sa> once you've got that kind of model, you can also
re-execute failed tasks... at the moment if one task fails, i have to
restart the workflow from scratch....
17:39 < dannon> pvh_sa: That's the plan
17:39 < jmchilton> You can restart workflows now, dannon has added that.
17:39 < kellrott> I kind of like the 'separate tasks' workflow model,
because I'm looking into managing 'workflows' using external clients
through the API
17:39 < dannon> Actually, right now, you can restart workflows.
17:39 < dannon> yep.
17:39 < kellrott> that way I can read a workflow file, and then use
the query engine to find previously run jobs that could fullfill the
input needs of that workflow
17:40 < jmchilton> Pausing workflows seems like a reasonable request
though... maybe more advanced UI that lets you visualize and interact
with the workflow as a unit.
17:40 < dannon> And I think it's actually great that that sort of
thing *does* run externally Kyle
17:40 < pvh_sa> jmchilton, yep, something UI related would be good for that.
17:40 < dannon> Very near up on my list is picking up some previous
work with galaxy/messaging to integrate celery tasks instead of having
all these status loops
17:41 < pvh_sa> dannon, yup for celery
17:41 < kellrott> it lets me restart workflows, even if is a
completley different run of the workflow, and I 'forgot' about the
17:41 < dannon> Yep, using celery, for sure.
17:41 < pvh_sa> i'm also thinking that we want to reason across
provenance graphs
17:42 < pvh_sa> so e.g. a certain transform need not be repeated if it
already exists in the set of data products... e.g. we've already
created that BLAST db, just re-use it
17:42 < kellrott> thats exactly what I want (and parallel tools ;-)
17:42 < dannon> Right, and I think that's the sort of thing Kyle's
query work will really enable.
17:43 < pvh_sa> kellrott, have you read the paper on using... datalog
i think its called... for provenance recording?
17:43 < kellrott> I'm pretty sure we can do all of this via the api
17:43 < dannon> That's the idea, at least.
17:43 < kellrott> I don't think I've seen that one
17:43 < pvh_sa> yeah the API is king... a powerful API also lets us
cleanly split UI from backend
17:44 < dannon> Exactly
17:44 < kellrott> I'm not even thinking UI. I'm thinking about script
controlled workflows
17:44 < pvh_sa> "Datalog as a Lingua Franca for provenance querying
and reasoning"
17:45 < pvh_sa> seems lots of talking the same language going on. yay.
i'm busy hiring developers to work on exactly this kind of stuff
17:45 < pvh_sa> but yeah my 3-part agenda is basically 1) type system
2) execution engine 3) provenance representation
17:46 < kellrott> We are building toward running workflows on TCGA
data, so I need a system where I can call a mutation calling workflow
~4000 times
17:47 < jmchilton> pvn_sa: Enhancing Galaxy or replacing it? :)
17:47 < pvh_sa> jmchilton, ripping out bits, keeping the project together though
17:47 < kellrott> Hopefully enhancing Galaxy
17:47 < pvh_sa> jmchilton, you've got 130 000 lines of code
17:47 < pvh_sa> and a vibrant community
17:48 < pvh_sa> any way forward needs to build on that. there's lots
to do, but galaxy is like a central beacon we can all gravitate
17:49 < pvh_sa> anyway, the current galaxy is already v2.0 compared to
the original galaxy described in the literature

On Sat, Oct 26, 2013 at 2:43 PM, Kyle Ellrott <kellr...@soe.ucsc.edu> wrote:
> I think one of the aspects where Galaxy is a bit soft is the ability to do
> distributed tasks. The current system of split/replicate/merge tasks based
> on file type is a bit limited and hard for tool developers to expand upon.
> Distributed computing is a non-trival thing to implement and I think it
> would be a better use of our time to use an already existing framework. And
> it would also mean one less API for tool writers to have to develop for.
> I was wondering if anybody has looked at Mesos ( http://mesos.apache.org/ ).
> You can see an overview of the Mesos architecture at
> https://github.com/apache/mesos/blob/master/docs/Mesos-Architecture.md
> The important thing about Mesos is that it provides an API for C/C++,
> Java/Scala and Python to write distributed frameworks. There are already
> implementations of frameworks for common parallel programming systems such
> as:
>  - Hadoop (https://github.com/mesos/hadoop)
>  - MPI
> (https://github.com/apache/mesos/blob/master/docs/Running-torque-or-mpi-on-mesos.md)
>  - Spark (http://spark-project.org)
> And you can find example Python framework at
> https://github.com/apache/mesos/tree/master/src/examples/python
> Integration with Galaxy would have three parts:
> 1) Add a system config variable to Galaxy called 'MESOS_URL' that is then
> passed to tool wrappers and allows them to contact the local mesos
> infrastructure (assuming the system has been configured) or pass a null if
> the system isn't available.
> 2) Write a tool runner that works as a mesos framework to executes single
> cpu jobs on the distributed system.
> 3) For instances where mesos is not available at a system wide level (say
> they only have access to an SGE based cluster), but the user wants to run
> distributed jobs, write a wrapper that can create a mesos cluster using the
> existing queueing system. For example, right now I run a Mesos system under
> the SGE queue system.
> I'm curious to see what other people think.
> Kyle
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