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 <chilton@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
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
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
On Tue, Dec 17, 2013 at 11:15 AM, Ben Gift <corn8bit2@gmail.com> wrote: the 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.
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