Merge pull request #68 from yuehhua/update_cuda

Update to CUDA.jl 1.2 and Flux 0.11

Author: yuehhua

Manifest.toml

@@ -14,9 +14,9 @@ version = "0.3.3"
 
 [[Adapt]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "fd04049c7dd78cfef0b06cdc1f0f181467655712"
+git-tree-sha1 = "0fac443759fa829ed8066db6cf1077d888bb6573"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "1.1.0"
+version = "2.0.2"
 
 [[ArnoldiMethod]]
 deps = ["DelimitedFiles", "LinearAlgebra", "Random", "SparseArrays", "StaticArrays", "Test"]
@@ -26,9 +26,9 @@ version = "0.0.4"
 
 [[ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra"]
-git-tree-sha1 = "a3254b3780a3544838ca0b7e23b1e9b06eb71bd8"
+git-tree-sha1 = "6f6e33efac70fc24c1f2a654a090b7af01690ffe"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
-version = "0.3.5"
+version = "0.3.7"
 
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -40,45 +40,27 @@ uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
 version = "0.5.10"
 
 [[CEnum]]
-git-tree-sha1 = "1b77a77c3b28e0b3f413f7567c9bb8dd9bdccd14"
+git-tree-sha1 = "215a9aa4a1f23fbd05b92769fdd62559488d70e9"
 uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
-version = "0.3.0"
-
-[[CUDAapi]]
-deps = ["Libdl", "Logging"]
-git-tree-sha1 = "831b825d10104bd29e28f6da93312a976830717b"
-uuid = "3895d2a7-ec45-59b8-82bb-cfc6a382f9b3"
-version = "4.0.0"
+version = "0.4.1"
 
-[[CUDAdrv]]
-deps = ["CEnum", "CUDAapi", "Printf"]
-git-tree-sha1 = "f56bbf18c86bcff7a961a32a4947a5abb2963a29"
-uuid = "c5f51814-7f29-56b8-a69c-e4d8f6be1fde"
-version = "6.3.0"
-
-[[CUDAnative]]
-deps = ["Adapt", "BinaryProvider", "CEnum", "CUDAapi", "CUDAdrv", "ExprTools", "GPUCompiler", "LLVM", "Libdl", "Pkg", "Printf"]
-git-tree-sha1 = "ac86db2b05fdfec96b011e25a504ffe7476e8a68"
-uuid = "be33ccc6-a3ff-5ff2-a52e-74243cff1e17"
-version = "3.1.0"
+[[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"
+uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
+version = "1.2.0"
 
 [[ChainRules]]
-deps = ["ChainRulesCore", "LinearAlgebra", "Reexport", "Requires", "Statistics"]
-git-tree-sha1 = "76cd719cb7ab57bd2687dcb3b186c4f99820a79d"
+deps = ["ChainRulesCore", "LinearAlgebra", "Random", "Reexport", "Requires", "Statistics"]
+git-tree-sha1 = "fbc6ca7a758b15cbb18df4936b2f588fbf3abdda"
 uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
-version = "0.6.5"
+version = "0.7.10"
 
 [[ChainRulesCore]]
 deps = ["MuladdMacro"]
-git-tree-sha1 = "c384e0e4fe6bfeb6bec0d41f71cc5e391cd110ba"
+git-tree-sha1 = "87e289253a5fc690c4860a41bbd427e16576f716"
 uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "0.8.1"
-
-[[CodeTracking]]
-deps = ["InteractiveUtils", "UUIDs"]
-git-tree-sha1 = "9c173f62af93cce8af2bd3527d160b6ddd6eaf81"
-uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
-version = "1.0.0"
+version = "0.9.3"
 
 [[CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
@@ -110,17 +92,11 @@ git-tree-sha1 = "7c4f882c41faa72118841185afc58a2eb00ef612"
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
 version = "0.3.3+0"
 
-[[Cthulhu]]
-deps = ["CodeTracking", "FoldingTrees", "InteractiveUtils", "REPL", "UUIDs", "Unicode"]
-git-tree-sha1 = "34bf82a46f0600727673e3cbed9a5908efff3c0c"
-uuid = "f68482b8-f384-11e8-15f7-abe071a5a75f"
-version = "1.2.0"
-
-[[CuArrays]]
-deps = ["AbstractFFTs", "Adapt", "CEnum", "CUDAapi", "CUDAdrv", "CUDAnative", "DataStructures", "GPUArrays", "Libdl", "LinearAlgebra", "MacroTools", "NNlib", "Pkg", "Printf", "Random", "Reexport", "Requires", "SparseArrays", "Statistics", "TimerOutputs"]
-git-tree-sha1 = "55ab24cc3fcf96f74246cf7e14bc9c2f818facbc"
-uuid = "3a865a2d-5b23-5a0f-bc46-62713ec82fae"
-version = "2.2.2"
+[[CpuId]]
+deps = ["Markdown", "Test"]
+git-tree-sha1 = "f0464e499ab9973b43c20f8216d088b61fda80c6"
+uuid = "adafc99b-e345-5852-983c-f28acb93d879"
+version = "0.2.2"
 
 [[DataAPI]]
 git-tree-sha1 = "176e23402d80e7743fc26c19c681bfb11246af32"
@@ -157,6 +133,12 @@ version = "1.0.1"
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
+[[DocStringExtensions]]
+deps = ["LibGit2", "Markdown", "Pkg", "Test"]
+git-tree-sha1 = "c5714d9bcdba66389612dc4c47ed827c64112997"
+uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+version = "0.8.2"
+
 [[ExprTools]]
 git-tree-sha1 = "6f0517056812fd6aa3af23d4b70d5325a2ae4e95"
 uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
@@ -170,9 +152,9 @@ version = "1.3.0"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "4783bbbeade37f2a8bd82af6c112510fde78e532"
+git-tree-sha1 = "be4180bdb27a11188d694ee3773122f4921f1a62"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.8.12"
+version = "0.8.13"
 
 [[FixedPointNumbers]]
 deps = ["Statistics"]
@@ -181,38 +163,38 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 version = "0.8.2"
 
 [[Flux]]
-deps = ["AbstractTrees", "Adapt", "CodecZlib", "Colors", "CuArrays", "DelimitedFiles", "Juno", "MacroTools", "NNlib", "Pkg", "Printf", "Random", "Reexport", "SHA", "Statistics", "StatsBase", "Test", "ZipFile", "Zygote"]
-git-tree-sha1 = "eb5801eea6294851dc2b16b20669f91776e79a3b"
+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"
 uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c"
-version = "0.10.4"
-
-[[FoldingTrees]]
-deps = ["AbstractTrees", "REPL"]
-git-tree-sha1 = "9a1e497cba7c33e5951aaffd9a421fa713acba0b"
-uuid = "1eca21be-9b9b-4ed8-839a-6d8ae26b1781"
-version = "1.0.0"
+version = "0.11.0"
 
 [[ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"]
 git-tree-sha1 = "1d090099fb82223abc48f7ce176d3f7696ede36d"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
 version = "0.10.12"
 
+[[Functors]]
+deps = ["MacroTools"]
+git-tree-sha1 = "f40adc6422f548176bb4351ebd29e4abf773040a"
+uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
+version = "0.1.0"
+
 [[Future]]
 deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[GPUArrays]]
 deps = ["AbstractFFTs", "Adapt", "LinearAlgebra", "Printf", "Random", "Serialization"]
-git-tree-sha1 = "d887693eb1bd5e1fd573262a978745481895ec7d"
+git-tree-sha1 = "0aaa4ff7001086e190a00180495b93b00df8bb43"
 uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "3.4.1"
+version = "4.0.1"
 
 [[GPUCompiler]]
-deps = ["Cthulhu", "DataStructures", "InteractiveUtils", "LLVM", "Libdl", "TimerOutputs"]
-git-tree-sha1 = "5275aa268ecd09640b32560e1eae90c78816e4d1"
+deps = ["DataStructures", "InteractiveUtils", "LLVM", "Libdl", "TimerOutputs", "UUIDs"]
+git-tree-sha1 = "6f46f295e8e504fce363caf2a28a2a56270681c0"
 uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
-version = "0.2.0"
+version = "0.5.3"
 
 [[IRTools]]
 deps = ["InteractiveUtils", "MacroTools", "Test"]
@@ -243,9 +225,9 @@ version = "0.8.2"
 
 [[LLVM]]
 deps = ["CEnum", "Libdl", "Printf", "Unicode"]
-git-tree-sha1 = "d9c6e1efcaa6c2fcd043da812a62b3e489a109a3"
+git-tree-sha1 = "a662366a5d485dee882077e8da3e1a95a86d097f"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "1.7.0"
+version = "2.0.0"
 
 [[LibGit2]]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -266,6 +248,12 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
+[[LoopVectorization]]
+deps = ["DocStringExtensions", "LinearAlgebra", "OffsetArrays", "SIMDPirates", "SLEEFPirates", "UnPack", "VectorizationBase"]
+git-tree-sha1 = "4c002de66221639174e081ec74c156e9013e4afa"
+uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
+version = "0.8.17"
+
 [[MacroTools]]
 deps = ["Markdown", "Random"]
 git-tree-sha1 = "f7d2e3f654af75f01ec49be82c231c382214223a"
@@ -302,16 +290,27 @@ 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 = ["BinaryProvider", "Libdl", "LinearAlgebra", "Requires", "Statistics"]
-git-tree-sha1 = "d9f196d911f55aeaff11b11f681b135980783824"
+deps = ["Libdl", "LinearAlgebra", "LoopVectorization", "NNPACK_jll", "Pkg", "Requires", "Statistics"]
+git-tree-sha1 = "1d8128735fdf3ab1643dd8bc9499e4b34ccb718d"
 uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
-version = "0.6.6"
+version = "0.7.3"
 
 [[NaNMath]]
-git-tree-sha1 = "928b8ca9b2791081dc71a51c55347c27c618760f"
+git-tree-sha1 = "c84c576296d0e2fbb3fc134d3e09086b3ea617cd"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
-version = "0.3.3"
+version = "0.3.4"
+
+[[OffsetArrays]]
+git-tree-sha1 = "4ba4cd84c88df8340da1c3e2d8dcb9d18dd1b53b"
+uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+version = "1.1.1"
 
 [[OpenSpecFun_jll]]
 deps = ["CompilerSupportLibraries_jll", "Libdl", "Pkg"]
@@ -359,6 +358,18 @@ version = "1.0.1"
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
+[[SIMDPirates]]
+deps = ["VectorizationBase"]
+git-tree-sha1 = "cbe8797ac354d0b1dfe75d983429938db834b706"
+uuid = "21efa798-c60a-11e8-04d3-e1a92915a26a"
+version = "0.8.16"
+
+[[SLEEFPirates]]
+deps = ["Libdl", "SIMDPirates", "VectorizationBase"]
+git-tree-sha1 = "c750d618b7c8268a97e55c70e8c88e56080d30fa"
+uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa"
+version = "0.5.4"
+
 [[Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
@@ -433,9 +444,20 @@ version = "0.9.5"
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
+[[UnPack]]
+git-tree-sha1 = "d4bfa022cd30df012700cf380af2141961bb3bfb"
+uuid = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
+version = "1.0.1"
+
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
+[[VectorizationBase]]
+deps = ["CpuId", "Libdl", "LinearAlgebra"]
+git-tree-sha1 = "95c0c737c307dfd4f65ad50a79856b343fdb7959"
+uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f"
+version = "0.12.24"
+
 [[ZipFile]]
 deps = ["Libdl", "Printf", "Zlib_jll"]
 git-tree-sha1 = "254975fef2fc526583bb9b7c9420fe66ffe09f2f"
@@ -449,10 +471,10 @@ uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
 version = "1.2.11+14"
 
 [[Zygote]]
-deps = ["AbstractFFTs", "ArrayLayouts", "ChainRules", "FillArrays", "ForwardDiff", "Future", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NNlib", "Random", "Requires", "Statistics", "ZygoteRules"]
-git-tree-sha1 = "2e2c82549fb0414df10469082fd001e2ede8547c"
+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"
 uuid = "e88e6eb3-aa80-5325-afca-941959d7151f"
-version = "0.4.22"
+version = "0.5.3"
 
 [[ZygoteRules]]
 deps = ["MacroTools"]

Project.toml

@@ -4,9 +4,7 @@ authors = ["Yueh-Hua Tu <a504082002@gmail.com>"]
 version = "0.6.0"
 
 [deps]
-CUDAapi = "3895d2a7-ec45-59b8-82bb-cfc6a382f9b3"
-CUDAnative = "be33ccc6-a3ff-5ff2-a52e-74243cff1e17"
-CuArrays = "3a865a2d-5b23-5a0f-bc46-62713ec82fae"
+CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
@@ -23,9 +21,7 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
 
 [compat]
-CUDAapi = "3, 4.0"
-CUDAnative = "2.10, 3.0, 3.1"
-CuArrays = "1.7.1, 1.7.2, 2.0, 2.1, 2.2"
+CUDA = "1.2"
 DataStructures = "~0.17"
 FillArrays = "^0.8.5"
 Flux = "~0.10, 0.11"

examples/gae.jl

@@ -7,7 +7,7 @@ using Statistics: mean
 using SparseArrays
 using LightGraphs.SimpleGraphs
 using LightGraphs: adjacency_matrix
-using CuArrays
+using CUDA
 
 @load "data/cora_features.jld2" features
 @load "data/cora_graph.jld2" g

examples/gcn.jl

@@ -7,7 +7,7 @@ using Statistics: mean
 using SparseArrays
 using LightGraphs.SimpleGraphs
 using LightGraphs: adjacency_matrix
-using CuArrays
+using CUDA
 
 @load "data/cora_features.jld2" features
 @load "data/cora_labels.jld2" labels

src/GeometricFlux.jl

@@ -109,19 +109,6 @@ export
     gather,
     topk_index
 
-using CUDAapi
-if has_cuda()
-    try
-        using CuArrays
-        @eval has_cuarrays() = true
-    catch ex
-        @warn "CUDA is installed, but CuArrays.jl fails to load" exception=(ex,catch_backtrace())
-        @eval has_cuarrays() = false
-    end
-else
-    has_cuarrays() = false
-end
-
 const IntOrTuple = Union{Integer,Tuple}
 
 include("operations/scatter.jl")
@@ -145,16 +132,15 @@ include("graph/simplegraphs.jl")
 
 
 function __init__()
-    @require CuArrays = "3a865a2d-5b23-5a0f-bc46-62713ec82fae" begin
-        using CUDAnative
-        using CuArrays: CuArray, CuMatrix, CuVector
-        import CuArrays: cu
+    @require CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" begin
+        using CUDA
+        using CUDA: @cuda
+        import CUDA: cu
         include("cuda/scatter.jl")
         include("cuda/msgpass.jl")
         include("cuda/conv.jl")
         include("cuda/pool.jl")
         include("cuda/utils.jl")
-        CuArrays.cu(x::Array{<:Integer}) = CuArray(x)
     end
     @require SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622" begin
         include("graph/weightedgraphs.jl")