From 2cfd75cce8449781ad1383dba9d9a0ded260c0f6 Mon Sep 17 00:00:00 2001 From: Matt Cuffaro Date: Tue, 10 Dec 2024 12:43:48 -0500 Subject: [PATCH 1/6] wip need to make sure jupyter server starts with sysimage --- .gitignore | 3 + packages/algjulia-service/README.md | 11 + .../algjulia-service/run_jupyter_server.sh | 3 + packages/sysimages/Manifest.toml | 2264 +++++++++++++++++ packages/sysimages/Project.toml | 2 + packages/sysimages/init-sysimg.jl | 23 + 6 files changed, 2306 insertions(+) create mode 100755 packages/algjulia-service/run_jupyter_server.sh create mode 100644 packages/sysimages/Manifest.toml create mode 100644 packages/sysimages/Project.toml create mode 100755 packages/sysimages/init-sysimg.jl diff --git a/.gitignore b/.gitignore index 94a39a3d4..1ebd46023 100644 --- a/.gitignore +++ b/.gitignore @@ -81,3 +81,6 @@ web_modules/ .netlify /packages/frontend/docs/ /target/ + +# ignore sysimage +/packages/sysimages/*.so diff --git a/packages/algjulia-service/README.md b/packages/algjulia-service/README.md index 859f307de..9803c78ad 100644 --- a/packages/algjulia-service/README.md +++ b/packages/algjulia-service/README.md @@ -33,3 +33,14 @@ jupyter server --IdentityProvider.token="" --ServerApp.disable_check_xsrf=True - While the Jupyter server is running, the AlgebraicJulia service will be usable by CatColab served locally. + +## Compiling a Sysimage + +Julia precompilation for packages like `CairoMakie.jl` and `OrdinaryDiffEq.jl` +can be time-consuming. A **sysimage** is a file which stores precompilation +statements, making future invocations of `AlgebraicJuliaService` and its +dependencies immediate. + +In order to build a sysimage, navigate to `packages/sysimages` and run +`~/.init-sysimg.jl` as a script. This process may take upwards of six minutes or +longer, depending on your machine. diff --git a/packages/algjulia-service/run_jupyter_server.sh b/packages/algjulia-service/run_jupyter_server.sh new file mode 100755 index 000000000..075604e31 --- /dev/null +++ b/packages/algjulia-service/run_jupyter_server.sh @@ -0,0 +1,3 @@ +#!/bin/bash + +jupyter server --ServerApp.token="" --ServerApp.disable_check_xsrf=True --ServerApp.allow_origin="http://localhost:5173" --ServerApp.allow_credentials=True diff --git a/packages/sysimages/Manifest.toml b/packages/sysimages/Manifest.toml new file mode 100644 index 000000000..0bb4b761f --- /dev/null +++ b/packages/sysimages/Manifest.toml @@ -0,0 +1,2264 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.11.2" +manifest_format = "2.0" +project_hash = "f5b458af044feb986379e50be42244e11182a07a" + +[[deps.ACSets]] +deps = ["AlgebraicInterfaces", "Base64", "CompTime", "DataStructures", "JSON3", "MLStyle", "OrderedCollections", "PEG", "Permutations", "Pkg", "PrettyTables", "Random", "Reexport", "SHA", "StaticArrays", "StructEquality", "StructTypes", "Tables"] +git-tree-sha1 = "d071b7329e50bd4dbb7e3893d3bc209cc27d22ad" +uuid = "227ef7b5-1206-438b-ac65-934d6da304b8" +version = "0.2.21" + + [deps.ACSets.extensions] + NautyACSetsExt = "nauty_jll" + XLSXACSetsExt = "XLSX" + + [deps.ACSets.weakdeps] + XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0" + nauty_jll = "55c6dc9b-343a-50ca-8ff2-b71adb3733d5" + +[[deps.ADTypes]] +git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "1.11.0" +weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] + + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesConstructionBaseExt = "ConstructionBase" + ADTypesEnzymeCoreExt = "EnzymeCore" + +[[deps.ANSIColoredPrinters]] +git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" +uuid = 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+version = "1.59.0+0" + +[[deps.oneTBB_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2021.12.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" diff --git a/packages/sysimages/Project.toml b/packages/sysimages/Project.toml new file mode 100644 index 000000000..d432ae1ca --- /dev/null +++ b/packages/sysimages/Project.toml @@ -0,0 +1,2 @@ +[deps] +AlgebraicJuliaService = "9ecda8fb-39ab-46a2-a496-7285fa6368c1" diff --git a/packages/sysimages/init-sysimg.jl b/packages/sysimages/init-sysimg.jl new file mode 100755 index 000000000..ea62c00b7 --- /dev/null +++ b/packages/sysimages/init-sysimg.jl @@ -0,0 +1,23 @@ +#!/usr/bin/env julia + +@info "Verifying PackageCompiler is installed globally" +using Pkg; Pkg.activate(); Pkg.add("PackageCompiler") +using PackageCompiler + +@info "Activating sysimage environment" +Pkg.activate(@__DIR__) +Pkg.develop(path=joinpath(@__DIR__, "../algjulia-service")) + +@info "Creating the sysimage. This may take a while..." +sysimg="AlgebraicJuliaService.so" +create_sysimage(["AlgebraicJuliaService"], sysimage_path=sysimg) +sysimg_path=joinpath(@__DIR__, sysimg); + +@info "Adding $sysimg_path to IJulia kernel" +Pkg.activate(); Pkg.add("IJulia") +using IJulia + +installkernel("Julia AJaaSKernel", "--sysimage=$sysimg_path") + +@info "done!" +exit() From 7a742e6a661f689d7f1a0ebfa5171d44075ccbbe Mon Sep 17 00:00:00 2001 From: Matt Cuffaro Date: Tue, 10 Dec 2024 16:24:51 -0500 Subject: [PATCH 2/6] 9s startup versus 21s startup. adding helper script --- packages/algjulia-service/Project.toml | 1 + packages/algjulia-service/run_jupyter_server.sh | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/packages/algjulia-service/Project.toml b/packages/algjulia-service/Project.toml index 08fe06591..d3c2d4696 100644 --- a/packages/algjulia-service/Project.toml +++ b/packages/algjulia-service/Project.toml @@ -29,6 +29,7 @@ Decapodes = "0.5.6" DiagrammaticEquations = "0.1.7" Distributions = "0.25" GeometryBasics = "0.4" +IJulia = "1.26.0" JSON3 = "1" LinearAlgebra = "1" MLStyle = "0.4" diff --git a/packages/algjulia-service/run_jupyter_server.sh b/packages/algjulia-service/run_jupyter_server.sh index 075604e31..8461e0850 100755 --- a/packages/algjulia-service/run_jupyter_server.sh +++ b/packages/algjulia-service/run_jupyter_server.sh @@ -1,3 +1,3 @@ #!/bin/bash -jupyter server --ServerApp.token="" --ServerApp.disable_check_xsrf=True --ServerApp.allow_origin="http://localhost:5173" --ServerApp.allow_credentials=True +jupyter server --ServerApp.token="" --ServerApp.disable_check_xsrf=True --ServerApp.allow_origin="http://localhost:5173" --ServerApp.allow_credentials=True --MultiKernelManager.default_kernel_name="julia-ajaaskernel-1.11" From c9145b6b13ad8feb818b685f346fe00d2ad2b512 Mon Sep 17 00:00:00 2001 From: Matt Cuffaro Date: Fri, 13 Dec 2024 15:25:14 -0500 Subject: [PATCH 3/6] added test precompilation statements --- packages/sysimages/Project.toml | 11 +++++++++++ packages/sysimages/init-sysimg.jl | 10 ++++++++-- packages/sysimages/precompile.jl | 2 ++ 3 files changed, 21 insertions(+), 2 deletions(-) create mode 100755 packages/sysimages/precompile.jl diff --git a/packages/sysimages/Project.toml b/packages/sysimages/Project.toml index d432ae1ca..2e34dabe7 100644 --- a/packages/sysimages/Project.toml +++ b/packages/sysimages/Project.toml @@ -1,2 +1,13 @@ [deps] +ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8" AlgebraicJuliaService = "9ecda8fb-39ab-46a2-a496-7285fa6368c1" +CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2" +ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" +Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391" +DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317" +IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" +JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" +OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" +StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" diff --git a/packages/sysimages/init-sysimg.jl b/packages/sysimages/init-sysimg.jl index ea62c00b7..b4c369d01 100755 --- a/packages/sysimages/init-sysimg.jl +++ b/packages/sysimages/init-sysimg.jl @@ -10,14 +10,20 @@ Pkg.develop(path=joinpath(@__DIR__, "../algjulia-service")) @info "Creating the sysimage. This may take a while..." sysimg="AlgebraicJuliaService.so" -create_sysimage(["AlgebraicJuliaService"], sysimage_path=sysimg) +create_sysimage(["AlgebraicJuliaService"], sysimage_path=sysimg, + precompile_execution_file="precompile.jl") sysimg_path=joinpath(@__DIR__, sysimg); @info "Adding $sysimg_path to IJulia kernel" Pkg.activate(); Pkg.add("IJulia") using IJulia -installkernel("Julia AJaaSKernel", "--sysimage=$sysimg_path") +# let's check if we have a kernel +if any(!isnothing, match.(r"ajaaskernel", readdir(IJulia.kerneldir(), join=true))) + @info "Julia kernel which uses AlgebraicJuliaService sysimage already installed. Skipping..." +else + installkernel("Julia AJaaSKernel", "--sysimage=$sysimg_path") +end @info "done!" exit() diff --git a/packages/sysimages/precompile.jl b/packages/sysimages/precompile.jl new file mode 100755 index 000000000..3d2770e52 --- /dev/null +++ b/packages/sysimages/precompile.jl @@ -0,0 +1,2 @@ +import AlgebraicJuliaService +include(joinpath(pkgdir(AlgebraicJuliaService), "test", "runtests.jl")) From a21ccf3461202e672e146e822316f969825c18d8 Mon Sep 17 00:00:00 2001 From: Matt Cuffaro Date: Fri, 13 Dec 2024 15:33:49 -0500 Subject: [PATCH 4/6] removed kernel checking conditional --- packages/sysimages/init-sysimg.jl | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/packages/sysimages/init-sysimg.jl b/packages/sysimages/init-sysimg.jl index b4c369d01..fa6d47291 100755 --- a/packages/sysimages/init-sysimg.jl +++ b/packages/sysimages/init-sysimg.jl @@ -18,12 +18,7 @@ sysimg_path=joinpath(@__DIR__, sysimg); Pkg.activate(); Pkg.add("IJulia") using IJulia -# let's check if we have a kernel -if any(!isnothing, match.(r"ajaaskernel", readdir(IJulia.kerneldir(), join=true))) - @info "Julia kernel which uses AlgebraicJuliaService sysimage already installed. Skipping..." -else - installkernel("Julia AJaaSKernel", "--sysimage=$sysimg_path") -end +installkernel("Julia AJaaSKernel", "--sysimage=$sysimg_path") @info "done!" exit() From 624cf8af5720648d1ebe23d4437ce7ec49899f7d Mon Sep 17 00:00:00 2001 From: Matt Cuffaro Date: Fri, 13 Dec 2024 15:37:14 -0500 Subject: [PATCH 5/6] Delete packages/sysimages/Manifest.toml --- packages/sysimages/Manifest.toml | 2264 ------------------------------ 1 file changed, 2264 deletions(-) delete mode 100644 packages/sysimages/Manifest.toml diff --git a/packages/sysimages/Manifest.toml b/packages/sysimages/Manifest.toml deleted file mode 100644 index 0bb4b761f..000000000 --- a/packages/sysimages/Manifest.toml +++ /dev/null @@ -1,2264 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.11.2" -manifest_format = "2.0" -project_hash = "f5b458af044feb986379e50be42244e11182a07a" - -[[deps.ACSets]] -deps = ["AlgebraicInterfaces", "Base64", "CompTime", "DataStructures", "JSON3", "MLStyle", "OrderedCollections", "PEG", "Permutations", "Pkg", "PrettyTables", "Random", "Reexport", "SHA", "StaticArrays", "StructEquality", "StructTypes", "Tables"] -git-tree-sha1 = "d071b7329e50bd4dbb7e3893d3bc209cc27d22ad" -uuid = "227ef7b5-1206-438b-ac65-934d6da304b8" -version = "0.2.21" - - [deps.ACSets.extensions] - NautyACSetsExt = "nauty_jll" - XLSXACSetsExt = "XLSX" - - [deps.ACSets.weakdeps] - XLSX = "fdbf4ff8-1666-58a4-91e7-1b58723a45e0" - nauty_jll = "55c6dc9b-343a-50ca-8ff2-b71adb3733d5" - -[[deps.ADTypes]] -git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" -uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.11.0" -weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] - - [deps.ADTypes.extensions] - ADTypesChainRulesCoreExt = "ChainRulesCore" - ADTypesConstructionBaseExt = "ConstructionBase" - ADTypesEnzymeCoreExt = "EnzymeCore" - -[[deps.ANSIColoredPrinters]] -git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" -uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" -version = "0.0.1" - -[[deps.AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" -uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.5.0" -weakdeps = ["ChainRulesCore", "Test"] - - [deps.AbstractFFTs.extensions] - AbstractFFTsChainRulesCoreExt = "ChainRulesCore" - AbstractFFTsTestExt = "Test" - -[[deps.AbstractTrees]] -git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" -uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.4.5" - -[[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] -git-tree-sha1 = "96bed9b1b57cf750cca50c311a197e306816a1cc" -uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.39" - - [deps.Accessors.extensions] - AccessorsAxisKeysExt = "AxisKeys" - AccessorsDatesExt = "Dates" - AccessorsIntervalSetsExt = "IntervalSets" - AccessorsStaticArraysExt = "StaticArrays" - AccessorsStructArraysExt = "StructArrays" - AccessorsTestExt = "Test" - AccessorsUnitfulExt = "Unitful" - - [deps.Accessors.weakdeps] - AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" - Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" - IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" - Requires = "ae029012-a4dd-5104-9daa-d747884805df" - StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" - StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" - Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" - -[[deps.Adapt]] -deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" -uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.1.1" -weakdeps = ["StaticArrays"] - - [deps.Adapt.extensions] - AdaptStaticArraysExt = "StaticArrays" - -[[deps.AlgebraicInterfaces]] -git-tree-sha1 = "28cca88bde1068ccf57f950e639df67975517c25" -uuid = "23cfdc9f-0504-424a-be1f-4892b28e2f0c" -version = "0.1.4" - -[[deps.AlgebraicJuliaService]] -deps = ["ACSets", "CombinatorialSpaces", "ComponentArrays", "CoordRefSystems", "Decapodes", "DiagrammaticEquations", "Distributions", "GeometryBasics", "IJulia", "JSON3", "LinearAlgebra", "MLStyle", "OrdinaryDiffEq", "Reexport", "StaticArrays"] -path = "/home/you/Documents/work/topos/catcolab/sysimg/packages/sysimages/../algjulia-service" -uuid = "9ecda8fb-39ab-46a2-a496-7285fa6368c1" -version = "0.1.0" - 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ArrayInterfaceReverseDiffExt = "ReverseDiff" - ArrayInterfaceSparseArraysExt = "SparseArrays" - ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" - ArrayInterfaceTrackerExt = "Tracker" - - [deps.ArrayInterface.weakdeps] - BandedMatrices = "aae01518-5342-5314-be14-df237901396f" - BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" - ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" - StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - -[[deps.ArrayLayouts]] -deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "2bf6e01f453284cb61c312836b4680331ddfc44b" -uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.11.0" -weakdeps = ["SparseArrays"] - 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Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - -[[deps.ZygoteRules]] -deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.5" - -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.11.0+0" - -[[deps.libsodium_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f76d682d87eefadd3f165d8d9fda436464213142" -uuid = "a9144af2-ca23-56d9-984f-0d03f7b5ccf8" -version = "1.0.20+1" - -[[deps.nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.59.0+0" - -[[deps.oneTBB_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" -uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" -version = "2021.12.0+0" - -[[deps.p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+2" From 797c539f758f041e1d5329e13354780f616f56ae Mon Sep 17 00:00:00 2001 From: Evan Patterson Date: Mon, 16 Dec 2024 10:40:12 -0800 Subject: [PATCH 6/6] CLEANUP: Move sys image scripts to main Julia dir. Also, frontend now uses the default kernel set in the Jupyter server. --- .gitignore | 3 --- packages/algjulia-service/.gitignore | 3 +++ packages/algjulia-service/README.md | 20 +++++++++---------- packages/algjulia-service/jupyter_server.sh | 13 ++++++++++++ .../make_sysimage.jl} | 7 +++---- .../algjulia-service/run_jupyter_server.sh | 3 --- .../sysimage_precompile.jl} | 0 .../frontend/src/stdlib/analyses/jupyter.ts | 9 +++++++-- packages/sysimages/Project.toml | 13 ------------ 9 files changed, 36 insertions(+), 35 deletions(-) create mode 100755 packages/algjulia-service/jupyter_server.sh rename packages/{sysimages/init-sysimg.jl => algjulia-service/make_sysimage.jl} (73%) delete mode 100755 packages/algjulia-service/run_jupyter_server.sh rename packages/{sysimages/precompile.jl => algjulia-service/sysimage_precompile.jl} (100%) delete mode 100644 packages/sysimages/Project.toml diff --git a/.gitignore b/.gitignore index 1ebd46023..94a39a3d4 100644 --- a/.gitignore +++ b/.gitignore @@ -81,6 +81,3 @@ web_modules/ .netlify /packages/frontend/docs/ /target/ - -# ignore sysimage -/packages/sysimages/*.so diff --git a/packages/algjulia-service/.gitignore b/packages/algjulia-service/.gitignore index 29126e47b..7a339e682 100644 --- a/packages/algjulia-service/.gitignore +++ b/packages/algjulia-service/.gitignore @@ -22,3 +22,6 @@ docs/site/ # committed for packages, but should be committed for applications that require a static # environment. Manifest.toml + +# Julia sys images +*.so diff --git a/packages/algjulia-service/README.md b/packages/algjulia-service/README.md index 9803c78ad..3ff764358 100644 --- a/packages/algjulia-service/README.md +++ b/packages/algjulia-service/README.md @@ -25,22 +25,22 @@ julia --project -e 'import Pkg; Pkg.instantiate()' ## Usage -Navigate to this directory and run: +Navigate to this directory and launch the Jupyter serving by running: ```sh -jupyter server --IdentityProvider.token="" --ServerApp.disable_check_xsrf=True --ServerApp.allow_origin="http://localhost:5173" +./jupyter_server.sh ``` While the Jupyter server is running, the AlgebraicJulia service will be usable -by CatColab served locally. +by CatColab when served locally. ## Compiling a Sysimage -Julia precompilation for packages like `CairoMakie.jl` and `OrdinaryDiffEq.jl` -can be time-consuming. A **sysimage** is a file which stores precompilation -statements, making future invocations of `AlgebraicJuliaService` and its -dependencies immediate. +Precompiling dependencies like `CairoMakie.jl` and `OrdinaryDiffEq.jl` can be +time-consuming. A **sysimage** is a file that stores precompilation statements, +making future invocations of `AlgebraicJuliaService` and its dependencies +immediate. -In order to build a sysimage, navigate to `packages/sysimages` and run -`~/.init-sysimg.jl` as a script. This process may take upwards of six minutes or -longer, depending on your machine. +To build a sysimage, run the Julia program `./make_sysimage.jl` as a script. +This process may take upwards of five minutes or longer, depending on your +machine. diff --git a/packages/algjulia-service/jupyter_server.sh b/packages/algjulia-service/jupyter_server.sh new file mode 100755 index 000000000..291f79c4a --- /dev/null +++ b/packages/algjulia-service/jupyter_server.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +KERNEL_NAME="julia-1.11" +#KERNEL_NAME="julia-ajaas-1.11" + +ORIGIN="http://localhost:5173" + +jupyter server \ + --IdentityProvider.token="" \ + --ServerApp.disable_check_xsrf=True \ + --ServerApp.allow_origin="$ORIGIN" \ + --ServerApp.allow_credentials=True \ + --MultiKernelManager.default_kernel_name="$KERNEL_NAME" diff --git a/packages/sysimages/init-sysimg.jl b/packages/algjulia-service/make_sysimage.jl similarity index 73% rename from packages/sysimages/init-sysimg.jl rename to packages/algjulia-service/make_sysimage.jl index fa6d47291..58c6ba96f 100755 --- a/packages/sysimages/init-sysimg.jl +++ b/packages/algjulia-service/make_sysimage.jl @@ -6,19 +6,18 @@ using PackageCompiler @info "Activating sysimage environment" Pkg.activate(@__DIR__) -Pkg.develop(path=joinpath(@__DIR__, "../algjulia-service")) @info "Creating the sysimage. This may take a while..." sysimg="AlgebraicJuliaService.so" create_sysimage(["AlgebraicJuliaService"], sysimage_path=sysimg, - precompile_execution_file="precompile.jl") + precompile_execution_file="sysimage_precompile.jl") sysimg_path=joinpath(@__DIR__, sysimg); @info "Adding $sysimg_path to IJulia kernel" Pkg.activate(); Pkg.add("IJulia") using IJulia -installkernel("Julia AJaaSKernel", "--sysimage=$sysimg_path") +installkernel("Julia AJaaS", "--project=@.", "--sysimage=$sysimg_path") -@info "done!" +@info "Done!" exit() diff --git a/packages/algjulia-service/run_jupyter_server.sh b/packages/algjulia-service/run_jupyter_server.sh deleted file mode 100755 index 8461e0850..000000000 --- a/packages/algjulia-service/run_jupyter_server.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -jupyter server --ServerApp.token="" --ServerApp.disable_check_xsrf=True --ServerApp.allow_origin="http://localhost:5173" --ServerApp.allow_credentials=True --MultiKernelManager.default_kernel_name="julia-ajaaskernel-1.11" diff --git a/packages/sysimages/precompile.jl b/packages/algjulia-service/sysimage_precompile.jl similarity index 100% rename from packages/sysimages/precompile.jl rename to packages/algjulia-service/sysimage_precompile.jl diff --git a/packages/frontend/src/stdlib/analyses/jupyter.ts b/packages/frontend/src/stdlib/analyses/jupyter.ts index b085b1ed4..6e04f4f1c 100644 --- a/packages/frontend/src/stdlib/analyses/jupyter.ts +++ b/packages/frontend/src/stdlib/analyses/jupyter.ts @@ -39,9 +39,14 @@ export function createKernel( /** Create a Julia kernel in a reactive context. */ export function createJuliaKernel(serverOptions: ServerSettings) { + // XXX: How do we know... + // - which Julia version to use? + // - whether to use the standard kernel or one with our custom sys image? + // For now, we are omitting the kernel name completely and thus assuming + // that the correct default kernel has been set on the Jupyter server. + // Obviously this approach will not extend to multiple languages. return createKernel(serverOptions, { - // XXX: Do I have to specify the Julia version? - name: "julia-1.11", + //name: "julia-1.11", }); } diff --git a/packages/sysimages/Project.toml b/packages/sysimages/Project.toml deleted file mode 100644 index 2e34dabe7..000000000 --- a/packages/sysimages/Project.toml +++ /dev/null @@ -1,13 +0,0 @@ -[deps] -ACSets = "227ef7b5-1206-438b-ac65-934d6da304b8" -AlgebraicJuliaService = "9ecda8fb-39ab-46a2-a496-7285fa6368c1" -CombinatorialSpaces = "b1c52339-7909-45ad-8b6a-6e388f7c67f2" -ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -Decapodes = "679ab3ea-c928-4fe6-8d59-fd451142d391" -DiagrammaticEquations = "6f00c28b-6bed-4403-80fa-30e0dc12f317" -IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" -JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078" -OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"