Jeremy (from the team) ran a similar workshop several months ago and used some resource intensive tools (e.g., Tophat). We were concerned about the same scalability issues so we just started 4 separate clusters and divided the users across those. The approach worked well and it turned out we did not see any scalability issues. I think we went way overboard with 4 clusters but the approach did demonstrate an additional 'coolness' of the project allowing one to spin up 4 complete, identical clusters in a matter of minutes... So, I feel you could replicate a similar approach but could probably go with 2 clusters only? Jeremy can hopefully provide some first hand comments as well.

Yes, this approach worked well when I did it. I created all the data and workflows needed for the workshop on one Galaxy instance, shared/cloned that instance and set up 3 additional instances, and divided users evenly amongst the instances. 2-3 clusters will probably meet your needs with 50 participants.

Scalability issues are more likely to arise on the back end than the front end, so you'll want to ensure that you have enough compute nodes. BWA uses four nodes by default--Enis, does the cloud config change this parameter?--so you'll want 4x50 or 200 total nodes if you want everyone to be able to run a BWA job simultaneously.

Good luck, J.

Clare I wonder if you would be open to share the details of your setup and what you had to do for this once you are done. I think it would be incredibly useful to community (at least it would be for me ;-))

Thanks! On Nov 17, 2011, at 5:14 PM, Clare Sloggett wrote:

Hi Enis, Jeremy,

Thanks, that's really helpful! Jeremy do you remember what kind of instance you used per node, e.g. Amazon's 'large' (2 core / 4ECU / 7.5GB) or 'xlarge' (4 core / 8ECU / 15GB)? This would be a good sanity check for me.

Enis when you say a lot of memory, would you consider the 15GB nodes 'a lot'? I would generally consider that a lot in the context of a web server but not so much in NGS, so it's all relative! Amazon does have double-memory instances available.

Also, when you say a lot of memory especially for the master node - does this imply that I can choose a different specification for the master node than the compute nodes? I thought they had to be all identical, but just checking.

Thanks, Clare

On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks jeremy.goecks@emory.edu wrote:

...

...

Jeremy (from the team) ran a similar workshop several months ago and used some resource intensive tools (e.g., Tophat). We were concerned about the same scalability issues so we just started 4 separate clusters and divided the users across those. The approach worked well and it turned out we did not see any scalability issues. I think we went way overboard with 4 clusters but the approach did demonstrate an additional 'coolness' of the project allowing one to spin up 4 complete, identical clusters in a matter of minutes... So, I feel you could replicate a similar approach but could probably go with 2 clusters only? Jeremy can hopefully provide some first hand comments as well.

Yes, this approach worked well when I did it. I created all the data and workflows needed for the workshop on one Galaxy instance, shared/cloned that instance and set up 3 additional instances, and divided users evenly amongst the instances. 2-3 clusters will probably meet your needs with 50 participants.

Scalability issues are more likely to arise on the back end than the front end, so you'll want to ensure that you have enough compute nodes. BWA uses four nodes by default--Enis, does the cloud config change this parameter?--so you'll want 4x50 or 200 total nodes if you want everyone to be able to run a BWA job simultaneously.

Good luck, J.

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On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks jeremy.goecks@emory.edu wrote:

...

Scalability issues are more likely to arise on the back end than the front end, so you'll want to ensure that you have enough compute nodes. BWA uses four nodes by default--Enis, does the cloud config change this parameter?--so you'll want 4x50 or 200 total nodes if you want everyone to be able to run a BWA job simultaneously.

Actually, one other question - this paragraph makes me realise that I don't really understand how Galaxy is distributing jobs. I had thought that each job would only use one node, and in some cases take advantage of multiple cores within that node. I'm taking a "node" to be a set of cores with their own shared memory, so in this case a VM instance, is this right? If some types of jobs can be distributed over multiple nodes, can I configure, in Galaxy, how many nodes they should use?

You're right -- my word choices were poor. Replace 'node' with 'core' in my paragraph to get an accurate suggestion for resources.

Galaxy uses a job scheduler--SGE on the cloud--to distribute jobs to different cluster nodes. Jobs that require multiple cores typically run on a single node. Enis can chime in on whether CloudMan supports job submission over multiple nodes; this would require setup of an appropriate parallel environment and a tool that can make use of this environment.

Good luck, J.