Hi John, thanks for the reply. Yes, I mean Galaxy's default behavior of keeping all the data on all nodes of our condor cluster. So for instance if I run a job, then the output of that job is copied to every node in the cluster. Is this not the normal behavior?
On Tue, Dec 17, 2013 at 9:42 AM, John Chilton <chil...@msi.umn.edu> wrote: > Hey Ben, > > Thanks for the e-mail. I did not promise anything was coming soon, I > only said people were working on parts of it. It is not a feature yet > unfortunately - multiple people including myself are thinking about > various parts of this problem though. > > I would like to respond, but I am trying to understand this line: "We > can't do this because Galaxy copies all intermediate steps to all > no(d)es, which would bog down the servers too much." > > Can you describe how you are doing this staging for me? Is data > currently being copied around to all the nodes, if so how are you > doing that? Or are you trying to say that Galaxy requires the data to > be available on all of the nodes? > > -John > > On Tue, Dec 17, 2013 at 11:15 AM, Ben Gift <corn8b...@gmail.com> wrote: > > We've run into a scenario lately where we need to run a very large > workflow > > (huge data in intermediate steps) many times. We can't do this because > > Galaxy copies all intermediate steps to all notes, which would bog down > the > > servers too much. > > > > I asked about something similar before and John mentioned the feature to > > automatically delete intermediate step data in a workflow once it > completed, > > was coming soon. Is that a feature now? That would help. > > > > Ultimately though we can't be copying all this data around to all nodes. > The > > network just isn't good enough, so I have an idea. > > > > What if we have an option on the 'run workflow' screen to only run on one > > node (eliminating the neat Galaxy concurrency ability for that workflow > > unfortunately)? Then it just propagates the final step data. > > > > Or maybe only copy to a couple other nodes, to keep concurrency. > > > > If the job errored then in this case I think it should just throw out all > > the data, or propagate where it stopped. > > > > I've been trying to work on implementing this myself but it's taking me a > > long time. I only just started understanding the pyramid stack, and am > > putting in the checkbox in the run.mako template. I still need to learn > the > > database schema, message passing, and how jobs are stored, and how to > tell > > condor to only use 1 node, (and more I'm sure) in Galaxy. (I'm drowning) > > > > This seems like a really important feature though as Galaxy gains more > > traction as a research tool for bigger projects that demand working with > > huge data, and running huge workflows many many times. > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ >
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