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
On 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
> 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
> - Spark (http://spark-project.org)
> And you can find example Python framework at
> 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.
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Ravi K Madduri
MCS, Argonne National Laboratory
Computation Institute, University of Chicago
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