diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml new file mode 100644 index 000000000..27a66d7d1 --- /dev/null +++ b/.github/workflows/benchmark.yml @@ -0,0 +1,25 @@ +name: Run benchmarks + +on: + pull_request: + types: [labeled, opened, synchronize, reopened] + +# Only trigger the benchmark job when you add `run benchmark` label to the PR +jobs: + Benchmark: + runs-on: ubuntu-latest + if: contains(github.event.pull_request.labels.*.name, 'run benchmark') + steps: + - uses: actions/checkout@v2 + - uses: julia-actions/setup-julia@latest + with: + version: 1 + - uses: julia-actions/julia-buildpkg@latest + - name: Install dependencies + run: julia -e 'using Pkg; pkg"add PkgBenchmark BenchmarkCI@0.1"' + - name: Run benchmarks + run: julia -e 'using BenchmarkCI; BenchmarkCI.judge()' + - name: Post results + run: julia -e 'using BenchmarkCI; BenchmarkCI.postjudge()' + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore index 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"OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/perf/Project.toml b/benchmark/Project.toml similarity index 60% rename from perf/Project.toml rename to benchmark/Project.toml index ddbb1be6e..9e49aa3eb 100644 --- a/perf/Project.toml +++ b/benchmark/Project.toml @@ -1,6 +1,8 @@ [deps] BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" GraphNeuralNetworks = "cffab07f-9bc2-4db1-8861-388f63bf7694" +Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -Graphs = "093fc24a-ae57-5d10-9952-331d41423f4d" +PkgBenchmark = "32113eaa-f34f-5b0d-bd6c-c81e245fc73d" diff --git a/benchmark/bench_gcnconv.jl b/benchmark/bench_gcnconv.jl new file mode 100644 index 000000000..8b12e2936 --- /dev/null +++ b/benchmark/bench_gcnconv.jl @@ -0,0 +1,82 @@ +module BenchGCNConv +using GraphNeuralNetworks +using Random, Statistics, SparseArrays +using BenchmarkTools +using Flux, Graphs + + +function get_single_benchmark(sub, N, c, D, CONV; gtype=:lg) + data = erdos_renyi(N, c / (N-1), seed=17) + X = randn(Float32, D, N) + + g = GNNGraph(data; ndata=X, graph_type=gtype) + g_gpu = g |> gpu + + m = CONV(D => D) + ps = Flux.params(m) + + m_gpu = m |> gpu + ps_gpu = Flux.params(m_gpu) + + + sub["CPU_FWD"] = @benchmarkable $m($g) + sub["CPU_GRAD"] = @benchmarkable gradient(() -> sum($m($g).ndata.x), $ps) + + # try + # sub["GPU_FWD"] = @benchmark CUDA.@sync($m_gpu($g_gpu)) teardown=(GC.gc(); CUDA.reclaim()) + # catch + # sub["GPU_FWD"] = missing + # end + + # try + # sub["GPU_GRAD"] = @benchmark CUDA.@sync(gradient(() -> sum($m_gpu($g_gpu).ndata.x), $ps_gpu)) teardown=(GC.gc(); CUDA.reclaim()) + # catch + # # sub["GPU_GRAD"] = missing + # end + + return sub +end + + + +""" + run_benchmarks(; + Ns = [10, 100, 1000, 10000], + c = 6, + D = 100, + layers = [GCNConv, GraphConv, GATConv] + ) + +Benchmark GNN layers on Erdos-Renyi ranomd graphs +with average degree `c`. Benchmarks are perfomed for each graph size in the list `Ns`. +`D` is the number of node features. +""" +function get_benchmarks(; + # Ns = [10, 100, 1000, 10000], + Ns = [10, 100], + c = 6, + D = 100, + # layers = [GCNConv, GATConv], + # gtypes = [:coo, :sparse, :dense], + layers = [GCNConv,], + gtypes = [:coo,], + ) + + SUITE = BenchmarkGroup() + + for gtype in gtypes + for N in Ns + for CONV in layers + sub = SUITE["$(gtype)_$(N)_$(CONV)"] = BenchmarkGroup() + get_single_benchmark(sub, N, c, D, CONV; gtype) + end + end + end + return SUITE +end + +SUITE = get_benchmarks() + +end + +BenchGCNConv.SUITE \ No newline at end of file diff --git a/benchmark/bench_propagate.jl b/benchmark/bench_propagate.jl new file mode 100644 index 000000000..1ea5e7927 --- /dev/null +++ b/benchmark/bench_propagate.jl @@ -0,0 +1,44 @@ +module BenchPropagate +using GraphNeuralNetworks +using Random, Statistics, SparseArrays +using BenchmarkTools + +SUITE = BenchmarkGroup() + +Random.seed!(17) +n = 1024 +A = sprand(n, n, 0.01) +X = rand(100, n) +w = reshape(A.nzval, 1, :) +e = rand(1, length(A.nzval)) + +g = GNNGraph(A, ndata=(; X), edata=(; e, w), graph_type=:coo) + +spmm1(g) = propagate((xi, xj, e) -> e .* xj , g, +; xj=g.ndata.X, e=g.edata.w) +spmm2(g) = propagate(e_mul_xj, g, +; xj=g.ndata.X, e=vec(g.edata.w)) + +@assert spmm1(g) ≈ X * A +@assert spmm2(g) ≈ X * A + +let sub = SUITE["e_mul_xj"] = BenchmarkGroup() + sub["_baseline"] = @benchmarkable $X * $A + sub["unfused"] = @benchmarkable spmm1($g) + sub["fused"] = @benchmarkable spmm2($g) +end + +spmm_copyxj_fused(g) = propagate(copy_xj, g, +; xj=g.ndata.X) +spmm_copyxj_unfused(g) = propagate((xi, xj, e) -> xj, g, +; xj=g.ndata.X) + + +let sub = SUITE["copy_xj"] = BenchmarkGroup() + Adj = map(x -> x > 0 ? 1 : 0, A) + @assert spmm_copyxj_unfused(g) ≈ X * Adj + @assert spmm_copyxj_fused(g) ≈ X * Adj + + sub["_baseline"] = @benchmarkable $X * $Adj + sub["fused"] = @benchmarkable spmm_copyxj_fused($g) + sub["unfused"] = @benchmarkable spmm_copyxj_unfused($g) +end + +end +BenchPropagate.SUITE \ No newline at end of file diff --git a/benchmark/benchmark.md b/benchmark/benchmark.md new file mode 100644 index 000000000..e57a37b5b --- /dev/null +++ b/benchmark/benchmark.md @@ -0,0 +1,57 @@ +# Benchmark Report for */home/carlo/.julia/dev/GraphNeuralNetworks* + +## Job Properties +* Time of benchmark: 25 Feb 2022 - 16:17 +* Package commit: dirty +* Julia commit: ac5cc9 +* Julia command flags: None +* Environment variables: `OMP_NUM_THREADS => 1` `JULIA_NUM_THREADS => 1` + +## Results +Below is a table of this job's results, obtained by running the benchmarks. +The values listed in the `ID` column have the structure `[parent_group, child_group, ..., key]`, and can be used to +index into the BaseBenchmarks suite to retrieve the corresponding benchmarks. +The percentages accompanying time and memory values in the below table are noise tolerances. The "true" +time/memory value for a given benchmark is expected to fall within this percentage of the reported value. +An empty cell means that the value was zero. + +| ID | time | GC time | memory | allocations | +|------------------------------------------------------------------|----------------:|--------:|----------------:|------------:| +| `["gcnconv", "coo_100_GraphNeuralNetworks.GCNConv", "CPU_FWD"]` | 86.176 μs (5%) | | 249.62 KiB (1%) | 58 | +| `["gcnconv", "coo_100_GraphNeuralNetworks.GCNConv", "CPU_GRAD"]` | 2.688 ms (5%) | | 757.31 KiB (1%) | 1887 | +| `["gcnconv", "coo_10_GraphNeuralNetworks.GCNConv", "CPU_FWD"]` | 20.919 μs (5%) | | 27.80 KiB (1%) | 51 | +| `["gcnconv", "coo_10_GraphNeuralNetworks.GCNConv", "CPU_GRAD"]` | 910.193 μs (5%) | | 219.61 KiB (1%) | 1869 | +| `["propagate", "copy_xj", "_baseline"]` | 408.494 μs (5%) | | 800.05 KiB (1%) | 2 | +| `["propagate", "copy_xj", "fused"]` | 561.269 μs (5%) | | 1.21 MiB (1%) | 31 | +| `["propagate", "copy_xj", "unfused"]` | 2.065 ms (5%) | | 8.95 MiB (1%) | 10 | +| `["propagate", "e_mul_xj", "_baseline"]` | 373.447 μs (5%) | | 800.05 KiB (1%) | 2 | +| `["propagate", "e_mul_xj", "fused"]` | 552.230 μs (5%) | | 1.13 MiB (1%) | 32 | +| `["propagate", "e_mul_xj", "unfused"]` | 3.596 ms (5%) | | 17.11 MiB (1%) | 12 | + +## Benchmark Group List +Here's a list of all the benchmark groups executed by this job: + +- `["gcnconv", "coo_100_GraphNeuralNetworks.GCNConv"]` +- `["gcnconv", "coo_10_GraphNeuralNetworks.GCNConv"]` +- `["propagate", "copy_xj"]` +- `["propagate", "e_mul_xj"]` + +## Julia versioninfo +``` +Julia Version 1.7.1 +Commit ac5cc99908 (2021-12-22 19:35 UTC) +Platform Info: + OS: Linux (x86_64-pc-linux-gnu) + "Manjaro Linux" + uname: Linux 5.16.7-1-MANJARO #1 SMP PREEMPT Sun Feb 6 12:22:29 UTC 2022 x86_64 unknown + CPU: Intel(R) Core(TM) i7-10710U CPU @ 1.10GHz: + speed user nice sys idle irq + #1-12 1185 MHz 484978 s 9416 s 116850 s 2788141 s 43648 s + + Memory: 15.464141845703125 GB (286.4765625 MB free) + Uptime: 63306.98 sec + Load Avg: 3.98 3.07 3.06 + WORD_SIZE: 64 + LIBM: libopenlibm + LLVM: libLLVM-12.0.1 (ORCJIT, skylake) +``` \ No newline at end of file diff --git a/benchmark/benchmarks.jl b/benchmark/benchmarks.jl new file mode 100644 index 000000000..19fc9c666 --- /dev/null +++ b/benchmark/benchmarks.jl @@ -0,0 +1,9 @@ +using BenchmarkTools + +SUITE = BenchmarkGroup() +for file in readdir(@__DIR__) + if startswith(file, "bench_") && endswith(file, ".jl") + SUITE[file[length("bench_") + 1:end - length(".jl")]] = + include(file) + end +end diff --git a/perf/perf.jl b/benchmark/perf.jl similarity index 100% rename from perf/perf.jl rename to benchmark/perf.jl diff --git a/benchmark/runbenchmarks.jl b/benchmark/runbenchmarks.jl new file mode 100644 index 000000000..78dd89cd0 --- /dev/null +++ b/benchmark/runbenchmarks.jl @@ -0,0 +1,15 @@ +using PkgBenchmark + +results = benchmarkpkg( + dirname(@__DIR__), + BenchmarkConfig( + # id = "v0.3.13", + env = Dict( + "JULIA_NUM_THREADS" => "1", + "OMP_NUM_THREADS" => "1", + ), + ), + # resultfile = joinpath(@__DIR__, "result.json"), + ) + +export_markdown("benchmark.md", results) diff --git a/benchmark/tune.json b/benchmark/tune.json new file mode 100644 index 000000000..30740b995 --- /dev/null +++ b/benchmark/tune.json @@ -0,0 +1 @@ +[{"Julia":"1.7.1","BenchmarkTools":"1.0.0"},[["BenchmarkGroup",{"data":{"propagate":["BenchmarkGroup",{"data":{"e_mul_xj":["BenchmarkGroup",{"data":{"_baseline":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"fused":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"unfused":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"copy_xj":["BenchmarkGroup",{"data":{"_baseline":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"fused":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"unfused":["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":[]}],"gcnconv":["BenchmarkGroup",{"data":{"coo_100_GraphNeuralNetworks.GCNConv":["BenchmarkGroup",{"data":{"CPU_FWD":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"CPU_GRAD":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}]},"tags":[]}],"coo_10_GraphNeuralNetworks.GCNConv":["BenchmarkGroup",{"data":{"CPU_FWD":["Parameters",{"gctrial":true,"time_tolerance":0.05,"samples":10000,"evals":1,"gcsample":false,"seconds":5.0,"overhead":0.0,"memory_tolerance":0.01}],"CPU_GRAD":["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":[]}]},"tags":[]}]]] 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+[[ZygoteRules]] +deps = ["MacroTools"] +git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" +uuid = "700de1a5-db45-46bc-99cf-38207098b444" +version = "0.2.2" + +[[libblastrampoline_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" + +[[nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" + +[[p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" diff --git a/perf/bench_gnn.jl b/perf/bench_gnn.jl deleted file mode 100644 index 0e1b35208..000000000 --- a/perf/bench_gnn.jl +++ /dev/null @@ -1,73 +0,0 @@ -using SparseArrays -using GraphNeuralNetworks -using BenchmarkTools -import Random: seed! -using LinearAlgebra - -n = 1024 -seed!(0) -A = sprand(n, n, 0.01) -b = rand(1, n) -B = rand(100, n) - -g = GNNGraph( - A, - ndata=(; b=b, B=B), - edata=(; A=reshape(A.nzval, 1, :)), - graph_type=:coo # changing to :sparse has little effect on performance -) - -function spmv(g) - propagate( - (xi, xj, e) -> e .* xj , # same as e_mul_xj - g, +; xj=g.ndata.b, e=g.edata.A - ) -end - -function spmm1(g) - propagate( - (xi, xj, e) -> e .* xj , # same as e_mul_xj - g, +; xj=g.ndata.B, e=g.edata.A - ) -end -function spmm2(g) - propagate( - e_mul_xj, - g, +; xj=g.ndata.B, e=vec(g.edata.A) - ) -end - -# @assert isequal(spmv(g), b * A) # true -# @btime spmv(g) # ~5 ms -# @btime b * A # ~32 us - -@assert isequal(spmm1(g), B * A) # true -@assert isequal(spmm2(g), B * A) # true -@btime spmm1(g) # ~9 ms -@btime spmm2(g) # ~9 ms -@btime B * A # ~400 us - - -function spmm_copyxj_fused(g) - propagate( - copy_xj, - g, +; xj=g.ndata.B - ) -end - -function spmm_copyxj_unfused(g) - propagate( - (xi, xj, e) -> xj, - g, +; xj=g.ndata.B - ) -end - -Adj = map(x -> x > 0 ? 1 : 0, A) -@assert spmm_copyxj_unfused(g) ≈ B * Adj -@assert spmm_copyxj_fused(g) ≈ B * Adj # bug fixed in #107 - -@btime spmm_copyxj_fused(g) # 268.614 μs (22 allocations: 1.13 MiB) -@btime spmm_copyxj_unfused(g) # 4.263 ms (52855 allocations: 12.23 MiB) -@btime B * Adj # 196.135 μs (2 allocations: 800.05 KiB) - -println() \ No newline at end of file diff --git a/perf/perf_master_20210830_carlodsba.jld2 b/perf/perf_master_20210830_carlodsba.jld2 deleted file mode 100644 index 6669c889e..000000000 Binary files a/perf/perf_master_20210830_carlodsba.jld2 and /dev/null differ