adds QueueMethod to benchmark.

Author: gzagatti

benchmarks/Jumps/Diffusion_CTRW.jmd

@@ -21,7 +21,7 @@ N = 256
 h = 1 / N
 u0 = 10 * ones(Int64, N)
 tf = .01
-methods = (Direct(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR())
+methods = (Direct(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), QueueMethod())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 jprob = JumpProblemLibrary.prob_jump_diffnetwork
 rn = jprob.network(N)

benchmarks/Jumps/Manifest.toml

@@ -1,8 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.8.1"
+julia_version = "1.8.0"
 manifest_format = "2.0"
-project_hash = "013abde731b3d76e3dccfe35d36c5e64c73bb4e2"
+project_hash = "5455d431245955657e71819ee934b7a0d433989e"
 
 [[deps.AbstractAlgebra]]
 deps = ["GroupsCore", "InteractiveUtils", "LinearAlgebra", "MacroTools", "Markdown", "Random", "RandomExtensions", "SparseArrays", "Test"]
@@ -170,6 +170,12 @@ git-tree-sha1 = "5522c338564580adf5d58d91e43a55db0fa5fb39"
 uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9"
 version = "0.1.10"
 
+[[deps.CodeTracking]]
+deps = ["InteractiveUtils", "UUIDs"]
+git-tree-sha1 = "cc4bd91eba9cdbbb4df4746124c22c0832a460d6"
+uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
+version = "1.1.1"
+
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
 git-tree-sha1 = "ded953804d019afa9a3f98981d99b33e3db7b6da"
@@ -405,10 +411,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
 version = "0.4.1"
 
 [[deps.FFMPEG_jll]]
-deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
-git-tree-sha1 = "ccd479984c7838684b3ac204b716c89955c76623"
+deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
+git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
-version = "4.4.2+0"
+version = "4.4.2+2"
 
 [[deps.FastBroadcast]]
 deps = ["ArrayInterface", "ArrayInterfaceCore", "LinearAlgebra", "Polyester", "Static", "StrideArraysCore"]
@@ -704,6 +710,12 @@ git-tree-sha1 = "1ec2cb3b87d0c38e3b01c76d9b11639f1eaeec96"
 uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 version = "1.0.10"
 
+[[deps.JuliaInterpreter]]
+deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"]
+git-tree-sha1 = "a79c4cf60cc7ddcdcc70acbb7216a5f9b4f8d188"
+uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a"
+version = "0.9.16"
+
 [[deps.JumpProblemLibrary]]
 deps = ["Catalyst", "DiffEqBase", "RuntimeGeneratedFunctions"]
 git-tree-sha1 = "7fe2667d577812b285f0a8f30a1f16d779f9d0c6"
@@ -712,9 +724,9 @@ version = "0.1.3"
 
 [[deps.JumpProcesses]]
 deps = ["ArrayInterfaceCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"]
-git-tree-sha1 = "5a6e6c522e8a7b39b24be8eebcc13cc7885c6f2c"
+path = "/home/gzagatti/.julia/dev/JumpProcesses"
 uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
-version = "9.2.0"
+version = "9.2.3"
 
 [[deps.KLU]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"]
@@ -882,6 +894,12 @@ git-tree-sha1 = "7b97cfe6e51e4fde195b7654425aa84e527d9657"
 uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
 version = "0.12.128"
 
+[[deps.LoweredCodeUtils]]
+deps = ["JuliaInterpreter"]
+git-tree-sha1 = "dedbebe234e06e1ddad435f5c6f4b85cd8ce55f7"
+uuid = "6f1432cf-f94c-5a45-995e-cdbf5db27b0b"
+version = "2.2.2"
+
 [[deps.MacroTools]]
 deps = ["Markdown", "Random"]
 git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf"
@@ -1173,9 +1191,9 @@ uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
 
 [[deps.Qt5Base_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"]
-git-tree-sha1 = "c6c0f690d0cc7caddb74cef7aa847b824a16b256"
+git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5"
 uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1"
-version = "5.15.3+1"
+version = "5.15.3+2"
 
 [[deps.QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
@@ -1249,6 +1267,12 @@ git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7"
 uuid = "ae029012-a4dd-5104-9daa-d747884805df"
 version = "1.3.0"
 
+[[deps.Revise]]
+deps = ["CodeTracking", "Distributed", "FileWatching", "JuliaInterpreter", "LibGit2", "LoweredCodeUtils", "OrderedCollections", "Pkg", "REPL", "Requires", "UUIDs", "Unicode"]
+git-tree-sha1 = "dad726963ecea2d8a81e26286f625aee09a91b7c"
+uuid = "295af30f-e4ad-537b-8983-00126c2a3abe"
+version = "3.4.0"
+
 [[deps.Rmath]]
 deps = ["Random", "Rmath_jll"]
 git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f"

benchmarks/Jumps/Mendes_multistate_example.jmd

@@ -21,7 +21,7 @@ reactions(rn)
 
 # Plot solutions by each method
 ```julia
-methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR())
+methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), QueueMethod())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 tf      = 10.0 * jprob.tstop
 prob    = DiscreteProblem(rn, jprob.u0, (0.0, tf), jprob.rates)

benchmarks/Jumps/NegFeedback_GeneExpr.jmd

@@ -20,7 +20,7 @@ reactions(rn)
 # Plot solutions by each method
 
 ```julia
-methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR())
+methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), QueueMethod())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 prob    = prob_jump_dnarepressor.discrete_prob
 tf      = prob_jump_dnarepressor.tstop

benchmarks/Jumps/NegFeedback_GeneExpr_Marchetti.jmd

@@ -33,7 +33,7 @@ plot(solution, format=fmt)
 
 ```julia
 tf = 4000.
-methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR())
+methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), QueueMethod())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 prob = prob = DiscreteProblem(rn, u0, (0.0, tf), rnpar)
 ploth = plot(reuse=false)

benchmarks/Jumps/Project.toml

@@ -8,6 +8,7 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 SciMLBenchmarks = "31c91b34-3c75-11e9-0341-95557aab0344"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"