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Flamegraphs #137

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Commits on Jun 14, 2022

  1. Trim the whole GHA, use https://github.com/umccr/reusable-github-actions

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  2. Repoint reusable workflows as per https://github.com/umccr/htsget-rs/… 

    …actions/runs/2493214340
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  3. Comment indirection

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  4. derive Eq along w/ PartialEq: https://github.com/umccr/htsget-rs/runs… 

    …/6875010856?check_suite_focus=true#step:5:455
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  5. Comment the test and benchmarks for now, need to implement dependenci… 

    …es w/ reusable workflows, see https://stackoverflow.com/questions/58457140/dependencies-between-workflows-on-github-actions and https://docs.github.com/en/actions/using-workflows/reusing-workflows
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Commits on Jun 15, 2022

  1. PartialEq, Eq errors

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  2. Hopefully done with that Eq lint?

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Commits on Jun 16, 2022

  1. Remove stray char in Cloud

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Commits on Jun 20, 2022

  1. Avoid duplicate CI runs

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  2. Check passes, let's go for testing phase

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  3. Add job dependencies and drafting release module

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  4. Enable benchmarking phase

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  5. Trigger run

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  6. Redundant comment

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  7. Add a couple of TODO, test cargo-install for multiple crates at once

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  8. Will use slim Rust container for

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  9. Need to get acquainted with conventional commits too, TODO

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  10. Not fully convinced about shipping Docker too for devs, but giving it… 

    … a go
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Commits on Jun 21, 2022

  1. Adjust timing and number of samples to avoid criterion warnings/runou… 

    …ts, both locally and on the target CI environment (GHA).
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  2. Benches closer to plots with this PR

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  3. Original htsnexus implementation is gone from DNANexus, @mlin? /cc @o… 

    …hofmann
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Commits on Jun 23, 2022

  1. Commits are non-convetional still, but let's try the request/search b… 

    …enchmarks and see if release PR is working
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  2. Move rusable bits away from this repo

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  3. Release should depend on benchmarking regressions too

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Commits on Dec 14, 2022

  1. Merge branch 'main' into better_ci

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  2. futures.push_back might have been deprecated? Switching to .push

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Commits on Dec 15, 2022

  1. Inline format arguments (make clippy happy)

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  2. Cargo fmt

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  3. Back pedal on push vs push_back (the former actually being the one be… 

    …ing deprecated :-S)... more inline format clippy warnings that do not show locally despite cargo clean-ing and making sure same versions are running on CI and local :/
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  4. More inline format strings

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  5. Fixup clippy on nightly too, not only stable

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Commits on Dec 16, 2022

  1. Ignore secrets and data

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  2. Clarify which lambda runtime we are using

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  3. cargo clippy --fix for all features

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  4. Cargo clippy --fix has been stabilised now

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  5. Get rid of reusable workflows strategy

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Commits on Dec 19, 2022

  1. Focus on search benchmarks generation and storage

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  2. auto-push must be false when external-data-json-path is set since thi… 

    …s action reads/writes the given JSON file and never pushes to remote
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  3. Is the benchmark output being generated on stderr instead of stdout?

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  4. Update secret accordingly, valid only for 1 year for now

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Commits on Dec 20, 2022

  1. Undo stdout/stderr redirection for search-benchmarks

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  2. Going a bit more verbatim on github-action-benchmark docs, perhaps mi… 

    …ssed some assumption/convention?
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  3. Where is the benchmark output.txt and why is it not found?

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  4. Repeated htsget-rs/htsget-rs path segment in https://github.com/umccr… 

    …/htsget-rs/actions/runs/3737593760/jobs/6342928802#step:9:17...
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  5. Hopefully correct path now/

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Commits on Dec 21, 2022

  1. Hardcode output.txt path on the runner directory

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Commits on Dec 22, 2022

  1. Test github-action-benchmark fork and cargo-criterion tool feature ou… 

    …tlinedi n benchmark-action/github-action-benchmark#145
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  2. Use the right branch for the forked action

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Commits on Dec 23, 2022

  1. Forked GHA requires a runnable release to work

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Commits on Jan 3, 2023

  1. Test custom cargo criterion release: does the GHA refer to tags/relea… 

    …ses or branches?
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Commits on Jan 4, 2023

  1. Test all the changes introduced in the GHA

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Commits on Jan 5, 2023

  1. Testing native benchmark report keeping

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  2. Newer checkout migrates from deprecated Node12 to Node16

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  3. Merge branch 'main' into better_ci

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  4. Merge conflicts

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  5. Add release-plz, first run

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  6. error: all dependencies must have a version specified when publishing.

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  7. [skip ci] Repoint dependencies to its respective repos instead of loc… 

    …al paths, in preparation for (manual) crates.io release
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  8. he remote server responded with an error: missing or empty metadata f… 

    …ields: description, license. Please see https://doc.rust-lang.org/cargo/reference/manifest.html for how to upload metadata
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  9. Add missing licenses/descriptions pre-crates.io publishing [ci skip]

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  10. Adding the rest of attributes to avoid cargo publish warnings [ci skip]

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  11. Last metadata addition to avoid cargo publish warnings on htsget-test… 

    …-utils crate [ci skip]
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Commits on Jan 6, 2023

  1. Rename htsget-http-actix -> htsget-actix, htsget-http-lambda -> htsge… 

    …t-lambda, htsget-http-core -> htsget-http, and htsget-test-utils -> htsget-test
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  2. Version bump all deps

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  3. Better names for the lib side of this crate

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  4. Cleanup before release as described in MarcoIeni/release-plz-action#1… 

    …4 (comment)
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  5. Temporarily disable htsget-test as suggested by cargo maintainers

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  6. Revert "Temporarily disable htsget-test as suggested by cargo maintai… 

    …ners"

This reverts commit 585485e.
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  7. Stray fmt

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  8. Cargo clippy

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  9. This cargo fmt did not go through?

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Commits on Jan 7, 2023

  1. Only trigger on those branches as I'm testing, thanks @Marcoleni, let… 

    …'s see what happens now :)
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  2. Split monolith GHA workflow into 3 actions, was running out of space … 

    …by release
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  3. Drop custom generate token for release-plz

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Commits on Jan 9, 2023

  1. No more than 1 level for tests and benchmarks [ci skip]

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  2. No target/criterion/<name_of_bench>/flamegraph.svg found :/

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  3. I suspect that the profiler only generates .svg's under Linux?

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  4. Check if the flamegraph .svg has been generated alongside the JSONs

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  5. wrong location/bench name?

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Commits on Jan 10, 2023

  1. Rewire criterion function, just generates JSONs, no flamegraphs.svg y… 

    …et :/ [ci skip]
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  2. Simplify cargo bench flamegraphs bench example a bit further and run … 

    …it on Linux just in case pprof does not work on OSX? Also try to solve the --profile-time mystery argument on GHA
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Commits on Jan 15, 2023

  1. Merge deploy conflict(s)

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Commits on Jan 16, 2023

  1. Merge branch 'better_ci' into flamegraphs

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  2. Merge branch 'main' into flamegraphs

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  3. Switch from criterion-rs custom profiler strategy to cargo-flamegraph… 

    …s crate
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  4. Install cargo flamegraphs and match GHA names with jobs to avoid conf… 

    …usion
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  5. Implicit --flamegraph will not be recognised by CLI

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  6. CI job failed with Linux-specific kernel settings, apply https://gith… 

    …ub.com/flamegraph-rs/flamegraph#enabling-perf-for-use-by-unprivileged-users
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  7. Binary perfile data seems to be spewed on stdout for Linux, does not … 

    …happen in DTrace under OSX? See: flamegraph-rs/flamegraph#248

Also check contents of restricted GHA kernel memory map.
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Commits on Jan 17, 2023

  1. What are the previous settings?

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Commits on May 12, 2023

  1. Merge branch 'main' into flamegraphs

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Commits on May 16, 2023

  1. [ci skip] ResolveResponse trait having some weird import issues... re… 

    …factoring into htsget-benchmarks after signing up for bencher.dev
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  2. fix(benchmarks): set correct feature flags for htsget dependencies

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  3. [ci skip] (fix): Crate typo, htsget-config instead of htsget-search /cc 

    @mmalenic
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  4. Add bencher.dev CI/CD

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Commits on May 17, 2023

  1. Correct GHA syntax for bencher

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  2. Adding uses as bencher.dev docs assume, I think they are wrong though?

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  3. Move requests benchmarks to htsget-benchmarks crate and **separate** … 

    …htsget-rs+htsget-refserver benchmark pairing. Aim is for them to run separatedly so that they are easier to paralelise on GHA CI/CD, otherwise we'll see timeouts often (we just had one now as I was integrating bencher.dev). Also we'll have a template for third party comparisons. Commented most of the search benchmarks to iterate more quickly now
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Commits on May 22, 2023

  1. [ci skip] Experiment with criterion-rs external profiler hooks (https… 

    …://bheisler.github.io/criterion.rs/book/user_guide/profiling.html#implementing-in-process-profiling-hooks) and extending @koute's not-perf accordingly in https://github.com/brainstorm/not-perf/tree/external_profiler_for_criterion
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Commits on May 29, 2023

  1. Change benchmark adapter/harness as suggested by @epompeii (thx)

    @brainstorm
    brainstorm committed May 29, 2023
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