Merge pull request #80 from yuehhua/develop

Add ScatterNNlib and GraphSignals as deps

Author: yuehhua

.travis.yml

@@ -9,6 +9,7 @@ os:
 
 julia:
   - 1.4
+  - 1.5
   - nightly
 
 branches:
@@ -22,9 +23,6 @@ after_success:
 notifications:
   email: false
 
-git:
-  depth: 99999999
-
 env:
   - JULIA_CUDA_SILENT=true
 
@@ -34,7 +32,7 @@ jobs:
   fast_finish: true
   include:
     - stage: Documentation
-      julia: 1.4
+      julia: 1.5
       script: julia --project=docs -e '
           using Pkg;
           Pkg.develop(PackageSpec(path=pwd()));

Manifest.toml

@@ -26,9 +26,9 @@ version = "0.0.4"
 
 [[ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra"]
-git-tree-sha1 = "6f6e33efac70fc24c1f2a654a090b7af01690ffe"
+git-tree-sha1 = "951c3fc1ff93497c88fb1dfa893f4de55d0b38e3"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
-version = "0.3.7"
+version = "0.3.8"
 
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -46,21 +46,21 @@ version = "0.4.1"
 
 [[CUDA]]
 deps = ["AbstractFFTs", "Adapt", "BinaryProvider", "CEnum", "DataStructures", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "Logging", "MacroTools", "NNlib", "Pkg", "Printf", "Random", "Reexport", "Requires", "SparseArrays", "Statistics", "TimerOutputs"]
-git-tree-sha1 = "66dbcc0d8e9470358d57aa52dbe74f97bab31a7f"
+git-tree-sha1 = "2c007bb3931360013d32bcd53a727e0a7f144e00"
 uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
-version = "1.2.0"
+version = "1.2.1"
 
 [[ChainRules]]
 deps = ["ChainRulesCore", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"]
-git-tree-sha1 = "fbc6ca7a758b15cbb18df4936b2f588fbf3abdda"
+git-tree-sha1 = "f54401294c1ed68d7cc2a7ea280ec101bca722bc"
 uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
-version = "0.7.10"
+version = "0.7.12"
 
 [[ChainRulesCore]]
 deps = ["MuladdMacro"]
-git-tree-sha1 = "87e289253a5fc690c4860a41bbd427e16576f716"
+git-tree-sha1 = "971b03f25bdf2acab79f1c51afc717f9dccf43c2"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "0.9.3"
+version = "0.9.5"
 
 [[CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
@@ -70,9 +70,9 @@ version = "0.7.0"
 
 [[ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
-git-tree-sha1 = "6e7aa35d0294f647bb9c985ccc34d4f5d371a533"
+git-tree-sha1 = "607c0ea16cb32af49ea2976f90c0c5acbca37d21"
 uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
-version = "0.10.6"
+version = "0.10.8"
 
 [[Colors]]
 deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Reexport"]
@@ -105,9 +105,9 @@ version = "1.3.0"
 
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "edad9434967fdc0a2631a65d902228400642120c"
+git-tree-sha1 = "88d48e133e6d3dd68183309877eac74393daa7eb"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.17.19"
+version = "0.17.20"
 
 [[Dates]]
 deps = ["Printf"]
@@ -146,27 +146,27 @@ version = "0.1.1"
 
 [[FileIO]]
 deps = ["Pkg"]
-git-tree-sha1 = "202335fd24c2776493e198d6c66a6d910400a895"
+git-tree-sha1 = "1e7e88a949b52e6f7f589041bd60928322414997"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.3.0"
+version = "1.4.1"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "be4180bdb27a11188d694ee3773122f4921f1a62"
+git-tree-sha1 = "4863cbb7910079369e258dee4add9d06ead5063a"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.8.13"
+version = "0.8.14"
 
 [[FixedPointNumbers]]
 deps = ["Statistics"]
-git-tree-sha1 = "266baee2e9d875cb7a3bfdcc6cab553c543ff8ab"
+git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc"
 uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
-version = "0.8.2"
+version = "0.8.4"
 
 [[Flux]]
 deps = ["AbstractTrees", "Adapt", "CUDA", "CodecZlib", "Colors", "DelimitedFiles", "Functors", "Juno", "LinearAlgebra", "MacroTools", "NNlib", "Pkg", "Printf", "Random", "Reexport", "SHA", "Statistics", "StatsBase", "Test", "ZipFile", "Zygote"]
-git-tree-sha1 = "a95bba0ee46dc320b34969fa246cc965c20c2c10"
+git-tree-sha1 = "ceb09ce8510ef31fd86a791bbd0e1d72a60f27d7"
 uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c"
-version = "0.11.0"
+version = "0.11.1"
 
 [[ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"]
@@ -186,15 +186,27 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[GPUArrays]]
 deps = ["AbstractFFTs", "Adapt", "LinearAlgebra", "Printf", "Random", "Serialization"]
-git-tree-sha1 = "0aaa4ff7001086e190a00180495b93b00df8bb43"
+git-tree-sha1 = "9027d6128645d227fa9ba7d5b3aa00af696b9aaf"
 uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "4.0.1"
+version = "5.0.0"
 
 [[GPUCompiler]]
 deps = ["DataStructures", "InteractiveUtils", "LLVM", "Libdl", "TimerOutputs", "UUIDs"]
-git-tree-sha1 = "6f46f295e8e504fce363caf2a28a2a56270681c0"
+git-tree-sha1 = "d6db068d8373bb45ac17e14744cc1d3681d0dbc7"
 uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
-version = "0.5.3"
+version = "0.5.5"
+
+[[GraphLaplacians]]
+deps = ["LightGraphs", "LinearAlgebra", "MetaGraphs", "SimpleWeightedGraphs", "SparseArrays", "Zygote"]
+git-tree-sha1 = "83881eb8eda839992f6310d9c4514b7ffb5498fe"
+uuid = "a1251efa-393a-423f-9d7b-faaecba535dc"
+version = "0.1.0"
+
+[[GraphSignals]]
+deps = ["GraphLaplacians", "LightGraphs", "LinearAlgebra", "SimpleWeightedGraphs", "Zygote"]
+git-tree-sha1 = "6e62e16c779458412951a71f4d535f05a1e0bb89"
+uuid = "3ebe565e-a4b5-49c6-aed2-300248c3a9c1"
+version = "0.1.1"
 
 [[IRTools]]
 deps = ["InteractiveUtils", "MacroTools", "Test"]
@@ -213,15 +225,15 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
 [[JLD2]]
 deps = ["CodecZlib", "DataStructures", "FileIO", "Mmap", "Pkg", "Printf", "UUIDs"]
-git-tree-sha1 = "e03e697cf84c275ece9cbefd1eabaf49bf5e7254"
+git-tree-sha1 = "9353b717ee4e27beab4e902c92a06bb5f160d2cf"
 uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-version = "0.1.13"
+version = "0.1.14"
 
 [[Juno]]
 deps = ["Base64", "Logging", "Media", "Profile"]
-git-tree-sha1 = "a686b0cf235fa3e491b79b4783c2d2382292b436"
+git-tree-sha1 = "90976c3ab792a98d240d42f9df07420ccfc60668"
 uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d"
-version = "0.8.2"
+version = "0.8.3"
 
 [[LLVM]]
 deps = ["CEnum", "Libdl", "Printf", "Unicode"]
@@ -230,6 +242,7 @@ uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
 version = "2.0.0"
 
 [[LibGit2]]
+deps = ["Printf"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
 [[Libdl]]
@@ -250,9 +263,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[LoopVectorization]]
 deps = ["DocStringExtensions", "LinearAlgebra", "OffsetArrays", "SIMDPirates", "SLEEFPirates", "UnPack", "VectorizationBase"]
-git-tree-sha1 = "4c002de66221639174e081ec74c156e9013e4afa"
+git-tree-sha1 = "df625d1ac07cb4b630ec1c024a42b8bc6ee9927f"
 uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
-version = "0.8.17"
+version = "0.8.23"
 
 [[MacroTools]]
 deps = ["Markdown", "Random"]
@@ -290,27 +303,21 @@ git-tree-sha1 = "c6190f9a7fc5d9d5915ab29f2134421b12d24a68"
 uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 version = "0.2.2"
 
-[[NNPACK_jll]]
-deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "c3d1a616362645754b18e12dbba96ec311b0867f"
-uuid = "a6bfbf70-4841-5cb9-aa18-3a8ad3c413ee"
-version = "2018.6.22+0"
-
 [[NNlib]]
-deps = ["Libdl", "LinearAlgebra", "LoopVectorization", "NNPACK_jll", "Pkg", "Requires", "Statistics"]
-git-tree-sha1 = "1d8128735fdf3ab1643dd8bc9499e4b34ccb718d"
+deps = ["Libdl", "LinearAlgebra", "Pkg", "Requires", "Statistics"]
+git-tree-sha1 = "8ec4693a5422f0b064ce324f59351f24aa474893"
 uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
-version = "0.7.3"
+version = "0.7.4"
 
 [[NaNMath]]
 git-tree-sha1 = "c84c576296d0e2fbb3fc134d3e09086b3ea617cd"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 version = "0.3.4"
 
 [[OffsetArrays]]
-git-tree-sha1 = "4ba4cd84c88df8340da1c3e2d8dcb9d18dd1b53b"
+git-tree-sha1 = "2066e16af994955287f2e03ba1d9e890eb43b0dd"
 uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-version = "1.1.1"
+version = "1.1.2"
 
 [[OpenSpecFun_jll]]
 deps = ["CompilerSupportLibraries_jll", "Libdl", "Pkg"]
@@ -324,7 +331,7 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.3.0"
 
 [[Pkg]]
-deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Test", "UUIDs"]
+deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [[Printf]]
@@ -360,15 +367,21 @@ uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
 [[SIMDPirates]]
 deps = ["VectorizationBase"]
-git-tree-sha1 = "cbe8797ac354d0b1dfe75d983429938db834b706"
+git-tree-sha1 = "26ccdd1466f3071e27e81b43216ea238b62c0c42"
 uuid = "21efa798-c60a-11e8-04d3-e1a92915a26a"
-version = "0.8.16"
+version = "0.8.24"
 
 [[SLEEFPirates]]
 deps = ["Libdl", "SIMDPirates", "VectorizationBase"]
-git-tree-sha1 = "c750d618b7c8268a97e55c70e8c88e56080d30fa"
+git-tree-sha1 = "67ae90a18aa8c22bf159318300e765fbd89ddf6e"
 uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa"
-version = "0.5.4"
+version = "0.5.5"
+
+[[ScatterNNlib]]
+deps = ["CUDA", "DataStructures", "FillArrays", "StaticArrays", "Statistics", "Zygote", "ZygoteRules"]
+git-tree-sha1 = "4e1d9dcde9d934fc2e38013d4d49277f09556529"
+uuid = "b1168b60-8710-48c1-88d2-5c53ae207dd0"
+version = "0.1.1"
 
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
@@ -445,18 +458,18 @@ deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[UnPack]]
-git-tree-sha1 = "d4bfa022cd30df012700cf380af2141961bb3bfb"
+git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b"
 uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
-version = "1.0.1"
+version = "1.0.2"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[VectorizationBase]]
 deps = ["CpuId", "Libdl", "LinearAlgebra"]
-git-tree-sha1 = "95c0c737c307dfd4f65ad50a79856b343fdb7959"
+git-tree-sha1 = "314bf15162034f846720ee1c3c3300dffd462253"
 uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
-version = "0.12.24"
+version = "0.12.31"
 
 [[ZipFile]]
 deps = ["Libdl", "Printf", "Zlib_jll"]
@@ -466,15 +479,15 @@ version = "0.9.2"
 
 [[Zlib_jll]]
 deps = ["Libdl", "Pkg"]
-git-tree-sha1 = "622d8b6dc0c7e8029f17127703de9819134d1b71"
+git-tree-sha1 = "d5bba6485811931e4b8958e2d7ca3738273ac468"
 uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.11+14"
+version = "1.2.11+15"
 
 [[Zygote]]
 deps = ["AbstractFFTs", "ArrayLayouts", "ChainRules", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "Future", "IRTools", "InteractiveUtils", "LinearAlgebra", "LoopVectorization", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"]
-git-tree-sha1 = "16a7228209e6f457e9d71c39a58965616425384e"
+git-tree-sha1 = "0079d92995b0fbcffd5d475d49ec8ca49375c471"
 uuid = "e88e6eb3-aa80-5325-afca-941959d7151f"
-version = "0.5.3"
+version = "0.5.4"
 
 [[ZygoteRules]]
 deps = ["MacroTools"]

Project.toml

@@ -8,11 +8,13 @@ CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
+GraphSignals = "3ebe565e-a4b5-49c6-aed2-300248c3a9c1"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+ScatterNNlib = "b1168b60-8710-48c1-88d2-5c53ae207dd0"
 SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -22,17 +24,19 @@ ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
 
 [compat]
 CUDA = "1.2"
-DataStructures = "~0.17"
-FillArrays = "^0.8.5"
-Flux = "~0.10, 0.11"
+DataStructures = "0.17"
+FillArrays = "0.8 - 0.9"
+Flux = "0.10 - 0.11"
+GraphSignals = "0.1"
 LightGraphs = "1.3"
 MetaGraphs = "0.6"
-Requires = "^1.0.0"
+Requires = "1.0.0"
+ScatterNNlib = "0.1"
 SimpleWeightedGraphs = "1.1"
-StaticArrays = "^0.12.1"
-Zygote = "~0.4, 0.5"
-ZygoteRules = "~0.2"
-julia = "1.4"
+StaticArrays = "0.12"
+Zygote = "0.4 - 0.5"
+ZygoteRules = "0.2"
+julia = "1.4 - 1.5"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

README.md

@@ -59,15 +59,3 @@ evalcb() = @show(accuracy(train_X, train_y))
 
 Flux.train!(loss, ps, train_data, opt, cb=throttle(evalcb, 10))
 ```
-
-## Benchmark
-
-Scatter operations are fundamental to GeometricFlux.jl and they are implemented in CPU and CUDA version. Benchmarks of scatter operations are done with scripts in benchmark folder. Statistics, includes max, min and mean, are shown in the following plots.
-
-![](benchmark/pics/gpu_scatter.svg)
-
-Performance of scatter add operations in GeometricFlux is better than pytorch_scatter on cuda.
-
-![](benchmark/pics/cpu_scatter.svg)
-
-However, performance in GeometricFlux is even worse than pytorch_scatter on cpu/threading.