Hi Kyle,

We have a similar ongoing development wherein we are working on integrating our Swift framework ( swift-lang.org ) with Galaxy. The goal is to enable Galaxy based applications to run on a variety of distributed resources via various integration schemes as suitable to application and underlying execution environment. 

Here is an abstract of a paper (co-authored with Ravi, who responded on this thread) we will be presenting in a workshop at the upcoming SC 13 conference:

"The Galaxy platform is a web-based science portal for scientific computing supporting Life Sciences users community. While user-friendly and intuitive for doing small to medium scale computations, it currently has a limited support for large-scale, parallel and distributed computing. The Swift parallel scripting framework is capable of composing ordinary applications into parallel scripts that can be run on multi-scale distributed and performance computing platforms. In complex distributed environments, often the user end of application lifecycle slows down because of the technical complexities brought in by the scale, access methods and resource management nuances. Galaxy offers a simple way of designing, composing, executing, reusing, and reproducing application runs. An integration between Swift and Galaxy systems can accelerate science as well as bring the respective user communities together in an interactive, user-friendly, parallel and distributed data analysis environment enabled on a broad range of computational infrastructures."

Kindly let us know if you need a hands on for the various tools we have already developed.


Best,
Ketan



On Mon, Oct 28, 2013 at 3:07 PM, Kyle Ellrott <kellrott@soe.ucsc.edu> wrote:
I don't think implementation will be very difficult. The bigger question is this a technology people are open to?
The nearest competitor is YARN (http://hadoop.apache.org/docs/current/hadoop-yarn/hadoop-yarn-site/YARN.html). Mesos seems a bit more geared toward general purpose usage (with several existing frameworks), while YARN seems more specific to Hadoop. But I'd be glad to hear some other thoughts.

Kyle


On Mon, Oct 28, 2013 at 12:55 PM, Ravi K Madduri <madduri@mcs.anl.gov> wrote:
Kyle
This is something I am very interested in. The three parts below make sense to me. I would be very happy to discuss further and provide any help to move this forward.

Regards
On Oct 26, 2013, at 2:43 PM, Kyle Ellrott <kellrott@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:
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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Ravi K Madduri
MCS, Argonne National Laboratory
Computation Institute, University of Chicago



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Ketan