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Future/Distributed Galaxy

Saving small snippets of the discussion for future reference:


I think the most important thing that we need to start thinking about is the how to create a distributed computational system. Think about a thousand users all wanting to start 10 queries. How do we do it? How could we implement a demonstration prototype of this in say one month? It is doable if we keep things simple.


take a look at http://www.bx.psu.edu/~rico/galaxy


But what about if the front end is running on multiple nodes? Sharing a BDB file over NFS is a _bad idea_ for this case. A database that all the front ends can talk to gives more flexibility. It can implement table/row level locking and other nice things to allow multiple processes to keep their data synchronized easily.

I think we need to strike the right balance. Perhaps every query the user is working on doesn't need to go to the database, they can be stored in the users current session, but user accounts, saved histories, and in general things that persist across multiple user sessions should be stored in a way that can be easily shared across many systems.

Also, a SQL database makes analysis of the data easy. When you want to aggregate what sorts of queries users are running, how long the take, et cetera it is very useful -- and we will want to do these things.

At some point we're going to run up against the dreaded GIL, or some other limit with one server and one python interpreter. We should plan to easily accomodate running N web servers with M interpreters on each behind a session-affinity preserving load balancer. Similarly, we may want to look at a less thread heavy job queueing strategy so that expensive compute jobs can be offloaded to other systems.


What both of you are proposing relies on sophisticated servers that are needed to take care of buisness which is a very solid strategy and some things can only be done that way.

But there is this other approach where every client is a lot more independent, like bittorrent, or to a lesser extent seti@home, architectures where simple systems can come together and become substantially more efficient.

Where you could just start a "trusted" galaxy server anywhere in the world, they would check in with a main server so that it will be forwarded new users, while in the background synchronization processes would start transferring the new data that gets entered into them to a main repository. If this new system needs to be taken offline it will notify the main server and would exit once all of its data is transferred all the while the main server would uppload the data to someone else's system so that when the user comes back they don't notice anything.

This is one of the reasons I'd like to see galaxy entirely self contained and independent.

Rico :

The method used to store all of the "real" data (alignments, sequences, annotation, etc. what else?) can for the most part be factored out of the discussion regarding the Web and Compute servers.

One solution is to separate the storage from the Web and Compute servers. In order to maintain scalability, and availability we could go with something like Luster: http://www.clusterfs.com. Essentially, there would be another cluster dedicated to providing access to the "real" data to the Web and Compute servers. With this architecture, and proper planning, the failure of a machine in the infrastructure is non-fatal. A failed Web, Compute, or Storage server is simply replaced, or removed from service.

Another solution would be to use PVFS: http://www.pvfs.org/pvfs2. This solution would distribute the data across all of the Nodes in the Compute Cluster. I'd have to look at pfvs again to intelligently comment on it's fault-tolerance capabilities. We wouldn't want a failed Compute Node to prevent us from accessing some of the "real" data.