First try on benchmark CI #315

filchristou · 2023-11-16T12:32:12Z

Options

As mentioned in the discourse thread https://discourse.julialang.org/t/recommendation-for-ci-benchmark-to-catch-regression/104698 the available options to have CI benchmarks are

PkgBenchmark.jl : a thin layer on top of BenchmarkTools.jl
BenchmarkCI.jl : an opinionated CI workflow using PkgBenchmark.jl
benchmark-action/github-action-benchmark : a CI machinery on top of BenchmarkTools.jl
AirspeedVelocity.jl : inspired by python's asv

Implementation

In this approach PkgBenchmark.jl and BenchmarkCI.jl are used.

Benchmarks

Regarding the benchmarks in ./benchmark/* directory I did nothing but translating them to a compatible formulation.
This means that the SUITE:BenchmarkGroup must be defined in ./benchmark/benchmark.jl
All options above need the same form (with minor changes for benchmark-action/github-action-benchmark).
This means that we can continue authoring more benchmarks with the security that the code is reusable even if in the CI approach changes in the future.

CI

This is described in the single file /.github/workflows/benchmark.yaml
There are 2 paths: if the event is a pull_request or if it is a push.

If the event is a pull_request a comparison is made (using BenchmarkCI.judge) between the base and the target refs.
This will also post a summary in the PR as a comment.
The base and target benchmarks are uploaded as artifacts in the workflow.

If the event is a push (or a merge) the benchmarks from the commit are run (using PkgBenchmark.benchmarkpkg).
A median estimation of the benchmarks is uploaded as an artifact in the workflow.

Further discussion

Strategy

Benchmarks are just running on ubuntu-latest and julia-v1.
I don't see any reason to populate the workflow with more data.

Artifacts uploads

Artifacts uploads remain available only for 90 days.
After that, the only thing that will stay are the comment-posts in the PRs.
If we want to store all benchmarks we can discuss on some alternatives.

uploading them in another github repo
uploading them as part of the current repo (the files need to be small (that's the thinking behind the median estimations)
uploading in another cloud service

I would like that to be part of the repo, since it's way easier to manage, but it's also completely useless for the users to get.

Permissions and approval

Right now the PR benchmark is run everytime a new update of the branch is pushed.
That might not be necessary.
I think it would be better to have some kind of a manual trigger to start the machinery when other more obvious issues are already resolved.
Also, it is insecure to allow everyone to run or modify the workflow, but I think that's already solved in the organization level.

Single and multithread

Right now both single and multithread benchmarking code is given 2 threads.
We can seperate that.

Example

See how a PR can look
filchristou#3
which triggers the workflow
https://github.com/filchristou/Graphs.jl/actions/runs/6889672830
After a PR is merged, a benchmark will run again
https://github.com/filchristou/Graphs.jl/actions/runs/6889854479

Overall I cannot promise it will work perfectly directly, since I was testing stuff in the fork and not on the main or protected branch. Also, I am not very familiar with the Graphs.jl way of things, so I guess we can tune several preferences in the future.

filchristou · 2023-11-16T12:40:49Z

For experimentation reasons we can make a benchx branch here actually.

codecov · 2023-11-16T15:41:21Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Comparison is base (cc3052f) 97.26% compared to head (e1e7882) 97.26%.
Report is 1 commits behind head on benchx.

❗ Current head e1e7882 differs from pull request most recent head bf18af6. Consider uploading reports for the commit bf18af6 to get more accurate results

Additional details and impacted files

@@           Coverage Diff           @@
##           benchx     #315   +/-   ##
=======================================
  Coverage   97.26%   97.26%           
=======================================
  Files         115      115           
  Lines        6795     6795           
=======================================
  Hits         6609     6609           
  Misses        186      186

☔ View full report in Codecov by Sentry.
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gdalle

Thank you so much for taking this on! The general setup seems okay to me, I didn't review the benchmark contents in detail because that's not the point of this PR: let's first get it working

gdalle · 2023-11-21T12:38:16Z

benchmark/benchmarks.jl

-suite = BenchmarkGroup()
-include("core.jl")
+serialbenchmarks = [
+    "serial/core.jl",


use joinpath?

ah yeah. with benchdir = dirname(@__FILE__) and the joinpath(benchdir, ...). yeah that's the way it should be.

gdalle · 2023-11-21T12:40:43Z

benchmark/tune.json

@@ -0,0 +1 @@
+[{"Julia":"1.9.4","BenchmarkTools":"1.0.0"},[["BenchmarkGroup",{"data":{"centrality":["BenchmarkGroup",{"data":{"graphs":["BenchmarkGroup",{"data":{"closeness_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"betweenness_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"katz_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"degree_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":15,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"digraphs":["BenchmarkGroup",{"data":{"closeness_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"betweenness_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"katz_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"degree_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":10,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"pagerank":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}]},"tags":[]}],"parallel":["BenchmarkGroup",{"data":{"egonet":["BenchmarkGroup",{"data":{"vertexfunction":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"twohop":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}]},"tags":[]}],"core":["BenchmarkGroup",{"data":{"nv":["BenchmarkGroup",{"data":{"graphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":723,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"digraphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":784,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"edges":["BenchmarkGroup",{"data":{"graphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":7,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"digraphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":8,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"has_edge":["BenchmarkGroup",{"data":{"graphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":7,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"digraphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":8,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}]},"tags":[]}],"connectivity":["BenchmarkGroup",{"data":{"graphs":["BenchmarkGroup",{"data":{"connected_components":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"digraphs":["BenchmarkGroup",{"data":{"strongly_connected_components":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}]},"tags":[]}],"insertions":["BenchmarkGroup",{"data":{"SG(n,e) 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do we need this?

Yes. Why is described on the Caching Parameters docs of BenchmarkTools.jl. Basically we win in twofold:

tuning is slow and it doesn't have to happen everytime when benchmark.

better consistency as the same evaluations/samples are being done in every benchmark

Can we find a way to automate the re-generation of the json every time the suite object is updated? Otherwise people will forget

gdalle · 2023-11-21T12:41:05Z

benchmark/benchmarks.jl

    "complete100" => complete_digraph(100), "path500" => path_digraph(500)
 )

-GRAPHS = Dict{String,Graph}(
+const GRAPHS = Dict{String,Graph}(


IIUC benchmarking is always done on all of these, and the total time is reported?

Yes. The benchmark results are accumulated across all Graphs and DiGraphs. I find it too granular to get benchmarks for each one of the Graphs. For me, It's better to add them up.
Now the const is not really needed I think, since the Graph is always interpolated in the benchmark, but it also doesn't harm.

gdalle · 2023-11-21T12:43:42Z

Benchmarks are just running on ubuntu-latest and julia-v1.

Agreed

Artifacts uploads remain available only for 90 days.

It would be useful to track the performance of the main branch over longer periods of time. For pull requests however we don't really care. Where are benchmarks for Julia itself stored for example?

Right now the PR benchmark is run everytime a new update of the branch is pushed.

Can we base this on a GitHub label, like benchmark, which repo admins would add to a PR when it's nearly ready?

For experimentation reasons we can make a benchx branch here actually.

Knock yourself out!

gdalle · 2023-11-21T12:43:57Z

I'd be curious to have @simonschoelly's opinion on the general approach

filchristou · 2023-11-22T07:23:54Z

Can we base this on a GitHub label, like benchmark, which repo admins would add to a PR when it's nearly ready?

I believe that is technically possible. Maybe the label should be more like to-benchmark because with benchmark there might be confusion that the PR itself was made for performance/benchmarking reasons ?

filchristou · 2023-11-22T07:28:16Z

The PR is failing because the benchmark baseline (i.e. the master branch) doesn't follow the requirements. I believe this is okey, and I wouldn't want to introduce complicated if statements just for this first PR. From the second on, once the master branch is properly structured, there should be no problem.
But as I said before we can test it further in a seperate benchx branch.

filchristou · 2023-11-23T16:32:21Z

Where are benchmarks for Julia itself stored for example?

In a separate github repo
https://github.com/JuliaCI/NanosoldierReports

gdalle · 2023-11-23T17:45:10Z

See JuliaGraphs/JuliaGraphs-meta#12 for the roadmap

(WIP) TODO: store results and PR label triggering

filchristou · 2023-11-28T15:12:40Z

I merged on the branch with the following TODOs pending before pushing to master:

make sure consecutive PRs benchmarks work as intended
find a way to trigger PR benchmarks (e.g. labels)
long store benchmark results upon push to master (github post or other repo)

* First try on benchmark CI (#315) (WIP) TODO: store results and PR label triggering * Test consecutive PR (#346) Merge all new advancements on the `benchx` branch in order to do a follow up consecutive PR to test github actions * Trivial change, test PR (#347) * Trivial change, test PR * Add PR write permission * Test full permissions * Granular permissions * try write-all * try label event * labeled in pull_request * Store results as artifact and trigger a consecutive workflow_run * Workflow chain almost complete (WIP) * correct .benchmarkci path * Add benchx support branch * Just try pull_request_target instead * Remove target * Get rid of s to get the chain going --------- Co-authored-by: Guillaume Dalle <[email protected]> * Simplify for master merge * Fixed formatting * Integrate review comments --------- Co-authored-by: Guillaume Dalle <[email protected]>

gdalle reviewed Nov 21, 2023

View reviewed changes

gdalle mentioned this pull request Nov 22, 2023

Add FrozenVector to wrap neighbors #317

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gdalle mentioned this pull request Nov 23, 2023

Community call - 2023.11.23 JuliaGraphs/JuliaGraphs-meta#12

Open

filchristou changed the base branch from master to benchx November 28, 2023 09:29

First try on benchmark CI

bf18af6

(WIP) TODO: store results and PR label triggering

filchristou force-pushed the benchx branch from e1e7882 to bf18af6 Compare November 28, 2023 15:03

filchristou merged commit b274d35 into JuliaGraphs:benchx Nov 28, 2023
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First try on benchmark CI #315

First try on benchmark CI #315

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		@@ -0,0 +1 @@
		[{"Julia":"1.9.4","BenchmarkTools":"1.0.0"},[["BenchmarkGroup",{"data":{"centrality":["BenchmarkGroup",{"data":{"graphs":["BenchmarkGroup",{"data":{"closeness_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"betweenness_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"katz_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"degree_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":15,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"digraphs":["BenchmarkGroup",{"data":{"closeness_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"betweenness_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"katz_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"degree_centrality":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":10,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"pagerank":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}]},"tags":[]}],"parallel":["BenchmarkGroup",{"data":{"egonet":["BenchmarkGroup",{"data":{"vertexfunction":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"twohop":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}]},"tags":[]}],"core":["BenchmarkGroup",{"data":{"nv":["BenchmarkGroup",{"data":{"graphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":723,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"digraphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":784,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"edges":["BenchmarkGroup",{"data":{"graphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":7,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"digraphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":8,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"has_edge":["BenchmarkGroup",{"data":{"graphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":7,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"digraphs":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":8,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}]},"tags":[]}],"connectivity":["BenchmarkGroup",{"data":{"graphs":["BenchmarkGroup",{"data":{"connected_components":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"digraphs":["BenchmarkGroup",{"data":{"strongly_connected_components":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}]},"tags":[]}],"insertions":["BenchmarkGroup",{"data":{"SG(n,e) 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First try on benchmark CI #315

First try on benchmark CI #315

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filchristou commented Nov 16, 2023 • edited Loading

Options

Implementation

Benchmarks

CI

Further discussion

Strategy

Artifacts uploads

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Single and multithread

Example

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