Comments (11)
natir
commented on September 24, 2024
1
If you give me some sample dataset I can try to perform runtime analysis and try to improve running time by parallelized or not.
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danydoerr
commented on September 24, 2024
There is potential for speedup by multithreading parts of GFAffix, especially if the bottle neck is the graph traversal. I'd be interested in knowing which step in the algorithm affects the running time on these deep graphs. The graph traversal can be parallelized, but it's not embarrassingly parallelizable, as the graph editing (which is intertwined in the graph traversal) can only be done safely in a single thread.
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danydoerr
commented on September 24, 2024
@ekg do you have such a "deep graph" handy?
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natir
commented on September 24, 2024
Or just smaller but similar graph.
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ekg
commented on September 24, 2024
Yes, but they are big. I don't think you need to use a deep graph to see if
parallelism can help. Probably a chunk of the MHC will be enough to
profile, or any graph that you've already used for testing that takes e.g.
5-10s to process.
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@ekg <https://github.com/ekg> do you have such a "deep graph" handy?
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danydoerr
commented on September 24, 2024
Do these deep graphs have a particular high node degree, or is the number of nodes exceptionally high?
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ekg
commented on September 24, 2024
High node degree and path depth. 2k fold coverage
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Do these deep graphs have a particular high node degree, or is the number
of nodes exceptionally high?
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danydoerr
commented on September 24, 2024
GFAffix should scale linearly with path depth, overall this shouldn't dominate the runtime. But node degree is certainly a bottle neck.
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natir
commented on September 24, 2024
@ekg Could you give me advise how to build a similar graph, type of data, pipeline, tools, etc…
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ekg
commented on September 24, 2024
@natir sorry to take a while here. I may need to share this somehow, but the graph is rather large and will take 4 days to build if you do so from scratch. I'll see if I can get a simpler test case together.
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danydoerr
commented on September 24, 2024
@ekg Just so you know that your issue is not forgotten: I have a solution for parallelizing GFAffix and will work on this sometime soonish.
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