├── .gitignore ├── .gitmodules ├── .travis.yml ├── LICENSE ├── README.md ├── deps.edn ├── dockerfiles └── Dockerfile ├── docs ├── css │ └── default.css ├── gc.html ├── highlight │ ├── highlight.min.js │ └── solarized-light.css ├── index.html ├── js │ ├── jquery.min.js │ └── page_effects.js ├── libjulia-clj.java-api.html ├── libjulia-clj.julia.html └── signals.html ├── examples └── fractal │ ├── README.md │ ├── deps.edn │ └── src │ └── julia_fractals.clj ├── resources ├── clj_julia_helper.jl └── symbols.txt ├── scripts ├── activate-julia ├── activate-openj9 ├── build-docker ├── deploy ├── local-julia-env ├── openj9-java ├── remote-repl └── run-docker ├── src └── libjulia_clj │ ├── impl │ ├── base.clj │ ├── collections.clj │ ├── ffi.clj │ ├── gc.clj │ └── protocols.clj │ ├── java_api.clj │ ├── julia.clj │ └── modules │ ├── Base.clj │ ├── Core.clj │ └── LinearAlgebra.clj ├── test └── libjulia_clj │ ├── api_test.clj │ └── julia_test.clj └── topics ├── gc.md ├── images └── julia.png └── signals.md /.gitignore: -------------------------------------------------------------------------------- 1 | /target 2 | /classes 3 | /checkouts 4 | profiles.clj 5 | pom.xml 6 | pom.xml.asc 7 | *.jar 8 | *.class 9 | /.lein-* 10 | .nrepl-port 11 | .hgignore 12 | .hg/ 13 | julia-1.5.3* 14 | julia 15 | openj9 16 | .cpcache 17 | *.png 18 | julia-1.* 19 | *.asc -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cnuernber/libjulia-clj/42685f6bc13d141522783efbf827d70c4d895336/.gitmodules -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: julia 2 | 3 | os: 4 | - linux 5 | - osx 6 | - windows 7 | 8 | dist: focal 9 | 10 | 11 | julia: 12 | - 1.5.3 13 | 14 | env: 15 | - JULIA_COPY_STACKS=0 16 | - JULIA_COPY_STACKS=1 17 | 18 | before_install: 19 | - wget https://raw.githubusercontent.com/technomancy/leiningen/stable/bin/lein 20 | - chmod a+x lein 21 | - export JULIA_HOME=$TRAVIS_HOME/julia 22 | - echo $TRAVIS_OS_NAME 23 | - if [ "$TRAVIS_OS_NAME" = "windows" ]; then choco install jdk8; fi 24 | - if [ "$TRAVIS_OS_NAME" = "windows" ]; then export PATH=$PATH:"/C/Program Files/Java/jdk1.8.0_211/bin"; fi 25 | - if [ "$TRAVIS_OS_NAME" = "windows" ]; then java -version; fi 26 | - if [ "$TRAVIS_OS_NAME" = "windows" ]; then export JULIA_HOME="/c/julia/"; fi 27 | - echo $($TRAVIS_BUILD_DIR/lein) 28 | 29 | 30 | script: 31 | - $TRAVIS_BUILD_DIR/lein test 32 | 33 | notifications: 34 | email: false 35 | 36 | jobs: 37 | allow_failures: 38 | - os: windows 39 | 40 | cache: 41 | directories: 42 | - "$HOME/.m2" 43 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Copyright 2021 Chris Nuernberger 2 | 3 | Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: 4 | 5 | The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. 6 | 7 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # julia-clj 2 | 3 | [![Clojars Project](https://img.shields.io/clojars/v/com.cnuernber/libjulia-clj.svg)](https://clojars.org/cnuernber/libjulia-clj) 4 | [![travis integration](https://travis-ci.com/cnuernber/libjulia-clj.svg?branch=master)](https://travis-ci.com/cnuernber/libjulia-clj) 5 | 6 | 7 | * [API docs](https://cnuernber.github.io/libjulia-clj/) 8 | * [In-Depth Example](https://github.com/cnuernber/kmeans-mnist) 9 | * We now support julia-1.7.X so you can use it with the latest Julia. 10 | 11 | ## Usage 12 | 13 | Install julia and set JULIA_HOME: 14 | 15 | ```console 16 | scripts/activate-julia 17 | ``` 18 | 19 | In your repl, load the julia base namespace and initialize the system. 20 | 21 | ```clojure 22 | user> (require '[libjulia-clj.julia :as julia]) 23 | nil 24 | user> (julia/initialize!) 25 | 07:07:06.228 [nREPL-session-e1c7b4a4-54f4-4298-80bb-972e83b902ff] INFO libjulia-clj.impl.base - Attempting to initialize Julia at /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so 26 | 07:07:07.121 [nREPL-session-e1c7b4a4-54f4-4298-80bb-972e83b902ff] INFO tech.v3.jna.base - Library /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so found at [:system "/home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so"] 27 | :ok 28 | user> (def ones-fn (julia/jl "Base.ones")) 29 | #'user/ones-fn 30 | user> (ones-fn 3 4) 31 | [1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0] 32 | user> (def julia-ary *1) 33 | #'user/julia-ary 34 | user> (require '[tech.v3.tensor :as dtt]) 35 | nil 36 | user> (dtt/ensure-tensor julia-ary) 37 | #tech.v3.tensor[3 4] 38 | [[1.000 1.000 1.000 1.000] 39 | [1.000 1.000 1.000 1.000] 40 | [1.000 1.000 1.000 1.000]] 41 | user> (def clj-tens *1) 42 | #'user/clj-tens 43 | user> (dtt/mset! clj-tens 0 25) 44 | #tech.v3.tensor[3 4] 45 | [[25.00 25.00 25.00 25.00] 46 | [1.000 1.000 1.000 1.000] 47 | [1.000 1.000 1.000 1.000]] 48 | user> julia-ary 49 | [25.0 25.0 25.0 25.0; 1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0] 50 | ``` 51 | 52 | ## Something Fun 53 | 54 | ```clojure 55 | user> (require '[tech.v3.libs.buffered-image :as bufimg]) 56 | nil 57 | user> (require '[tech.v3.datatype :as dtype]) 58 | nil 59 | user> (def fract-width 1920) 60 | (def fract-height 1080) 61 | (def i1 0.31) 62 | (def i2 -0.6) 63 | (def d 11) 64 | (def zoom-factor 0.2) 65 | #'user/fract-width#'user/fract-height#'user/i1#'user/i2#'user/d#'user/zoom-factor 66 | user> (def julia-code 67 | "function juliaSet(i1,i2,d,zoomFactor,imgWidth,imgHeight) 68 | # Allocating a widthxheight matrix as our Clojure client is row-major 69 | matrix = Array{UInt8}(undef,imgWidth,imgHeight) 70 | icomp = Complex{Float64}(i1,i2) 71 | Threads.@threads for i in CartesianIndices(matrix) 72 | ## Julia has 1-based indexing... 73 | pos = complex(((i[1]-1) - (0.5 * imgWidth)) / (zoomFactor * imgWidth), 74 | ((i[2]-1) - (0.5 * imgHeight)) / (zoomFactor * imgHeight)) 75 | 76 | for c in (1:d) pos = (pos * pos) + icomp end 77 | absval = abs(pos) 78 | if (absval != NaN && absval < (d-1)) 79 | matrix[i] = 255 80 | else 81 | matrix[i] = 0 82 | end 83 | end 84 | return matrix 85 | end") 86 | #'user/julia-code 87 | user> (def fractal-fn (julia/jl julia-code)) 88 | #'user/fractal-fn 89 | user> (defn jl-fractal 90 | [] 91 | (-> (fractal-fn i1 i2 d zoom-factor fract-width fract-height) 92 | (dtt/ensure-tensor) 93 | ;;Julia is column-major so our image comes out widthxheight 94 | ;;datatype is row major. 95 | (dtt/transpose [1 0]) 96 | ;;The tensor library *knows* the original was transposed so transposing the result 97 | ;;back into row-major means the memory can be read in order and thus 98 | ;;the copy operation below is one large memcopy into a jvm byte array. 99 | (dtype/copy! (bufimg/new-image fract-height fract-width :byte-gray)))) 100 | #'user/jl-fractal 101 | user> (jl-fractal) 102 | #object[java.awt.image.BufferedImage 0x4d63b28f "BufferedImage@4d63b28f: type = 10 ColorModel: #pixelBits = 8 numComponents = 1 color space = java.awt.color.ICC_ColorSpace@2703464d transparency = 1 has alpha = false isAlphaPre = false ByteInterleavedRaster: width = 1920 height = 1080 #numDataElements 1 dataOff[0] = 0"] 103 | ;; Roughly 1920*1080*11*3, or 68428800 complex number operations 104 | user> (time (def ignored (jl-fractal))) 105 | "Elapsed time: 31.487044 msecs" 106 | #'user/ignored 107 | user> (bufimg/save! (jl-fractal) "julia.png") 108 | true 109 | ``` 110 | 111 | ![julia-img](topics/images/julia.png) 112 | 113 | 114 | ## License 115 | 116 | Copyright © 2021 Chris Nuernberger 117 | 118 | * [MIT](LICENSE) 119 | -------------------------------------------------------------------------------- /deps.edn: -------------------------------------------------------------------------------- 1 | {:paths ["src"] 2 | :deps {org.clojure/clojure {:mvn/version "1.10.2" :scope "provided"} 3 | cnuernber/dtype-next {:mvn/version "8.062"} 4 | net.java.dev.jna/jna {:mvn/version "5.10.0"}} 5 | :aliases 6 | {:jdk-17 7 | {:jvm-opts ["--add-modules" "jdk.incubator.foreign" 8 | "--enable-native-access=ALL-UNNAMED"]} 9 | :test 10 | {:extra-deps {com.cognitect/test-runner 11 | {:git/url "https://github.com/cognitect-labs/test-runner" 12 | :sha "209b64504cb3bd3b99ecfec7937b358a879f55c1"} 13 | ch.qos.logback/logback-classic {:mvn/version "1.1.3"}} 14 | :extra-paths ["test"] 15 | :main-opts ["-m" "cognitect.test-runner"]} 16 | :depstar 17 | {:replace-deps {com.github.seancorfield/depstar {:mvn/version "2.0.193"}} 18 | :ns-default hf.depstar 19 | :exec-fn hf.depstar/jar 20 | :exec-args {:group-id "com.cnuernber" 21 | :artifact-id "libjulia-clj" 22 | :version "1.000-beta-8" 23 | :aot true 24 | :compile-ns [libjulia-clj.java-api] 25 | :sync-pom true 26 | :jar "target/libjulia-clj.jar"}} 27 | 28 | :deploy 29 | {:replace-deps {slipset/deps-deploy {:mvn/version "0.1.5"}} 30 | :exec-fn deps-deploy.deps-deploy/deploy 31 | :exec-args {:installer :remote 32 | :sign-releases? true 33 | :artifact "target/libjulia-clj.jar"}} 34 | 35 | :install 36 | {:replace-deps {slipset/deps-deploy {:mvn/version "0.1.5"}} 37 | :exec-fn deps-deploy.deps-deploy/deploy 38 | :exec-args {:installer :local 39 | :artifact "target/libjulia-clj.jar"}} 40 | :codox 41 | {:extra-deps {codox-theme-rdash/codox-theme-rdash {:mvn/version "0.1.2"} 42 | com.cnuernber/codox {:mvn/version "1.001"} 43 | cider/cider-nrepl {:mvn/version "0.26.0"}} 44 | :extra-paths ["test" "resources"] 45 | :exec-fn codox.main/-main 46 | :exec-args {:arg-paths [[:aliases :depstar :exec-args]] 47 | :description "Julia bindings for Clojure and the JVM" 48 | :metadata {:doc/format :markdown} 49 | :themes [:rdash] 50 | :source-paths ["src"] 51 | :output-path "docs" 52 | :doc-paths ["topics"] 53 | :source-uri "https://github.com/cnuernber/libjulia-clj/blob/master/{filepath}#L{line}" 54 | :namespaces [libjulia-clj.julia 55 | libjulia-clj.java-api]}}} 56 | } 57 | -------------------------------------------------------------------------------- /dockerfiles/Dockerfile: -------------------------------------------------------------------------------- 1 | # We will use Ubuntu for our image 2 | FROM ubuntu:latest 3 | 4 | # Updating Ubuntu packages 5 | 6 | ARG CLOJURE_TOOLS_VERSION=1.10.1.507 7 | 8 | 9 | RUN apt-get -qq update && apt-get -qq -y install curl wget bzip2 openjdk-8-jdk-headless \ 10 | && curl -o install-clojure https://download.clojure.org/install/linux-install-${CLOJURE_TOOLS_VERSION}.sh \ 11 | && chmod +x install-clojure \ 12 | && ./install-clojure && rm install-clojure \ 13 | && wget https://raw.githubusercontent.com/technomancy/leiningen/stable/bin/lein \ 14 | && chmod a+x lein \ 15 | && mv lein /usr/bin \ 16 | && apt-get -qq -y autoremove \ 17 | && apt-get autoclean \ 18 | && rm -rf /var/lib/apt/lists/* /var/log/dpkg.log 19 | 20 | 21 | ARG USERID 22 | ARG GROUPID 23 | ARG USERNAME 24 | 25 | RUN groupadd -g $GROUPID $USERNAME 26 | RUN useradd -u $USERID -g $GROUPID $USERNAME 27 | RUN mkdir /home/$USERNAME && chown $USERNAME:$USERNAME /home/$USERNAME 28 | USER $USERNAME 29 | 30 | WORKDIR /home/$USERNAME 31 | 32 | RUN wget https://julialang-s3.julialang.org/bin/linux/x64/1.5/julia-1.5.3-linux-x86_64.tar.gz \ 33 | && tar -xvzf julia-1.5.3-linux-x86_64.tar.gz 34 | 35 | ENV PATH /home/$USERNAME/julia-1.5.3/bin:$PATH 36 | ENV JULIA_HOME /home/$USERNAME/julia-1.5.3 37 | ENV LD_LIBRARY_PATH /home/$USERNAME/julia-1.5.3/lib 38 | ENV JULIA_COPY_STACKS=yes 39 | 40 | RUN lein -v -------------------------------------------------------------------------------- /docs/css/default.css: -------------------------------------------------------------------------------- 1 | @import url('https://fonts.googleapis.com/css?family=PT+Sans'); 2 | 3 | body { 4 | font-family: 'PT Sans', Helvetica, sans-serif; 5 | font-size: 14px; 6 | } 7 | 8 | a { 9 | color: #337ab7; 10 | text-decoration: none; 11 | } 12 | 13 | a:hover { 14 | color: #30426a; 15 | text-decoration: underline; 16 | } 17 | 18 | pre, code { 19 | font-family: Monaco, DejaVu Sans Mono, Consolas, monospace; 20 | font-size: 9pt; 21 | margin: 15px 0; 22 | } 23 | 24 | h1 { 25 | font-weight: normal; 26 | font-size: 29px; 27 | margin: 10px 0 2px 0; 28 | padding: 0; 29 | } 30 | 31 | h2 { 32 | font-weight: normal; 33 | font-size: 25px; 34 | } 35 | 36 | h3 > a:hover { 37 | text-decoration: none; 38 | } 39 | 40 | .document h1, .namespace-index h1 { 41 | font-size: 32px; 42 | margin-top: 12px; 43 | } 44 | 45 | #header, #content, .sidebar { 46 | position: fixed; 47 | } 48 | 49 | #header { 50 | top: 0; 51 | left: 0; 52 | right: 0; 53 | height: 22px; 54 | color: #f5f5f5; 55 | padding: 5px 7px; 56 | } 57 | 58 | #content { 59 | top: 32px; 60 | right: 0; 61 | bottom: 0; 62 | overflow: auto; 63 | background: #fff; 64 | color: #333; 65 | padding: 0 18px; 66 | } 67 | 68 | .sidebar { 69 | position: fixed; 70 | top: 32px; 71 | bottom: 0; 72 | overflow: auto; 73 | } 74 | 75 | .sidebar.primary { 76 | background: #30426a; 77 | border-right: solid 1px #cccccc; 78 | left: 0; 79 | width: 250px; 80 | color: white; 81 | font-size: 110%; 82 | } 83 | 84 | .sidebar.secondary { 85 | background: #f2f2f2; 86 | border-right: solid 1px #d7d7d7; 87 | left: 251px; 88 | width: 200px; 89 | font-size: 110%; 90 | } 91 | 92 | #content.namespace-index, #content.document { 93 | left: 251px; 94 | } 95 | 96 | #content.namespace-docs { 97 | left: 452px; 98 | } 99 | 100 | #content.document { 101 | padding-bottom: 10%; 102 | } 103 | 104 | #header { 105 | background: #2d3e63; 106 | box-shadow: 0 0 8px rgba(0, 0, 0, 0.4); 107 | z-index: 100; 108 | } 109 | 110 | #header h1 { 111 | margin: 0; 112 | padding: 0; 113 | font-size: 18px; 114 | font-weight: lighter; 115 | text-shadow: -1px -1px 0px #333; 116 | } 117 | 118 | #header h1 .project-version { 119 | font-weight: normal; 120 | } 121 | 122 | .project-version { 123 | padding-left: 0.15em; 124 | } 125 | 126 | #header a, .sidebar a { 127 | display: block; 128 | text-decoration: none; 129 | } 130 | 131 | #header a { 132 | color: #f5f5f5; 133 | } 134 | 135 | .sidebar.primary, .sidebar.primary a { 136 | color: #b2bfdc; 137 | } 138 | 139 | .sidebar.primary a:hover { 140 | color: white; 141 | } 142 | 143 | .sidebar.secondary, .sidebar.secondary a { 144 | color: #738bc0; 145 | } 146 | 147 | .sidebar.secondary a:hover { 148 | color: #2d3e63; 149 | } 150 | 151 | #header h2 { 152 | float: right; 153 | font-size: 9pt; 154 | font-weight: normal; 155 | margin: 4px 3px; 156 | padding: 0; 157 | color: #bbb; 158 | } 159 | 160 | #header h2 a { 161 | display: inline; 162 | } 163 | 164 | .sidebar h3 { 165 | margin: 0; 166 | padding: 10px 13px 0 13px; 167 | font-size: 19px; 168 | font-weight: lighter; 169 | } 170 | 171 | .sidebar.primary h3.no-link { 172 | text-transform: uppercase; 173 | font-size: 12px; 174 | color: #738bc0; 175 | } 176 | 177 | .sidebar.secondary h3 a { 178 | text-transform: uppercase; 179 | font-size: 12px; 180 | color: #2d3e63; 181 | } 182 | 183 | .sidebar ul { 184 | padding: 7px 0 6px 0; 185 | margin: 0; 186 | } 187 | 188 | .sidebar ul.index-link { 189 | padding-bottom: 4px; 190 | } 191 | 192 | .sidebar li { 193 | display: block; 194 | vertical-align: middle; 195 | } 196 | 197 | .sidebar li a, .sidebar li .no-link { 198 | border-left: 3px solid transparent; 199 | padding: 0 10px; 200 | white-space: nowrap; 201 | } 202 | 203 | .sidebar li .inner { 204 | display: inline-block; 205 | padding-top: 7px; 206 | height: 24px; 207 | } 208 | 209 | .sidebar li a, .sidebar li .tree { 210 | height: 31px; 211 | } 212 | 213 | .depth-1 .inner { padding-left: 2px; } 214 | .depth-2 .inner { padding-left: 6px; } 215 | .depth-3 .inner { padding-left: 20px; } 216 | .depth-4 .inner { padding-left: 34px; } 217 | .depth-5 .inner { padding-left: 48px; } 218 | .depth-6 .inner { padding-left: 62px; } 219 | 220 | .sidebar li .tree { 221 | display: block; 222 | float: left; 223 | position: relative; 224 | top: -10px; 225 | margin: 0 4px 0 0; 226 | padding: 0; 227 | } 228 | 229 | .sidebar li.depth-1 .tree { 230 | display: none; 231 | } 232 | 233 | .sidebar li .tree .top, .sidebar li .tree .bottom { 234 | display: block; 235 | margin: 0; 236 | padding: 0; 237 | width: 7px; 238 | } 239 | 240 | .sidebar li .tree .top { 241 | border-left: 1px solid #aaa; 242 | border-bottom: 1px solid #aaa; 243 | height: 19px; 244 | } 245 | 246 | .sidebar li .tree .bottom { 247 | height: 22px; 248 | } 249 | 250 | .sidebar li.branch .tree .bottom { 251 | border-left: 1px solid #aaa; 252 | } 253 | 254 | .sidebar.primary li.current a { 255 | border-left: 3px solid #e99d1a; 256 | color: white; 257 | } 258 | 259 | .sidebar.secondary li.current a { 260 | border-left: 3px solid #2d3e63; 261 | color: #33a; 262 | } 263 | 264 | .namespace-index h2 { 265 | margin: 30px 0 0 0; 266 | } 267 | 268 | .namespace-index h3 { 269 | font-size: 16px; 270 | font-weight: bold; 271 | margin-bottom: 0; 272 | letter-spacing: 0.05em; 273 | border-bottom: solid 1px #ddd; 274 | max-width: 680px; 275 | background-color: #fafafa; 276 | padding: 0.5em; 277 | } 278 | 279 | .namespace-index .topics { 280 | padding-left: 30px; 281 | margin: 11px 0 0 0; 282 | } 283 | 284 | .namespace-index .topics li { 285 | padding: 5px 0; 286 | } 287 | 288 | .namespace-docs h3 { 289 | font-size: 18px; 290 | font-weight: bold; 291 | } 292 | 293 | .public h3 { 294 | margin: 0; 295 | float: left; 296 | } 297 | 298 | .usage { 299 | clear: both; 300 | } 301 | 302 | .public { 303 | margin: 0; 304 | border-top: 1px solid #e0e0e0; 305 | padding-top: 14px; 306 | padding-bottom: 6px; 307 | } 308 | 309 | .public:last-child { 310 | margin-bottom: 20%; 311 | } 312 | 313 | .members .public:last-child { 314 | margin-bottom: 0; 315 | } 316 | 317 | .members { 318 | margin: 15px 0; 319 | } 320 | 321 | .members h4 { 322 | color: #555; 323 | font-weight: normal; 324 | font-variant: small-caps; 325 | margin: 0 0 5px 0; 326 | } 327 | 328 | .members .inner { 329 | padding-top: 5px; 330 | padding-left: 12px; 331 | margin-top: 2px; 332 | margin-left: 7px; 333 | border-left: 1px solid #bbb; 334 | } 335 | 336 | #content .members .inner h3 { 337 | font-size: 12pt; 338 | } 339 | 340 | .members .public { 341 | border-top: none; 342 | margin-top: 0; 343 | padding-top: 6px; 344 | padding-bottom: 0; 345 | } 346 | 347 | .members .public:first-child { 348 | padding-top: 0; 349 | } 350 | 351 | h4.type, 352 | h4.dynamic, 353 | h4.added, 354 | h4.deprecated { 355 | float: left; 356 | margin: 3px 10px 15px 0; 357 | font-size: 15px; 358 | font-weight: bold; 359 | font-variant: small-caps; 360 | } 361 | 362 | .public h4.type, 363 | .public h4.dynamic, 364 | .public h4.added, 365 | .public h4.deprecated { 366 | font-size: 13px; 367 | font-weight: bold; 368 | margin: 3px 0 0 10px; 369 | } 370 | 371 | .members h4.type, 372 | .members h4.added, 373 | .members h4.deprecated { 374 | margin-top: 1px; 375 | } 376 | 377 | h4.type { 378 | color: #717171; 379 | } 380 | 381 | h4.dynamic { 382 | color: #9933aa; 383 | } 384 | 385 | h4.added { 386 | color: #508820; 387 | } 388 | 389 | h4.deprecated { 390 | color: #880000; 391 | } 392 | 393 | .namespace { 394 | margin-bottom: 30px; 395 | } 396 | 397 | .namespace:last-child { 398 | margin-bottom: 10%; 399 | } 400 | 401 | .index { 402 | padding: 0; 403 | font-size: 80%; 404 | margin: 15px 0; 405 | line-height: 1.6em; 406 | } 407 | 408 | .index * { 409 | display: inline; 410 | } 411 | 412 | .index p { 413 | padding-right: 3px; 414 | } 415 | 416 | .index li { 417 | padding-right: 5px; 418 | } 419 | 420 | .index ul { 421 | padding-left: 0; 422 | } 423 | 424 | .type-sig { 425 | clear: both; 426 | color: #088; 427 | } 428 | 429 | .type-sig pre { 430 | padding-top: 10px; 431 | margin: 0; 432 | } 433 | 434 | .usage code { 435 | display: block; 436 | color: #008; 437 | margin: 2px 0; 438 | } 439 | 440 | .usage code:first-child { 441 | padding-top: 10px; 442 | } 443 | 444 | p { 445 | margin: 15px 0; 446 | } 447 | 448 | .public p:first-child, .public pre.plaintext { 449 | margin-top: 12px; 450 | } 451 | 452 | .doc { 453 | margin: 0 0 26px 0; 454 | clear: both; 455 | } 456 | 457 | .public .doc { 458 | margin: 0; 459 | } 460 | 461 | .namespace-index { 462 | font-size: 120%; 463 | } 464 | 465 | .namespace-index .doc { 466 | margin-bottom: 20px; 467 | } 468 | 469 | .namespace-index .namespace .doc { 470 | margin-bottom: 10px; 471 | } 472 | 473 | .markdown p, .markdown li, .markdown dt, .markdown dd, .markdown td { 474 | line-height: 1.6em; 475 | } 476 | 477 | .markdown h2 { 478 | font-weight: normal; 479 | font-size: 25px; 480 | } 481 | 482 | #content .markdown h3 { 483 | font-size: 20px; 484 | } 485 | 486 | .markdown h4 { 487 | font-size: 15px; 488 | } 489 | 490 | .doc, .public, .namespace .index { 491 | max-width: 680px; 492 | overflow-x: visible; 493 | } 494 | 495 | .markdown pre > code { 496 | display: block; 497 | padding: 10px; 498 | } 499 | 500 | .markdown pre > code, .src-link a { 501 | border: 1px solid #e4e4e4; 502 | border-radius: 2px; 503 | } 504 | 505 | .src-link a { 506 | background: #f6f6f6; 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618 | } 619 | 620 | .namespace-index > h1 { 621 | display: none; 622 | } 623 | 624 | .public, .doc, .namespace > .index, .namespace > .doc, .namespace > h3 { 625 | max-width: initial; 626 | } 627 | 628 | .doc { 629 | text-align: justify; 630 | } 631 | 632 | .public { 633 | padding-top: 2em; 634 | padding-bottom: 2em; 635 | } 636 | 637 | .public > h3 { 638 | font-size: 300%; 639 | } 640 | 641 | .public > h4.type, .public > h4.added, .public > h4.deprecated { 642 | font-size: 150%; 643 | margin-top: 1em; 644 | } 645 | 646 | pre > code { 647 | font-size: 200%; 648 | } 649 | } 650 | -------------------------------------------------------------------------------- /docs/gc.html: -------------------------------------------------------------------------------- 1 | 3 | JVM/Julia Garbage Collection Integration

Project

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Namespaces

JVM/Julia Garbage Collection Integration

4 |

Both the JVM and julia rely on garbage collection in order to decided 5 | when and how to cleanup objects. This means that we need a mechanism 6 | to ensure that objects visible across language boundaries are not cleaned 7 | up prematurely.

8 |

Julia Objects in the JVM

9 |

When a new julia object is returned from a function we first check 10 | if this is a primitive or atomic type - numbers, symbols, strings. 11 | If so, we convert the value into the JVM immediately. Else we 12 | return a JVM object and root the julia object in a datastructure 13 | we declared to julia.

14 |

The user has a choice to link the Julia object to the JVM's GC mechanism 15 | such that when the JVM decided the object is no longer reachable we will 16 | then unroot the Julia object. This is default and requires the user 17 | to periodically call 18 | cycle-gc! 19 | in order to unroot objects as the JVM's callback happens in another thread and 20 | thus we can only mark objects that should be unrooted automatically. The 21 | gc based unrooting needs to be cooperative at this point to ensure it happens 22 | in whichever thread is currently using Julia.

23 |

There is also a stack based mechanism, 24 | with-stack-context 25 | by which we can ensure that Julia objects rooted within a given stack 26 | scope are unrooted when programmatic flow exits that scope either 27 | normally or via an exception.

28 |

JVM Objects in Julia

29 |
    30 |
  • TODO - not sure if this is very necessary or the best way to handle this. 31 | Currently you can pass functions to Julia but this isn't very fleshed 32 | out and it is most likely not bullet-proof. If they are called from tasks 33 | then there is a decent chance they will be silently ignored. Most likely 34 | you, from the JVM side, will need to ensure they do not leave JVM scope 35 | while you think they are in scope in Julia.
    • 36 |
37 |
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Project

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1.000-beta-8

Julia bindings for Clojure and the JVM.

Topics

Namespaces

libjulia-clj.java-api

Java Users - Use the -aot postfixed version of the jar on clojars. Then import 4 | libjulia_clj.java_api. Each method in this namespace is exposed as a public static 5 | method on the java_api class so for instance -initialize is exposed as:

6 |

Public variables and functions:

libjulia-clj.julia

Public API for Julia functionality. Initialize! must be called before any other functions 7 | and there are a choice of garbgage collection mechanisms (see topic in docs). 8 | is probably a bad idea to call Julia from multiple threads so access to julia 9 | should be from one thread or protected via a mutex.

10 |

Public variables and functions:

-------------------------------------------------------------------------------- /docs/js/page_effects.js: -------------------------------------------------------------------------------- 1 | function visibleInParent(element) { 2 | var position = $(element).position().top 3 | return position > -50 && position < ($(element).offsetParent().height() - 50) 4 | } 5 | 6 | function hasFragment(link, fragment) { 7 | return $(link).attr("href").indexOf("#" + fragment) != -1 8 | } 9 | 10 | function findLinkByFragment(elements, fragment) { 11 | return $(elements).filter(function(i, e) { return hasFragment(e, fragment)}).first() 12 | } 13 | 14 | function scrollToCurrentVarLink(elements) { 15 | var elements = $(elements); 16 | var parent = elements.offsetParent(); 17 | 18 | if (elements.length == 0) return; 19 | 20 | var top = elements.first().position().top; 21 | var bottom = elements.last().position().top + elements.last().height(); 22 | 23 | if (top >= 0 && bottom <= parent.height()) return; 24 | 25 | if (top < 0) { 26 | parent.scrollTop(parent.scrollTop() + top); 27 | } 28 | else if (bottom > parent.height()) { 29 | parent.scrollTop(parent.scrollTop() + bottom - parent.height()); 30 | } 31 | } 32 | 33 | function setCurrentVarLink() { 34 | $('.secondary a').parent().removeClass('current') 35 | $('.anchor'). 36 | filter(function(index) { return visibleInParent(this) }). 37 | each(function(index, element) { 38 | findLinkByFragment(".secondary a", element.id). 39 | parent(). 40 | addClass('current') 41 | }); 42 | scrollToCurrentVarLink('.secondary .current'); 43 | } 44 | 45 | var hasStorage = (function() { try { return localStorage.getItem } catch(e) {} }()) 46 | 47 | function scrollPositionId(element) { 48 | var directory = window.location.href.replace(/[^\/]+\.html$/, '') 49 | return 'scroll::' + $(element).attr('id') + '::' + directory 50 | } 51 | 52 | function storeScrollPosition(element) { 53 | if (!hasStorage) return; 54 | localStorage.setItem(scrollPositionId(element) + "::x", $(element).scrollLeft()) 55 | localStorage.setItem(scrollPositionId(element) + "::y", $(element).scrollTop()) 56 | } 57 | 58 | function recallScrollPosition(element) { 59 | if (!hasStorage) return; 60 | $(element).scrollLeft(localStorage.getItem(scrollPositionId(element) + "::x")) 61 | $(element).scrollTop(localStorage.getItem(scrollPositionId(element) + "::y")) 62 | } 63 | 64 | function persistScrollPosition(element) { 65 | recallScrollPosition(element) 66 | $(element).scroll(function() { storeScrollPosition(element) }) 67 | } 68 | 69 | function sidebarContentWidth(element) { 70 | var widths = $(element).find('.inner').map(function() { return $(this).innerWidth() }) 71 | return Math.max.apply(Math, widths) 72 | } 73 | 74 | function calculateSize(width, snap, margin, minimum) { 75 | if (width == 0) { 76 | return 0 77 | } 78 | else { 79 | return Math.max(minimum, (Math.ceil(width / snap) * snap) + (margin * 2)) 80 | } 81 | } 82 | 83 | function resizeSidebars() { 84 | var primaryWidth = sidebarContentWidth('.primary') 85 | var secondaryWidth = 0 86 | 87 | if ($('.secondary').length != 0) { 88 | secondaryWidth = sidebarContentWidth('.secondary') 89 | } 90 | 91 | // snap to grid 92 | primaryWidth = calculateSize(primaryWidth, 32, 13, 160) 93 | secondaryWidth = calculateSize(secondaryWidth, 32, 13, 160) 94 | 95 | $('.primary').css('width', primaryWidth) 96 | $('.secondary').css('width', secondaryWidth).css('left', primaryWidth + 1) 97 | 98 | if (secondaryWidth > 0) { 99 | $('#content').css('left', primaryWidth + secondaryWidth + 2) 100 | } 101 | else { 102 | $('#content').css('left', primaryWidth + 1) 103 | } 104 | } 105 | 106 | $(window).ready(resizeSidebars) 107 | $(window).ready(setCurrentVarLink) 108 | $(window).ready(function() { persistScrollPosition('.primary')}) 109 | $(window).ready(function() { 110 | $('#content').scroll(setCurrentVarLink) 111 | $(window).resize(setCurrentVarLink) 112 | $(window).resize(resizeSidebars) 113 | }) 114 | -------------------------------------------------------------------------------- /docs/libjulia-clj.java-api.html: -------------------------------------------------------------------------------- 1 | 3 | libjulia-clj.java-api documentation

Project

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Public Vars

libjulia-clj.java-api

Java Users - Use the -aot postfixed version of the jar on clojars. Then import 4 | libjulia_clj.java_api. Each method in this namespace is exposed as a public static 5 | method on the java_api class so for instance -initialize is exposed as:

6 | 
  java_api.initialize(options);
 7 |
8 |

-arrayToJVM

(-arrayToJVM jlary)

Returns a map with three keys - shape, datatype, and data. Shape is an integer array 9 | that is the reverse of the julia shape, datatype is a string denoting one of the supported 10 | datatypes, and data is a primitive array of data.

11 |
view source

-createArray

(-createArray datatype shape data)

Return julia array out of the tuple of datatype, shape, and data.

12 |
    13 |
  • datatype - must be one of the strings `"int8" "uint8" "int16" "uin16" 15 | "int32" "uint32" "int64" "uint64" "float32" "float64".
    • 16 |
  • shape - an array or implementation of java.util.List that specifies the row-major 17 | shape intended of the data. Note that Julia is column-major so this data will appear 18 | transposed when printed via Julia.
    • 19 |
  • data may be a java array or an implementation of java.util.List. Ideally data is 20 | of the same datatype as data.
    • 21 |
22 |
view source

-initialize

(-initialize options)

Initialize the julia interpreter. See documentation for libjulia-clj.julia/initialize!. 23 | Options may be null or must be a map of string->value for one of the supported initialization 24 | values. JULIA_HOME can be set by the user by setting the key "julia-home" in the 25 | options map to the desired value and this will supercede the environment variable 26 | version.

27 |

Example:

28 | 
  (japi/-initialize (jvm-map/hash-map {"n-threads" 8}))
29 |
30 |
view source

-inJlContext

(-inJlContext fn)

Execute a function in a context where all julia objects created will be released 31 | just after the function returns. The function must return pure JVM data - it cannot 32 | return a reference to a julia object.

33 |
view source

-namedTuple

(-namedTuple data)

Create a julia named tuple. This is required for calling keyword functions. The 34 | path for calling keyword functions looks something like:

35 |
    36 |
  • data - must be an implementation of java.util.Map with strings as keys.
    • 37 |
38 | 
(let [add-fn (jl "function teste(a;c = 1.0, b = 2.0)
39 |     a+b+c
40 | end")
41 |           kwfunc (jl "Core.kwfunc")
42 |           add-kwf (kwfunc add-fn)]
43 |       (is (= 38.0 (add-kwf (jl/named-tuple {'b 10 'c 20})
44 |                            add-fn
45 |                            8.0)))
46 |       (is (= 19.0 (add-kwf (jl/named-tuple {'b 10})
47 |                            add-fn
48 |                            8.0)))
49 |       (is (= 11.0 (add-kwf (jl/named-tuple)
50 |                            add-fn
51 |                            8.0)))
52 | 
53 |       (is (= 38.0 (add-fn 8.0 :b 10 :c 20)))
54 |       (is (= 19.0 (add-fn 8 :b 10)))
55 |       (is (= 11.0 (add-fn 8))))
56 |
57 |
view source

-runString

(-runString data)

Run a string in Julia returning a jvm object if the return value is simple or 58 | a julia object if not. The returned object will have a property overloaded 59 | toString method for introspection.

60 |
view source

requires*

view source
-------------------------------------------------------------------------------- /docs/libjulia-clj.julia.html: -------------------------------------------------------------------------------- 1 | 3 | libjulia-clj.julia documentation

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Public Vars

libjulia-clj.julia

Public API for Julia functionality. Initialize! must be called before any other functions 4 | and there are a choice of garbgage collection mechanisms (see topic in docs). 5 | is probably a bad idea to call Julia from multiple threads so access to julia 6 | should be from one thread or protected via a mutex.

7 |

Example:

8 | 
user> (require '[libjulia-clj.julia :as julia])
  9 | nil
 10 | user> (julia/initialize!)
 11 | :ok
 12 | user> (def ones-fn (julia/jl "Base.ones"))
 13 | Nov 27, 2020 12:39:39 PM clojure.tools.logging$eval6611$fn__6614 invoke
 14 | INFO: Rooting address  0x00007F3E092D6E40
 15 | #'user/ones-fn
 16 | user> (def jl-ary (ones-fn 3 4))
 17 | 
 18 | Nov 27, 2020 12:40:02 PM clojure.tools.logging$eval6611$fn__6614 invoke
 19 | INFO: Rooting address  0x00007F3DFF9C92A0
 20 | #'user/jl-ary
 21 | user> jl-ary
 22 | [1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0]
 23 | user> (type jl-ary)
 24 | libjulia_clj.impl.base.JuliaArray
 25 | user> (require '[tech.v3.tensor :as dtt])
 26 | nil
 27 | user> ;;zero-copy
 28 | user> (def tens (dtt/as-tensor jl-ary))
 29 | #'user/tens
 30 | user> tens
 31 | #tech.v3.tensor<float64>[3 4]
 32 | [[1.000 1.000 1.000 1.000]
 33 |  [1.000 1.000 1.000 1.000]
 34 |  [1.000 1.000 1.000 1.000]]
 35 | user> (dtt/mset! tens 0 25)
 36 | #tech.v3.tensor<float64>[3 4]
 37 | [[25.00 25.00 25.00 25.00]
 38 |  [1.000 1.000 1.000 1.000]
 39 |  [1.000 1.000 1.000 1.000]]
 40 | user> jl-ary
 41 | [25.0 25.0 25.0 25.0; 1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0]
 42 |
43 |

->array

(->array tens)

Create a new dense julia array that is the 'transpose' of the input tensor. 44 | Transposing ensures the memory alignment matches as Julia is column-major 45 | while datatype is row-major.

46 |
view source

apply-tuple-type

(apply-tuple-type & args)

Create a new Julia tuple type from a sequence of types.

47 |
view source

apply-type

(apply-type jl-type & args)

Create a new Julia type from an existing type and a sequence of other 48 | types.

49 |
view source

base-ary-type*

Resolves to the base julia array datatype

50 |
view source

call-function

(call-function fn-handle args options)(call-function fn-handle args)

Call a function. The result will be marshalled back to the jvm and if necessary, 51 | rooted. This method is normally not necessary but useful if you would like to 52 | use keywords in your argument list or specify to avoid rooting the result.

53 |
view source

call-function-kw

(call-function-kw fn-handle args kw-args options)(call-function-kw fn-handle args kw-args)(call-function-kw fn-handle args)

Call a julia function and pass in keyword arguments. This is useful if you 54 | would like to specify the arglist and kw-argmap. Normally this is done for 55 | you.

56 |
view source

cycle-gc!

(cycle-gc!)

Call periodically to release rooted Julia objects. We root return values if they 57 | aren't primitives and then hook them to the jvm GC such that they get put in a queue 58 | once they aren't reachable by the program. This call clears that queue and unroots 59 | them thus notifying the Julia GC that they aren't reachable any more.

60 |

In the future point this may be done for you.

61 |
view source

initialize!

(initialize! {:keys [julia-library-path], :as options})(initialize!)

Initialize julia optionally providing an explicit path which will override 62 | the julia library search mechanism.

63 |

Currently the search mechanism is:

64 |

user-path->JULIA_HOME->"julia"

65 |

Returns :ok on success else exception.

66 |

Options:

67 |
    68 |
  • :julia-home - Explicitly declare the env var julia-home.
    • 69 |
  • :n-threads - Set to -1 to set to n-cpus. Defaults to nil which means single threaded 70 | unless the JULIA_NUM_THREADS environment variable is set. Note that this has implications 71 | for application stability - see the signals.md topic.
    • 72 |
  • :signals-enabled? - Users do not usually need to set this. This allows users to disable 73 | all of Julia's signal handling most likely leading to a crash. See the signals.md topic.
    • 74 |
75 |
view source

jl

(jl str-data options)(jl str-data)

Eval a string in julia returning the result. If the result is callable in Julia, 76 | the result will be callable in Clojure.

77 |
view source

jl-undef*

Resolves to the julia undef type

78 |
view source

named-tuple

(named-tuple value-map)(named-tuple)

Create a julia named tuple from a map of values. The keys of the map must be 79 | keywords or symbols. A new named tuple type will be created and instantiated.

80 |
view source

new-array

(new-array shape datatype)(new-array shape)

Create a new, uninitialized dense julia array. Because Julia is column major 81 | while tech.v3.datatype is row major, the returned array's size will be the 82 | reverse of dtype/shape as that keeps the same in memory alignment of data.

83 |
view source

set-julia-gc-root-log-level!

(set-julia-gc-root-log-level! log-level)

Set the log level to use when rooting/unrooting julia objects. We automatically 84 | root julia objects in a julia id dictionary that we expose to JVM objects. 85 | This code isn't yet perfect, so sometimes it is worthwhile to log all 86 | root/unroot operations.

87 |

Valid log levels are valid log levels for 88 | clojure/tools.logging.

89 |
view source

struct

(struct struct-type & args)

Instantiate a Julia struct type (tuple, NamedTuple, etc). Use this after 90 | apply-tuple-type in order to create an instance of your new type.

91 |
view source

tuple

(tuple & args)

Create a julia tuple from a set of arguments. The tuple type will be the 92 | same datatype as the argument types.

93 |

This function converts the arguments to julia, calls apply-tuple-type 94 | on the resulting argument types, and then instantiates an instance of 95 | the given newly created tuple type.

96 |
view source

typeof

(typeof item)

Get the julia type of an item.

97 |
view source

with-stack-context

macro

(with-stack-context & body)

Run code in which all objects created within this context will be released once 98 | the stack unwinds where released means unrooted and thus potentially available to 99 | the next julia garbage collection run.

100 |
view source
-------------------------------------------------------------------------------- /docs/signals.html: -------------------------------------------------------------------------------- 1 | 3 | Julia, The JVM, and Signals

Project

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Julia, The JVM, and Signals

4 |

Julia and the JVM both rely on an operating concept called signals 5 | which are a simple method of IPC. If you aren't familiar with them 6 | it probably isn't necessary to get familiar right now but it is necessary 7 | in order to use libjulia-clj for you to understand how the signal mechanism 8 | in these two systems interact and what happens when they interact poorly.

9 |

Two Worlds Collide

10 |

When using both Julia and the JVM in the same process you are likely to run into 11 | instances where, during their normal course of operation their respective usage of 12 | signals conflict. For instance, the JVM uses SIGSEGV during it's normal course of 13 | operation and if the Julia handler for SIGSEGV is installed then things like a 14 | normal JVM garbage collection run can cause the process to unceremoniously exit:

15 | 
user> (require '[libjulia-clj.julia :as julia])
16 | nil
17 | user> (julia/initialize! {:signals-enabled? true})
18 | 16:14:40.838 [nRepl-session-926e4a65-853b-40b4-a182-0f4b8a0cdfa3] INFO libjulia-clj.impl.base - Attempting to initialize Julia at /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so
19 | 16:14:40.875 [nRepl-session-926e4a65-853b-40b4-a182-0f4b8a0cdfa3] INFO tech.v3.jna.base - Library /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so found at [:system "/home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so"]
20 | 16:14:40.881 [nRepl-session-926e4a65-853b-40b4-a182-0f4b8a0cdfa3] INFO libjulia-clj.impl.jna - Julia startup options: n-threads null, signals? true
21 | :ok
22 | user> (System/gc)
23 | 
24 | *** Closed on Mon Dec 14 16:14:45 2020 ***
25 |
26 |

Julia has an option to disable its use of signals but this results in a crash as it 27 | requires the use of at least SIGINT in order to manage garbage collection in 28 | multithreaded code.

29 |

If we simply disable Julia's use of signals then single-threaded code works fine. 30 | Multithreaded code, however, will eventually crash without warning:

31 | 
user> (require '[libjulia-clj.julia :as julia])
32 | nil
33 | user> (julia/initialize! {:n-threads 8 :signals-enabled? false})
34 | 16:28:10.854 [nRepl-session-a6713b61-bf94-4492-bcbb-7cc7e44c2a4f] INFO libjulia-clj.impl.base - Attempting to initialize Julia at /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so
35 | 16:28:10.908 [nRepl-session-a6713b61-bf94-4492-bcbb-7cc7e44c2a4f] INFO tech.v3.jna.base - Library /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so found at [:system "/home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so"]
36 | 16:28:10.925 [nRepl-session-a6713b61-bf94-4492-bcbb-7cc7e44c2a4f] INFO libjulia-clj.impl.jna - Julia startup options: n-threads 8, signals? false
37 | :ok
38 | user> (System/gc)
39 | nil
40 | user> (julia/eval-string "Threads.@threads for i in 1:1000; zeros(1024, 1024) .+ zeros(1024, 1024); end")
41 | 
42 | *** Closed on Mon Dec 14 16:28:25 2020 ***
43 |
44 |

The Work-Around For Now

45 |

The JVM has a facility for signal chaining. This allows us to launch the JVM 46 | in a particular way where installs a handler that listens for entities attempting 47 | to install a signal handler and it records these handlers. When a signal occurse, 48 | it can detect whether it came from the JVM or from an outside entity and thus route 49 | the correct signal to the correct handler as required.

50 |

Using this facility is fairly simple, setup an environment variable LD_PRELOAD that 51 | forces the operating system to load a shared library that exports functions that 52 | allow the JVM to chain signals as opposed to simply handling them.

53 |

If we modify our example from before with this pathway we can successfully run 54 | our example:

55 | 
chrisn@chrisn-lt-01:~/dev/cnuernber/libjulia-clj$ find /usr -name "*jsig*"
56 | /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjsig.so
57 | /usr/lib/jvm/java-11-openjdk-amd64/lib/libjsig.so
58 | /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjsig.so
59 | /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/libjsig.so
60 | chrisn@chrisn-lt-01:~/dev/cnuernber/libjulia-clj$ export LD_PRELOAD=/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/libjsig.so
61 |
62 | 
user> (require '[libjulia-clj.julia :as julia])
63 | nil
64 | user> ;;Signals are automatically enabled if n-threads has a value
65 | user> (julia/initialize! {:n-threads 8})
66 | 16:37:40.695 [nRepl-session-447a06c6-bf23-4338-9618-34e0f841c82b] INFO libjulia-clj.impl.base - Attempting to initialize Julia at /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so
67 | 16:37:40.741 [nRepl-session-447a06c6-bf23-4338-9618-34e0f841c82b] INFO tech.v3.jna.base - Library /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so found at [:system "/home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so"]
68 | 16:37:40.747 [nRepl-session-447a06c6-bf23-4338-9618-34e0f841c82b] INFO libjulia-clj.impl.jna - Julia startup options: n-threads 8, signals? true
69 | :ok
70 | user> (julia/eval-string "Threads.@threads for i in 1:1000; zeros(1024, 1024) .+ zeros(1024, 1024); end")
71 | nil
72 |
73 |

So, for now, we have to setup some nonstandard JVM state in order to use Julia to 74 | it's full potential. Still, it is pretty amazing that the chaining facility exists 75 | and that it works as advertised and at least we have a solid pathway forward in 76 | order to using Julia from the JVM or vice versa.

77 |
78 | -------------------------------------------------------------------------------- /examples/fractal/README.md: -------------------------------------------------------------------------------- 1 | # Simple Julia Example 2 | 3 | Ensure you have julia installed and JULIA_HOME exported to point to your 4 | installation directory. If you are on a linux system, from the top level 5 | run: 6 | 7 | ```console 8 | (base) chrisn@chrisn-lt3:~/dev/cnuernber/libjulia-clj/examples/fractal$ cd ../../ 9 | (base) chrisn@chrisn-lt3:~/dev/cnuernber/libjulia-clj$ source scripts/activate-julia 10 | (base) chrisn@chrisn-lt3:~/dev/cnuernber/libjulia-clj$ cd examples/fractal/ 11 | (base) chrisn@chrisn-lt3:~/dev/cnuernber/libjulia-clj/examples/fractal$ 12 | ``` 13 | 14 | 15 | ```console 16 | 17 | Downloading: com/cnuernber/libjulia-clj/1.000-beta-1/libjulia-clj-1.000-beta-1.pom from clojars 18 | Downloading: com/cnuernber/libjulia-clj/1.000-beta-1/libjulia-clj-1.000-beta-1.jar from clojars 19 | Clojure 1.10.3 20 | (require '[julia-fractals :as jf]) 21 | nil 22 | (jf/jl-fractal) 23 | Oct 25, 2021 12:14:59 PM clojure.tools.logging$eval3221$fn__3224 invoke 24 | INFO: Reference thread starting 25 | Oct 25, 2021 12:14:59 PM clojure.tools.logging$eval3221$fn__3224 invoke 26 | INFO: julia library arguments: ["--handle-signals=no" "--threads" "1"] 27 | #object[java.awt.image.BufferedImage 0x31ee5a9 "BufferedImage@31ee5a9: type = 10 ColorModel: #pixelBits = 8 numComponents = 1 color space = java.awt.color.ICC_ColorSpace@67add4c9 transparency = 1 has alpha = false isAlphaPre = false ByteInterleavedRaster: width = 1920 height = 1080 #numDataElements 1 dataOff[0] = 0"] 28 | (def img *1) 29 | #'user/img 30 | (require '[tech.v3.libs.buffered-image :as bufimg]) 31 | nil 32 | (bufimg/save! img "test.png") 33 | true 34 | ``` 35 | -------------------------------------------------------------------------------- /examples/fractal/deps.edn: -------------------------------------------------------------------------------- 1 | {:paths ["src"] 2 | :deps {com.cnuernber/libjulia-clj {:mvn/version "1.000-beta-3"}}} 3 | -------------------------------------------------------------------------------- /examples/fractal/src/julia_fractals.clj: -------------------------------------------------------------------------------- 1 | (ns julia-fractals 2 | (:require [tech.v3.tensor :as dtt] 3 | [tech.v3.datatype :as dtype] 4 | [tech.v3.libs.buffered-image :as bufimg] 5 | [libjulia-clj.julia :as julia]) 6 | (:import [org.apache.commons.math3.complex Complex])) 7 | 8 | (set! *unchecked-math* :warn-on-boxed) 9 | 10 | 11 | (def fract-width 1920) 12 | (def fract-height 1080) 13 | (def i1 0.31) 14 | (def i2 -0.6) 15 | (def d 11) 16 | (def zoom-factor 0.2) 17 | 18 | 19 | (defn fractal 20 | [] 21 | (let [icomp (Complex. i1 i2) 22 | ;;type out all the variables to avoid boxing 23 | zoom-factor (double zoom-factor) 24 | img-width (double fract-width) 25 | img-height (double fract-height) 26 | d (long d) 27 | hw (* 0.5 (double fract-width)) 28 | hh (* 0.5 (double fract-height)) 29 | zw (* zoom-factor img-width) 30 | zh (* zoom-factor img-height)] 31 | (-> (dtt/typed-compute-tensor 32 | :int64 33 | [img-height img-width] 34 | [y x] 35 | (loop [pos (Complex. (-> (- x hw) (/ zw)) (-> (- y hh) (/ zh))) 36 | c 0] 37 | (if (< c d) 38 | (recur (-> (.multiply pos pos) (.add icomp)) (inc c)) 39 | (let [val (.abs pos)] 40 | (if (and (Double/isFinite val) (< val (dec d))) 255 0))))) 41 | (dtype/copy! (bufimg/new-image img-height img-width :byte-gray))))) 42 | 43 | 44 | (comment 45 | 46 | (-> (fractal) 47 | (bufimg/save! "clj-fract.png")) 48 | 49 | (time (fractal)) 50 | ;;202 ms 51 | ) 52 | 53 | 54 | (def julia-code 55 | "function juliaSet(i1,i2,d,zoomFactor,imgWidth,imgHeight) 56 | # Allocating a widthxheight matrix as our Clojure client is row-major 57 | matrix = Array{UInt8}(undef,imgWidth,imgHeight) 58 | icomp = Complex{Float64}(i1,i2) 59 | Threads.@threads for i in CartesianIndices(matrix) 60 | ## Julia has 1-based indexing... 61 | pos = complex(((i[1]-1) - (0.5 * imgWidth)) / (zoomFactor * imgWidth), 62 | ((i[2]-1) - (0.5 * imgHeight)) / (zoomFactor * imgHeight)) 63 | 64 | for c in (1:d) pos = (pos * pos) + icomp end 65 | absval = abs(pos) 66 | if (absval != NaN && absval < (d-1)) 67 | matrix[i] = 255 68 | else 69 | matrix[i] = 0 70 | end 71 | end 72 | return matrix 73 | end") 74 | 75 | 76 | (def jl-fn* (delay (do (julia/initialize!) 77 | (julia/jl julia-code)))) 78 | 79 | 80 | (defn jl-fractal 81 | [] 82 | (let [jl-fn @jl-fn*] 83 | (-> (jl-fn i1 i2 d zoom-factor fract-width fract-height) 84 | (dtt/ensure-tensor) 85 | (dtype/copy! (bufimg/new-image fract-height fract-width :byte-gray))))) 86 | 87 | 88 | (comment 89 | 90 | (-> (jl-fractal) 91 | (bufimg/save! "jl-fract.png")) 92 | 93 | (time (jl-fractal)) 94 | ;;34 ms 95 | ) 96 | -------------------------------------------------------------------------------- /resources/clj_julia_helper.jl: -------------------------------------------------------------------------------- 1 | module clj_julia_helper 2 | "Ruthlessly stolen from pyjulia" 3 | 4 | 5 | """ 6 | num_utf8_trailing(d::Vector{UInt8}) 7 | 8 | If `d` ends with an incomplete UTF8-encoded character, return the number of trailing incomplete bytes. 9 | Otherwise, return `0`. 10 | 11 | Taken from IJulia.jl. 12 | """ 13 | function num_utf8_trailing(d::Vector{UInt8}) 14 | i = length(d) 15 | # find last non-continuation byte in d: 16 | while i >= 1 && ((d[i] & 0xc0) == 0x80) 17 | i -= 1 18 | end 19 | i < 1 && return 0 20 | c = d[i] 21 | # compute number of expected UTF-8 bytes starting at i: 22 | n = c <= 0x7f ? 1 : c < 0xe0 ? 2 : c < 0xf0 ? 3 : 4 23 | nend = length(d) + 1 - i # num bytes from i to end 24 | return nend == n ? 0 : nend 25 | end 26 | 27 | function pipe_stream(sender::IO, receiver, buf::IO = IOBuffer()) 28 | receiver("begin pipe stream") 29 | try 30 | while !eof(sender) 31 | receiver("in loop") 32 | nb = bytesavailable(sender) 33 | write(buf, read(sender, nb)) 34 | 35 | # Taken from IJulia.send_stream: 36 | d = take!(buf) 37 | n = num_utf8_trailing(d) 38 | dextra = d[end-(n-1):end] 39 | resize!(d, length(d) - n) 40 | s = String(copy(d)) 41 | 42 | write(buf, dextra) 43 | receiver(s) # check isvalid(String, s)? 44 | end 45 | catch e 46 | receiver("error detected") 47 | if !isa(e, InterruptException) 48 | rethrow() 49 | end 50 | pipe_stream(sender, receiver, buf) 51 | end 52 | end 53 | 54 | const read_stdout = Ref{Base.PipeEndpoint}() 55 | const read_stderr = Ref{Base.PipeEndpoint}() 56 | 57 | function pipe_std_outputs(out_receiver, err_receiver) 58 | global readout_task 59 | global readerr_task 60 | global out_rec = out_receiver 61 | global err_rec = err_receiver 62 | read_stdout[], = redirect_stdout() 63 | readout_task = @task pipe_stream(read_stdout[], out_receiver) 64 | read_stderr[], = redirect_stderr() 65 | readerr_task = @task pipe_stream(read_stderr[], err_receiver) 66 | (readout_task,readerr_task) 67 | end 68 | 69 | end 70 | -------------------------------------------------------------------------------- /resources/symbols.txt: -------------------------------------------------------------------------------- 1 | 00000000000435e0 T jl_ 2 | 00000000000fc060 T jl_abs_float 3 | 00000000000fbf40 T jl_abs_float_withtype 4 | 00000000004f2cf8 B jl_abstractarray_type 5 | 00000000004f2d90 B jl_abstractslot_type 6 | 00000000004f2c00 B jl_abstractstring_type 7 | 00000000000fabd0 T jl_add_float 8 | 00000000000fa960 T jl_add_int 9 | 000000000013c550 T jl_add_optimization_passes 10 | 00000000000fa980 T jl_add_ptr 11 | 00000000000ef250 T jl_add_standard_imports 12 | 00000000000fe5c0 T jl_alignment 13 | 00000000000d87b0 T jl_alloc_array_1d 14 | 00000000000d8b50 T jl_alloc_array_2d 15 | 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866 | 00000000000fb8d0 T jl_xor_int 867 | 0000000000110dc0 T jl_yield 868 | 00000000000fba80 T jl_zext_int 869 | -------------------------------------------------------------------------------- /scripts/activate-julia: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | if [ ! -e julia-1.7.0-rc2 ]; then 4 | wget https://julialang-s3.julialang.org/bin/linux/x64/1.7/julia-1.7.0-rc2-linux-x86_64.tar.gz 5 | tar -xvzf julia-1.7.0-rc2-linux-x86_64.tar.gz 6 | rm julia-1.7.0-rc2-linux-x86_64.tar.gz 7 | fi 8 | 9 | export JULIA_HOME=$(pwd)/julia-1.7.0-rc2 10 | export PATH=$PATH:$JULIA_HOME/bin -------------------------------------------------------------------------------- /scripts/activate-openj9: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | OPENJ9_VERSION="jdk8u275-b01" 4 | OPENJ9_VERSION_NODASH="8u275b01" 5 | J9_VERSION="0.23.0" 6 | J9_TARNAME="OpenJDK8U-jdk_x64_linux_openj9_$OPENJ9_VERSION_NODASH_openj9-$J9_VERSION.tar.gz" 7 | JAVA_PATH=$(pwd)/openj9/$OPENJ9_VERSION/bin 8 | 9 | if [ ! -e "$JAVA_PATH/java" ]; then 10 | mkdir -p openj9 11 | pushd openj9 12 | wget "https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/$OPENJ9_VERSION_openj9-$J9_VERSION/$J9_TARNAME" 13 | tar -xvzf $J9_TARNAME 14 | popd 15 | fi 16 | 17 | export LD_PRELOAD=$(pwd)/openj9/$OPENJ9_VERSION/jre/lib/amd64/j9vm/libjsig.so 18 | export PATH=$JAVA_PATH:$PATH 19 | 20 | -------------------------------------------------------------------------------- /scripts/build-docker: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | set -e 4 | 5 | 6 | pushd dockerfiles 7 | docker build -t julia-clj-docker -f Dockerfile --build-arg USERID=$(id -u) --build-arg GROUPID=$(id -u) --build-arg USERNAME=$USER . 8 | popd 9 | -------------------------------------------------------------------------------- /scripts/deploy: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | set -e 4 | 5 | rm -rf classes 6 | 7 | source scripts/local-julia-env 8 | 9 | clj -M:test 10 | clj -X:codox 11 | clj -X:depstar 12 | clj -X:deploy 13 | -------------------------------------------------------------------------------- /scripts/local-julia-env: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | source scripts/activate-julia 4 | export LD_PRELOAD=/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjsig.so 5 | -------------------------------------------------------------------------------- /scripts/openj9-java: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | source scripts/activate-openj9 4 | java $@ -------------------------------------------------------------------------------- /scripts/remote-repl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | export JULIA_COPY_STACKS=yes 4 | 5 | lein update-in :dependencies conj \[nrepl\ \"0.6.0\"\]\ 6 | -- update-in :plugins conj \[cider/cider-nrepl\ \"0.22.4\"\]\ 7 | -- repl :headless :host localhost 8 | 9 | -------------------------------------------------------------------------------- /scripts/run-docker: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | set -e 4 | 5 | scripts/build-docker 6 | 7 | ## Need this for julia magic 8 | export JULIA_COPY_STACKS=yes 9 | 10 | docker run --rm -it -u $(id -u):$(id -g) \ 11 | -v /$HOME/.m2:/home/$USER/.m2 \ 12 | -v $(pwd)/:/julia-clj \ 13 | --net=host -w /julia-clj \ 14 | julia-clj-docker lein update-in :dependencies conj \[nrepl\ \"0.6.0\"\]\ 15 | -- update-in :plugins conj \[cider/cider-nrepl\ \"0.22.4\"\]\ 16 | -- repl :headless :host localhost 17 | -------------------------------------------------------------------------------- /src/libjulia_clj/impl/base.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.impl.base 2 | (:require [tech.v3.datatype :as dtype] 3 | [tech.v3.datatype.ffi :as dt-ffi] 4 | [tech.v3.datatype.ffi.size-t :as ffi-size-t] 5 | [tech.v3.datatype.ffi.ptr-value :as ffi-ptr-value] 6 | [tech.v3.datatype.protocols :as dtype-proto] 7 | [tech.v3.datatype.errors :as errors] 8 | [tech.v3.datatype.casting :as casting] 9 | [tech.v3.datatype.pprint :as dtype-pp] 10 | [tech.v3.datatype.native-buffer :as native-buffer] 11 | [tech.v3.tensor.dimensions.analytics :as dims-analytics] 12 | [tech.v3.tensor :as dtt] 13 | [tech.v3.resource :as resource] 14 | [libjulia-clj.impl.gc :as gc] 15 | [libjulia-clj.impl.ffi :as julia-ffi] 16 | [libjulia-clj.impl.protocols :as julia-proto] 17 | [com.github.ztellman.primitive-math :as pmath] 18 | [clojure.tools.logging :as log]) 19 | (:import [tech.v3.datatype.ffi Pointer] 20 | [java.nio.file Paths] 21 | [java.util Map Iterator NoSuchElementException] 22 | [clojure.lang IFn Symbol Keyword]) 23 | (:refer-clojure :exclude [struct])) 24 | 25 | 26 | (set! *warn-on-reflection* true) 27 | 28 | 29 | (defonce jvm-julia-roots* (atom nil)) 30 | 31 | 32 | (declare call-function raw-call-function call-function-kw) 33 | 34 | 35 | (defn initialize-julia-root-map! 36 | [] 37 | (errors/when-not-error 38 | (nil? @jvm-julia-roots*) 39 | "Attempt to initialize julia root map twice") 40 | (let [refmap (julia-ffi/jl_eval_string "jvm_refs = IdDict()") 41 | set-index! (julia-ffi/jl_get_function (julia-ffi/jl_base_module) "setindex!") 42 | delete! (julia-ffi/jl_get_function (julia-ffi/jl_base_module) "delete!") 43 | haskey (julia-ffi/jl_get_function (julia-ffi/jl_base_module) "haskey")] 44 | (reset! jvm-julia-roots* 45 | {:jvm-refs refmap 46 | :set-index! set-index! 47 | :delete! delete! 48 | :haskey haskey}))) 49 | 50 | (defonce julia-gc-root-log-level* (atom nil)) 51 | 52 | (defn root-ptr! 53 | "Root a pointer and set a GC hook that will unroot it when the time comes. 54 | Defaults to :auto track type" 55 | ([^Pointer value options] 56 | (when-not (or (:unrooted? options) 57 | (== 0 (julia-ffi/jl_gc_is_enabled))) 58 | (let [{:keys [jvm-refs set-index! delete! haskey]} @jvm-julia-roots* 59 | native-value (.address value) 60 | untracked-value (Pointer. native-value) 61 | ;;Eventually we will turn off default logging... 62 | log-level (:log-level options @julia-gc-root-log-level*)] 63 | ;;We do not root pointers twice; that could cause a crash when 64 | ;;dereferencing 65 | (if-not (julia-proto/julia->jvm 66 | (julia-ffi/jl_call2 haskey jvm-refs untracked-value) 67 | {}) 68 | (do 69 | (when log-level 70 | (log/logf log-level "Rooting address 0x%016X - %s" 71 | native-value (julia-ffi/jl-ptr->typename value))) 72 | (julia-ffi/jl_call3 set-index! jvm-refs untracked-value value) 73 | (gc/track value (fn [] 74 | (when log-level 75 | (log/logf log-level 76 | "Unrooting address 0x%016X" 77 | native-value)) 78 | (julia-ffi/jl_call2 delete! jvm-refs untracked-value)))) 79 | ;;already rooted 80 | value)))) 81 | ([value] 82 | (root-ptr! value nil))) 83 | 84 | 85 | (defn combine-paths 86 | ^String [src-path & args] 87 | (-> (Paths/get (str src-path) ^"[java.lang.String;" 88 | (into-array String 89 | (map str args))) 90 | (.toString))) 91 | 92 | 93 | (defonce module-functions* (atom nil)) 94 | 95 | 96 | (defn initialize-module-functions! 97 | [] 98 | (let [basemod (julia-ffi/jl_base_module) 99 | coremod (julia-ffi/jl_core_module)] 100 | (reset! module-functions* 101 | {:sprint (julia-ffi/jl_get_function basemod "sprint") 102 | :showerror (julia-ffi/jl_get_function basemod "showerror") 103 | :catch-backtrace (julia-ffi/jl_get_function basemod "catch_backtrace") 104 | :dump (julia-ffi/jl_get_function basemod "dump") 105 | :print (julia-ffi/jl_get_function basemod "print") 106 | :methods (julia-ffi/jl_get_function basemod "methods") 107 | :length (julia-ffi/jl_get_function basemod "length") 108 | :names (julia-ffi/jl_get_function basemod "names") 109 | :kwfunc (julia-ffi/jl_get_function coremod "kwfunc") 110 | :isempty (julia-ffi/jl_get_function basemod "isempty") 111 | :setindex! (julia-ffi/jl_get_function basemod "setindex!") 112 | :getindex (julia-ffi/jl_get_function basemod "getindex") 113 | :fieldnames (julia-ffi/jl_get_function basemod "fieldnames") 114 | :getfield (julia-ffi/jl_get_function basemod "getfield") 115 | :keys (julia-ffi/jl_get_function basemod "keys") 116 | :values (julia-ffi/jl_get_function basemod "values") 117 | :haskey (julia-ffi/jl_get_function basemod "haskey") 118 | :get (julia-ffi/jl_get_function basemod "get") 119 | :append! (julia-ffi/jl_get_function basemod "append!") 120 | :delete! (julia-ffi/jl_get_function basemod "delete!") 121 | :iterate (julia-ffi/jl_get_function basemod "iterate") 122 | :pairs (julia-ffi/jl_get_function basemod "pairs") 123 | :eltype (julia-ffi/jl_get_function basemod "eltype")}))) 124 | 125 | 126 | (defn module-fn 127 | [fn-name & args] 128 | (if-let [fn-val (get @module-functions* fn-name)] 129 | (call-function fn-val args) 130 | (errors/throwf "Failed to find module function %s" fn-name))) 131 | 132 | 133 | (defn sprint-last-error 134 | ^String [exc] 135 | (when exc 136 | (let [{:keys [sprint showerror catch-backtrace]} @module-functions* 137 | bt (julia-ffi/jl_call0 catch-backtrace)] 138 | (-> (julia-ffi/jl_call3 sprint showerror exc bt) 139 | (julia-proto/julia->jvm nil))))) 140 | 141 | 142 | (defn check-last-error 143 | [] 144 | (when-let [exc (julia-ffi/jl_exception_occurred)] 145 | (errors/throwf "Julia error:\n%s" (or (sprint-last-error exc) 146 | "unable to print error")))) 147 | 148 | 149 | (defn jl-obj->str 150 | ^String [jl-ptr] 151 | (when jl-ptr 152 | (let [{:keys [sprint print]} @module-functions*] 153 | (-> (julia-ffi/jl_call2 sprint print jl-ptr) 154 | (julia-proto/julia->jvm nil))))) 155 | 156 | 157 | (defn windows-os? 158 | [] 159 | (.contains (.toLowerCase (System/getProperty "os.name")) 160 | "windows")) 161 | 162 | 163 | (defn initialize! 164 | "Initialize julia optionally providing an explicit path which will override 165 | the julia library search mechanism. 166 | 167 | Currently the search mechanism is: 168 | 169 | [user-path]->JULIA_HOME->\"julia\" 170 | 171 | Returns :ok on success else exception. 172 | 173 | Options: 174 | 175 | * `:julia-home` - Explicitly declare the env var julia-home. 176 | * `:n-threads` - Set to -1 to set to n-cpus. Defaults to nil which means single threaded 177 | unless the JULIA_NUM_THREADS environment variable is set. Note that this has implications 178 | for application stability - see the signals.md topic. 179 | * `:signals-enabled?` - Users do not usually need to set this. This allows users to disable 180 | all of Julia's signal handling most likely leading to a crash. See the signals.md topic." 181 | ([{:keys [julia-library-path] 182 | :as options}] 183 | (julia-ffi/initialize! options) 184 | (reset! julia-ffi/julia-library-path* julia-library-path) 185 | (when-not (== 1 (julia-ffi/jl_is_initialized)) 186 | ;;The JVM uses SIGSEGV signals during it's normal course of 187 | ;;operation. Without disabling Julia's signal handling this will 188 | ;;cause an instantaneous and unceremonious exit :-). 189 | (julia-ffi/init-process-options options) 190 | (julia-ffi/jl_init__threading) 191 | (julia-ffi/initialize-type-map!) 192 | (initialize-julia-root-map!) 193 | (initialize-module-functions!)) 194 | :ok) 195 | ([] 196 | (initialize! nil))) 197 | 198 | 199 | (def ptr-dtype (ffi-size-t/lower-ptr-type :pointer)) 200 | 201 | 202 | (defn module-symbol-names 203 | [module] 204 | (let [names-fn (:names @module-functions*) 205 | names-ary (julia-ffi/jl_call1 names-fn module) 206 | ary-data (native-buffer/wrap-address (ffi-ptr-value/ptr-value names-ary) 207 | 16 ptr-dtype :little-endian nil) 208 | data-ptr (ary-data 0) 209 | ;;If julia is compiled with STORE_ARRAY_LENGTH 210 | data-len (ary-data 1) 211 | data (native-buffer/wrap-address data-ptr 212 | (* data-len 213 | (casting/numeric-byte-width ptr-dtype)) 214 | ptr-dtype :little-endian nil)] 215 | (-> (dtype/emap (fn [^long sym-data] 216 | (-> (Pointer. sym-data) 217 | (julia-ffi/jl_symbol_name))) 218 | :string data) 219 | (dtype/clone)))) 220 | 221 | 222 | (deftype GenericJuliaObject [^Pointer handle gc-obj] 223 | julia-proto/PToJulia 224 | (->julia [item] handle) 225 | dt-ffi/PToPointer 226 | (convertible-to-pointer? [this] true) 227 | (->pointer [this] handle) 228 | Object 229 | (toString [this] 230 | (jl-obj->str handle))) 231 | 232 | (dtype-pp/implement-tostring-print GenericJuliaObject) 233 | 234 | 235 | (defn args->pos-kw-args 236 | "Utility function that, given a list of arguments, separates them 237 | into positional and keyword arguments. Throws an exception if the 238 | keyword argument is not followed by any more arguments." 239 | [arglist] 240 | (loop [args arglist 241 | pos-args [] 242 | kw-args nil 243 | found-kw? false] 244 | (if-not (seq args) 245 | [pos-args kw-args] 246 | (let [arg (first args) 247 | [pos-args kw-args args found-kw?] 248 | (if (keyword? arg) 249 | (if-not (seq (rest args)) 250 | (throw (Exception. 251 | (format "Keyword arguments must be followed by another arg: %s" 252 | (str arglist)))) 253 | [pos-args (assoc kw-args arg (first (rest args))) 254 | (drop 2 args) true]) 255 | (if found-kw? 256 | (throw (Exception. 257 | (format "Positional arguments are not allowed after keyword arguments: %s" 258 | arglist))) 259 | [(conj pos-args (first args)) 260 | kw-args 261 | (rest args) found-kw?]))] 262 | (recur args pos-args kw-args found-kw?))))) 263 | 264 | 265 | (defmacro ^:private impl-callable-julia-object 266 | [] 267 | `(deftype ~'CallableJuliaObject [~'handle ~'kw-fn-handle ~'gc-obj] 268 | julia-proto/PToJulia 269 | (->julia [item] ~'handle) 270 | julia-proto/PJuliaKWFn 271 | (kw-fn [item] ~'kw-fn-handle) 272 | dt-ffi/PToPointer 273 | (convertible-to-pointer? [this#] true) 274 | (->pointer [this#] ~'handle) 275 | Object 276 | (toString [this] 277 | (jl-obj->str ~'handle)) 278 | IFn 279 | ~@(->> (range 16) 280 | (map (fn [idx] 281 | (let [argsyms (->> (range idx) 282 | (mapv (fn [arg-idx] 283 | (symbol (str "arg-" arg-idx)))))] 284 | `(invoke ~(vec (concat ['this] argsyms)) 285 | (let [[pos-args# kw-args#] (args->pos-kw-args ~argsyms)] 286 | (if (nil? kw-args#) 287 | (call-function ~'handle ~argsyms nil) 288 | (call-function-kw ~'handle pos-args# kw-args#)))))))) 289 | (applyTo [this# argseq#] 290 | (let [[pos-args# kw-args#] (args->pos-kw-args argseq#)] 291 | (if (nil? kw-args#) 292 | (call-function ~'handle argseq# nil) 293 | (call-function-kw ~'kw-fn-handle ~'handle pos-args# kw-args#)))))) 294 | 295 | 296 | (impl-callable-julia-object) 297 | 298 | 299 | (dtype-pp/implement-tostring-print CallableJuliaObject) 300 | 301 | (defn jl-obj-callable? 302 | [jl-obj] 303 | (when jl-obj 304 | (let [{:keys [methods length]} @module-functions*] 305 | (try 306 | (not= 0 (long (call-function length 307 | [(raw-call-function methods [jl-obj])]))) 308 | (catch Throwable e false))))) 309 | 310 | 311 | (defn kw-fn 312 | ([jl-fn options] 313 | (let [{:keys [kwfunc]} @module-functions*] 314 | (call-function kwfunc [jl-fn] options))) 315 | ([jl-fn] 316 | (kw-fn jl-fn nil))) 317 | 318 | 319 | (extend-type Object 320 | julia-proto/PJuliaKWFn 321 | (kw-fn [item] 322 | (kw-fn item))) 323 | 324 | 325 | (defmethod julia-proto/julia->jvm :default 326 | [julia-val options] 327 | (when julia-val 328 | ;;Do not root when someone asks us not to or when 329 | ;;we have explicitly disabled the julia gc. 330 | (root-ptr! julia-val options) 331 | (if (jl-obj-callable? julia-val) 332 | (CallableJuliaObject. julia-val (kw-fn julia-val {:unrooted? true}) 333 | (:gc-obj options)) 334 | (GenericJuliaObject. julia-val 335 | (:gc-obj options))))) 336 | 337 | 338 | (extend-protocol julia-proto/PToJulia 339 | Boolean 340 | (->julia [item] (julia-ffi/jl_box_bool (if item 1 0))) 341 | Byte 342 | (->julia [item] (julia-ffi/jl_box_int8 item)) 343 | Short 344 | (->julia [item] (julia-ffi/jl_box_int16 item)) 345 | Integer 346 | (->julia [item] (julia-ffi/jl_box_int32 item)) 347 | Long 348 | (->julia [item] (julia-ffi/jl_box_int64 item)) 349 | Float 350 | (->julia [item] (julia-ffi/jl_box_float32 item)) 351 | Double 352 | (->julia [item] (julia-ffi/jl_box_float64 item)) 353 | String 354 | (->julia [item] (julia-ffi/jl_cstr_to_string item)) 355 | Symbol 356 | (->julia [item] (julia-ffi/jl_symbol (name item))) 357 | Keyword 358 | (->julia [item] (julia-ffi/jl_symbol (name item))) 359 | Pointer 360 | (->julia [item] item)) 361 | 362 | (defmethod julia-proto/julia->jvm :boolean 363 | [julia-val options] 364 | (if (== 0 (julia-ffi/jl_unbox_bool julia-val)) 365 | false 366 | true)) 367 | 368 | 369 | (defmethod julia-proto/julia->jvm :uint8 370 | [julia-val options] 371 | (pmath/byte->ubyte (julia-ffi/jl_unbox_uint8 julia-val))) 372 | 373 | (defmethod julia-proto/julia->jvm :uint16 374 | [julia-val options] 375 | (pmath/short->ushort (julia-ffi/jl_unbox_uint16 julia-val))) 376 | 377 | (defmethod julia-proto/julia->jvm :uint32 378 | [julia-val options] 379 | (pmath/int->uint (julia-ffi/jl_unbox_uint32 julia-val))) 380 | 381 | (defmethod julia-proto/julia->jvm :uint64 382 | [julia-val options] 383 | (julia-ffi/jl_unbox_uint64 julia-val)) 384 | 385 | 386 | (defmethod julia-proto/julia->jvm :int8 387 | [julia-val options] 388 | (julia-ffi/jl_unbox_int8 julia-val)) 389 | 390 | (defmethod julia-proto/julia->jvm :int16 391 | [julia-val options] 392 | (julia-ffi/jl_unbox_int16 julia-val)) 393 | 394 | (defmethod julia-proto/julia->jvm :int32 395 | [julia-val options] 396 | (julia-ffi/jl_unbox_int32 julia-val)) 397 | 398 | (defmethod julia-proto/julia->jvm :int64 399 | [julia-val options] 400 | (julia-ffi/jl_unbox_int64 julia-val)) 401 | 402 | (defmethod julia-proto/julia->jvm :float64 403 | [julia-val options] 404 | (julia-ffi/jl_unbox_float64 julia-val)) 405 | 406 | (defmethod julia-proto/julia->jvm :float32 407 | [julia-val options] 408 | (julia-ffi/jl_unbox_float32 julia-val)) 409 | 410 | (defmethod julia-proto/julia->jvm :string 411 | [julia-val options] 412 | (julia-ffi/jl_string_ptr julia-val)) 413 | 414 | (defmethod julia-proto/julia->jvm :jl-nothing-type 415 | [julia-val options] 416 | nil) 417 | 418 | 419 | (defn jvm-args->julia 420 | [args] 421 | (mapv #(if % 422 | (julia-proto/->julia %) 423 | (julia-ffi/jl_nothing)) args)) 424 | 425 | 426 | #_(defn lookup-julia-type 427 | "Lookup a julia type from a clojure type keyword." 428 | [clj-type-kwd] 429 | (if-let [retval (get-in @julia-ffi/julia-typemap* [:typename->typeid clj-type-kwd])] 430 | (julia-proto/julia->jvm retval {:unrooted? true}) 431 | (errors/throwf "Failed to find julia type %s" clj-type-kwd))) 432 | 433 | 434 | (defn jvm-args->julia-types 435 | [args] 436 | (mapv #(if % 437 | (julia-proto/->julia %) 438 | (julia-ffi/jl_nothing)) 439 | args)) 440 | 441 | 442 | (defn jvm-args->julia-symbols 443 | [args] 444 | (mapv #(cond (string? %) (julia-ffi/jl_symbol %) 445 | (or (keyword? %) (symbol? %)) (julia-proto/->julia %) 446 | :else (errors/throwf "%s is not convertible to a julia symbol" %)) 447 | args)) 448 | 449 | 450 | (defn raw-call-function 451 | "Call the function. We disable the Julia GC when marshalling arguments but 452 | the GC is enabled for the actual julia function call. The result is returned 453 | to the user as a Pointer." 454 | ^Pointer [fn-handle args] 455 | (resource/stack-resource-context 456 | ;;do not GC my stuff when I am marshalling function arguments to julia 457 | (let [jl-args (julia-ffi/with-disabled-julia-gc (jvm-args->julia args))] 458 | (let [retval 459 | (case (count jl-args) 460 | 0 (julia-ffi/jl_call0 fn-handle) 461 | 1 (julia-ffi/jl_call1 fn-handle (first jl-args)) 462 | 2 (julia-ffi/jl_call2 fn-handle (first jl-args) (second jl-args)) 463 | 3 (apply julia-ffi/jl_call3 fn-handle jl-args) 464 | (let [n-args (count args) 465 | ;;This will be cleaned up when the resource stack context unwraps. 466 | ptr-buf (dtype/make-container :native-heap ptr-dtype 467 | {:resource-type :stack} 468 | (mapv #(if % 469 | (ffi-ptr-value/ptr-value %) 470 | 0) 471 | jl-args))] 472 | (julia-ffi/jl_call fn-handle ptr-buf n-args)))] 473 | (check-last-error) 474 | retval)))) 475 | 476 | 477 | (defn call-function 478 | "Call a function. The result will be marshalled back to the jvm and if necessary, 479 | rooted. This method is normally not necessary but useful if you would like to 480 | use keywords in your argument list or specify to avoid rooting the result." 481 | ([fn-handle args options] 482 | (let [retval (raw-call-function fn-handle args)] 483 | (julia-proto/julia->jvm retval options))) 484 | ([fn-handle args] 485 | (call-function fn-handle args nil))) 486 | 487 | (defn apply-tuple-type 488 | "Create a new Julia tuple type from a sequence of types." 489 | ^Pointer [args & [options]] 490 | (resource/stack-resource-context 491 | (let [jl-args (julia-ffi/with-disabled-julia-gc (jvm-args->julia-types args)) 492 | n-args (count args) 493 | ptr-buf (dtype/make-container :native-heap ptr-dtype 494 | {:resource-type :stack} 495 | (mapv #(if % 496 | (ffi-ptr-value/ptr-value %) 497 | 0) 498 | jl-args)) 499 | retval (julia-ffi/jl_apply_tuple_type_v ptr-buf n-args)] 500 | (check-last-error) 501 | (julia-proto/julia->jvm retval options)))) 502 | 503 | 504 | (defn apply-type 505 | "Create a new Julia type from an existing type and a sequence of other 506 | types." 507 | ^Pointer [jl-type args] 508 | (resource/stack-resource-context 509 | (let [args (julia-ffi/with-disabled-julia-gc (jvm-args->julia-types args)) 510 | retval 511 | (case (count args) 512 | 1 (julia-ffi/jl_apply_type1 jl-type (first args)) 513 | 2 (julia-ffi/jl_apply_type2 jl-type (first args) (second args)) 514 | (let [n-args (count args) 515 | ptr-buf (dtype/make-container 516 | :native-heap ptr-dtype 517 | {:resource-type :stack} 518 | (mapv #(if % 519 | (ffi-ptr-value/ptr-value %) 520 | 0) 521 | args))] 522 | (julia-ffi/jl_apply_type jl-type ptr-buf n-args)))] 523 | (check-last-error) 524 | (julia-proto/julia->jvm retval nil)))) 525 | 526 | 527 | (defn struct 528 | "Instantiate a Julia struct type (tuple, NamedTuple, etc). Use this after 529 | apply-tuple-type in order to create an instance of your new type." 530 | ^Pointer [jl-type args] 531 | (resource/stack-resource-context 532 | (let [args (julia-ffi/with-disabled-julia-gc (jvm-args->julia args)) 533 | n-args (count args) 534 | ptr-buf (dtype/make-container :native-heap ptr-dtype 535 | {:resource-type :stack} 536 | (mapv #(if % 537 | (ffi-ptr-value/ptr-value %) 538 | 0) 539 | args)) 540 | retval (julia-ffi/jl_new_structv jl-type ptr-buf n-args)] 541 | (check-last-error) 542 | (julia-proto/julia->jvm retval nil)))) 543 | 544 | 545 | (defn tuple 546 | "Create a julia tuple from a set of arguments. The tuple type will be the 547 | same datatype as the argument types. 548 | 549 | This function converts the arguments to julia, calls `apply-tuple-type` 550 | on the resulting argument types, and then instantiates an instance of 551 | the given newly created tuple type." 552 | [args] 553 | (let [[jl-args tuple-type] 554 | (julia-ffi/with-disabled-julia-gc 555 | (let [jl-args (jvm-args->julia args)] 556 | [jl-args 557 | (apply-tuple-type (map julia-ffi/jl_typeof jl-args))]))] 558 | (struct tuple-type jl-args))) 559 | 560 | 561 | (defn named-tuple 562 | "Create a julia named tuple from a map of values. The keys of the map must be 563 | keywords or symbols. A new named tuple type will be created and instantiated." 564 | ([value-map] 565 | (let [generic-nt-type (julia-ffi/lookup-library-type :jl-namedtuple-type) 566 | [jl-values nt-type] 567 | (julia-ffi/with-disabled-julia-gc 568 | (let [item-keys (tuple (jvm-args->julia-symbols (keys value-map))) 569 | map-vals (vals value-map) 570 | jl-values (jvm-args->julia map-vals) 571 | item-type-tuple (apply-tuple-type (map julia-ffi/jl_typeof jl-values)) 572 | nt-type (apply-type generic-nt-type [item-keys item-type-tuple])] 573 | [jl-values nt-type]))] 574 | (check-last-error) 575 | ;;And now, with gc (potentially) enabled, attempt to create the struct 576 | (struct nt-type jl-values))) 577 | ([] 578 | (named-tuple nil))) 579 | 580 | 581 | (defn kw-args->named-tuple 582 | [kw-args] 583 | (if (instance? Map kw-args) 584 | (named-tuple kw-args) 585 | (julia-proto/->julia kw-args))) 586 | 587 | 588 | (defn call-function-kw 589 | "Call a julia function and pass in keyword arguments. This is useful if you 590 | would like to specify the arglist and kw-argmap. Normally this is done for 591 | you." 592 | ([fn-handle args kw-args options] 593 | (call-function (julia-proto/kw-fn fn-handle) 594 | (concat [(julia-ffi/with-disabled-julia-gc 595 | (kw-args->named-tuple kw-args)) 596 | fn-handle] 597 | args) 598 | options)) 599 | ([fn-handle args kw-args] 600 | (call-function-kw fn-handle args kw-args nil)) 601 | ([fn-handle args] 602 | (call-function-kw fn-handle args nil nil))) 603 | 604 | 605 | (dtype-pp/implement-tostring-print Pointer) 606 | 607 | 608 | (defn module-publics 609 | [module] 610 | (->> (module-symbol-names module) 611 | (map (fn [sym-name] 612 | (let [global-sym (julia-ffi/jl_get_function module sym-name)] 613 | (when global-sym 614 | [(symbol sym-name) 615 | {:symbol-type (julia-ffi/jl-ptr->typename global-sym) 616 | :symbol global-sym}])))) 617 | (remove nil?) 618 | (sort-by first))) 619 | 620 | 621 | (defmacro define-module-publics 622 | [module-name unsafe-name-map] 623 | (if-let [mod (julia-ffi/jl_eval_string module-name)] 624 | (let [publics (module-publics mod) 625 | docs-fn (julia-ffi/jl_eval_string "Base.Docs.doc")] 626 | `(do 627 | (def ~'module (julia-ffi/jl_eval_string ~module-name)) 628 | ~@(->> publics 629 | (map (fn [[sym {jl-symbol :symbol}]] 630 | (when jl-symbol 631 | (try 632 | (let [sym-name (name sym) 633 | sym-rawname sym-name 634 | sym-name (.replace ^String sym-name "@" "AT") 635 | sym-name (get unsafe-name-map sym-name sym-name) 636 | docs (jl-obj->str (raw-call-function docs-fn [jl-symbol]))] 637 | `(def ~(with-meta (symbol sym-name) 638 | {:doc docs}) 639 | (try 640 | (julia-proto/julia->jvm 641 | (julia-ffi/jl_get_function ~'module ~sym-rawname) 642 | {:unrooted? true}) 643 | (catch Exception e# 644 | (log/warnf e# "Julia symbol %s(%s) will be unavailable" 645 | ~sym-name ~sym-rawname))))) 646 | (catch Exception e 647 | (log/warnf e "Julia symbol %s will unavailable" (name sym))))))) 648 | (remove nil?)))) 649 | (errors/throwf "Failed to find module: %s" module-name))) 650 | 651 | 652 | (defn julia-array->nd-descriptor 653 | [ary-ptr] 654 | (let [rank (julia-ffi/jl_array_rank ary-ptr) 655 | shape (vec (reverse 656 | (map #(julia-ffi/jl_array_size ary-ptr %) 657 | (range rank)))) 658 | data (julia-ffi/jl_array_ptr ary-ptr) 659 | dtype (-> (julia-ffi/jl_array_eltype ary-ptr) 660 | (julia-ffi/julia-eltype->datatype)) 661 | byte-width (casting/numeric-byte-width dtype) 662 | ;;TODO - Figure out to handle non-packed data. This is a start, however. 663 | strides (->> (dims-analytics/shape-ary->strides shape) 664 | (mapv #(* byte-width (long %))))] 665 | {:ptr (ffi-ptr-value/ptr-value data) 666 | :elemwise-datatype dtype 667 | :shape shape 668 | :strides strides 669 | :julia-array ary-ptr})) 670 | 671 | 672 | (deftype JuliaArray [^Pointer handle] 673 | julia-proto/PToJulia 674 | (->julia [item] handle) 675 | dt-ffi/PToPointer 676 | (convertible-to-pointer? [item] true) 677 | (->pointer [this] handle) 678 | dtype-proto/PElemwiseDatatype 679 | (elemwise-datatype [this] 680 | (-> (julia-ffi/jl_array_eltype handle) 681 | (julia-ffi/julia-eltype->datatype))) 682 | dtype-proto/PShape 683 | (shape [this] 684 | (let [rank (julia-ffi/jl_array_rank handle)] 685 | (mapv #(julia-ffi/jl_array_size handle %) 686 | (reverse (range rank))))) 687 | dtype-proto/PECount 688 | (ecount [this] 689 | (long (apply * (dtype-proto/shape this)))) 690 | dtype-proto/PToTensor 691 | (as-tensor [this] 692 | (-> (julia-array->nd-descriptor handle) 693 | (dtt/nd-buffer-descriptor->tensor))) 694 | dtype-proto/PToNDBufferDesc 695 | (convertible-to-nd-buffer-desc? [this] true) 696 | (->nd-buffer-descriptor [this] (julia-array->nd-descriptor handle)) 697 | dtype-proto/PToBuffer 698 | (convertible-to-buffer? [this] true) 699 | (->buffer [this] (dtype-proto/->buffer (dtt/as-tensor this))) 700 | dtype-proto/PToNativeBuffer 701 | (convertible-to-native-buffer? [this] true) 702 | (->native-buffer [this] (-> (dtype-proto/as-tensor this) 703 | (dtype-proto/->native-buffer))) 704 | Object 705 | (toString [this] 706 | (jl-obj->str handle))) 707 | 708 | 709 | (dtype-pp/implement-tostring-print JuliaArray) 710 | 711 | 712 | (defn- wrap-array 713 | [jl-ptr options] 714 | (root-ptr! jl-ptr options) 715 | (JuliaArray. jl-ptr)) 716 | 717 | 718 | (defmethod julia-proto/julia->jvm "Array" [jl-ptr options] 719 | (wrap-array jl-ptr options)) 720 | 721 | (defmethod julia-proto/julia->jvm :jl-array-int-64-type [jl-ptr options] 722 | (wrap-array jl-ptr options)) 723 | 724 | (defmethod julia-proto/julia->jvm :jl-array-uint-64-type [jl-ptr options] 725 | (wrap-array jl-ptr options)) 726 | 727 | (defmethod julia-proto/julia->jvm :jl-array-int-32-type [jl-ptr options] 728 | (wrap-array jl-ptr options)) 729 | 730 | (defmethod julia-proto/julia->jvm :jl-array-uint-32-type [jl-ptr options] 731 | (wrap-array jl-ptr options)) 732 | 733 | (defmethod julia-proto/julia->jvm :jl-array-int-16-type [jl-ptr options] 734 | (wrap-array jl-ptr options)) 735 | 736 | (defmethod julia-proto/julia->jvm :jl-array-uint-16-type [jl-ptr options] 737 | (wrap-array jl-ptr options)) 738 | 739 | (defmethod julia-proto/julia->jvm :jl-array-int-8-type [jl-ptr options] 740 | (wrap-array jl-ptr options)) 741 | 742 | (defmethod julia-proto/julia->jvm :jl-array-uint-8-type [jl-ptr options] 743 | (wrap-array jl-ptr options)) 744 | 745 | 746 | (deftype JLIterator [iter 747 | ^:unsynchronized-mutable iter-state 748 | ^:unsynchronized-mutable last-value] 749 | Iterator 750 | (hasNext [this] 751 | (boolean (not (nil? iter-state)))) 752 | (next [this] 753 | (when-not iter-state 754 | (throw (NoSuchElementException.))) 755 | (let [next-tuple (module-fn :iterate iter iter-state) 756 | retval last-value] 757 | (if next-tuple 758 | (do 759 | (set! last-value (module-fn :getindex next-tuple 1)) 760 | (set! iter-state (module-fn :getindex next-tuple 2))) 761 | (do 762 | (set! last-value nil) 763 | (set! iter-state nil))) 764 | retval))) 765 | 766 | 767 | (defn julia-obj->iterable 768 | ^Iterable [jl-obj] 769 | (reify Iterable 770 | (iterator [this] 771 | (let [first-tuple (module-fn :iterate jl-obj)] 772 | (if first-tuple 773 | (JLIterator. jl-obj 774 | (module-fn :getindex first-tuple 2) 775 | (module-fn :getindex first-tuple 1)) 776 | (JLIterator. jl-obj nil nil)))))) 777 | 778 | (def comp-iface-def (dt-ffi/define-foreign-interface :int32 [:pointer :pointer])) 779 | 780 | 781 | (defn fn->jl 782 | "Convert a clojure function to a Julia void-ptr." 783 | ([clj-fn {:keys [no-coerce?] :as options}] 784 | (errors/when-not-errorf (instance? IFn clj-fn) 785 | "Item %s is not an instance of IFn" 786 | clj-fn) 787 | (let [inst 788 | (dt-ffi/instantiate-foreign-interface 789 | comp-iface-def 790 | (if no-coerce? 791 | clj-fn 792 | (fn [jl-args] 793 | (try 794 | (let [retval (apply clj-fn (julia-proto/julia->jvm 795 | jl-args options))] 796 | ;;Explicit nil check so we can return booleans. 797 | (if (nil? retval) 798 | (julia-ffi/jl_nothing) 799 | (julia-proto/->julia retval))) 800 | (catch Throwable e 801 | (log/warnf e "Clojure fn errored during julia call") 802 | (julia-ffi/jl_nothing)))))) 803 | 804 | fn-ptr (dt-ffi/foreign-interface-instance->c comp-iface-def inst)] 805 | (julia-proto/julia->jvm (julia-ffi/jl_box_voidpointer fn-ptr) 806 | {:gc-obj [clj-fn fn-ptr]}))) 807 | ([clj-fn] 808 | (fn->jl clj-fn nil))) 809 | 810 | 811 | (def fn-wrapper* (delay (-> 812 | (julia-ffi/jl_eval_string "function(fn_ptr::Ptr{Nothing}) return function(a...) return ccall(fn_ptr, Any, (Any,), a) end end") 813 | (julia-proto/julia->jvm nil)))) 814 | 815 | ;;Object default protocol implementation 816 | (extend-type Object 817 | julia-proto/PToJulia 818 | (->julia [item] 819 | (if (instance? IFn item) 820 | (let [jl-fn (fn->jl item) 821 | ^CallableJuliaObject wrapped-fn (@fn-wrapper* jl-fn)] 822 | (CallableJuliaObject. (.handle wrapped-fn) (.kw-fn-handle wrapped-fn) 823 | [jl-fn (.gc-obj wrapped-fn)])) 824 | (errors/throwf "Item %s is not convertible to julia" item)))) 825 | -------------------------------------------------------------------------------- /src/libjulia_clj/impl/collections.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.impl.collections 2 | (:require [libjulia-clj.impl.base :as base] 3 | [libjulia-clj.impl.protocols :as julia-proto] 4 | [libjulia-clj.impl.ffi :as julia-ffi] 5 | [tech.v3.datatype.pprint :as dtype-pp] 6 | [tech.v3.datatype.ffi :as dt-ffi]) 7 | (:import [java.util Map Iterator] 8 | [clojure.lang ILookup ISeq MapEntry] 9 | [com.sun.jna Pointer] 10 | [tech.v3.datatype ObjectReader])) 11 | 12 | 13 | (deftype JuliaDict [^Pointer handle] 14 | julia-proto/PToJulia 15 | (->julia [item] handle) 16 | dt-ffi/PToPointer 17 | (convertible-to-pointer? [this] true) 18 | (->pointer [this] handle) 19 | Map 20 | (size [this] (int (base/module-fn :length handle))) 21 | (isEmpty [this] (boolean (base/module-fn :isempty handle))) 22 | (containsKey [this k] (boolean (base/module-fn :haskey handle k))) 23 | (containsValue [this v] (throw (UnsupportedOperationException. "Unimplemented"))) 24 | (get [this k] (base/module-fn :get handle k)) 25 | (put [this k v] (base/module-fn :setindex! handle v k)) 26 | (remove [this k] (base/module-fn :delete! handle k)) 27 | (putAll [this m] (throw (UnsupportedOperationException.))) 28 | (clear [this] (throw (UnsupportedOperationException.))) 29 | (keySet [this] 30 | (throw (UnsupportedOperationException.))) 31 | (values [this] (throw (UnsupportedOperationException.))) 32 | (entrySet [this] 33 | (throw (UnsupportedOperationException.))) 34 | Iterable 35 | (iterator [this] 36 | (let [pairs (base/module-fn :pairs handle) 37 | base-iterator (.iterator (base/julia-obj->iterable pairs))] 38 | (reify Iterator 39 | (hasNext [iter] (.hasNext base-iterator)) 40 | (next [iter] 41 | (let [next-pair (.next base-iterator)] 42 | (MapEntry. (base/module-fn :getindex next-pair 1) 43 | (base/module-fn :getindex next-pair 2))))))) 44 | Object 45 | (toString [this] 46 | (base/jl-obj->str handle))) 47 | 48 | 49 | (dtype-pp/implement-tostring-print JuliaDict) 50 | 51 | 52 | (defmethod julia-proto/julia->jvm "Dict" 53 | [jl-ptr options] 54 | (base/root-ptr! jl-ptr options) 55 | (JuliaDict. jl-ptr)) 56 | 57 | 58 | (deftype JuliaTuple [^Pointer handle] 59 | julia-proto/PToJulia 60 | (->julia [item] handle) 61 | dt-ffi/PToPointer 62 | (convertible-to-pointer? [this] true) 63 | (->pointer [this] handle) 64 | ObjectReader 65 | (elemwiseDatatype [this] 66 | (-> (base/module-fn :eltype handle) 67 | (julia-ffi/julia-eltype->datatype))) 68 | (lsize [this] (long (base/module-fn :length handle))) 69 | (readObject [this idx] 70 | (base/module-fn :getindex handle (int (inc idx)))) 71 | Object 72 | (toString [this] 73 | (base/jl-obj->str handle))) 74 | 75 | 76 | (dtype-pp/implement-tostring-print JuliaTuple) 77 | 78 | 79 | (defmethod julia-proto/julia->jvm "Tuple" 80 | [jl-ptr options] 81 | (base/root-ptr! jl-ptr options) 82 | (JuliaTuple. jl-ptr)) 83 | -------------------------------------------------------------------------------- /src/libjulia_clj/impl/ffi.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.impl.ffi 2 | "Low level raw JNA bindings and some basic initialization facilities" 3 | (:require [tech.v3.datatype.pprint :as dtype-pp] 4 | [tech.v3.datatype.ffi :as dt-ffi] 5 | [tech.v3.datatype.ffi.size-t :as ffi-size-t] 6 | [tech.v3.datatype.ffi.ptr-value :as ffi-ptr-value] 7 | [tech.v3.datatype.errors :as errors] 8 | [tech.v3.datatype.native-buffer :as native-buffer] 9 | [tech.v3.datatype.casting :as casting] 10 | [tech.v3.datatype :as dt] 11 | [tech.v3.datatype.jvm-map :as jvm-map] 12 | [tech.v3.resource :as resource] 13 | [camel-snake-kebab.core :as csk] 14 | [clojure.string :as s] 15 | [clojure.set :as set] 16 | [clojure.tools.logging :as log])) 17 | 18 | 19 | (set! *warn-on-reflection* true) 20 | 21 | 22 | (defonce julia-library-path* (atom "julia")) 23 | 24 | 25 | (def julia-fns-def 26 | {:jl_parse_opts {:rettype :void 27 | :argtypes [['argcp :pointer] 28 | ['argvp :pointer]] 29 | :doc "parse argc/argv pair"} 30 | :jl_init__threading {:rettype :void 31 | :doc "Initialize julia"} 32 | :jl_is_initialized {:rettype :int32 33 | :doc "Returns 1 if julia is initialized, 0 otherwise"} 34 | :jl_eval_string {:rettype :pointer 35 | :argtypes [['data :string]] 36 | :doc "Eval a string returning a julia object"} 37 | :jl_atexit_hook {:rettype :void 38 | :argytpes [['data :pointer]] 39 | :doc "Register a julia fn to run at program exit"} 40 | :jl_typename_str {:rettype :string 41 | :argtypes [['v :pointer]] 42 | :doc "Return the object typename as a string"} 43 | :jl_typeof_str {:rettype :string 44 | :argtypes [['v :pointer]] 45 | :doc "Return the type of an object as a string"} 46 | :jl_exception_occurred {:rettype :pointer? 47 | :doc "Return the current in-flight exception or nil"} 48 | :jl_symbol {:rettype :pointer 49 | :argtypes [['symbol-name :string]] 50 | :doc "Create a julia symbol from a string"} 51 | :jl_symbol_lookup {:rettype :pointer 52 | :argtypes [['symbol-name :string]] 53 | :doc "Find a julia symbol in the runtime"} 54 | :jl_symbol_n {:rettype :pointer 55 | :argtypes [['symbol-name :pointer] 56 | ['name-len :int64]] 57 | :doc "Create a julia symbol from a string"} 58 | :jl_gensym {:rettype :pointer 59 | :doc "Generate an opaque julia symbol"} 60 | :jl_typeof {:rettype :pointer 61 | :argtypes [['t :pointer]] 62 | :doc "Return the type of a thing as a julia symbol"} 63 | :jl_get_global {:rettype :pointer 64 | :argtypes [['m :pointer] 65 | ['s :pointer]] 66 | :doc "Get reference to module symbol"} 67 | :jl_module_name {:rettype :pointer 68 | :argytpes [['m :pointer]] 69 | :doc "Return the module name as a symbol"} 70 | 71 | :jl_get_module_binding {:doc "Return the module name as a symbol" 72 | :rettype :pointer 73 | :argtypes [['m :pointer] 74 | ['s :pointer]]} 75 | 76 | :jl_module_build_id {:doc "Return the module name as a symbol" 77 | :rettype :int64 78 | :argtypes [['m :pointer]]} 79 | :jl_get_default_sysimg_path {:doc "Get the default sysimg path" 80 | :rettype :string} 81 | 82 | 83 | :jl_subtype {:doc "Return 1 if this is a subtype of that" 84 | :rettype :int32 85 | :argtypes [['a :pointer] 86 | ['b :pointer]]} 87 | :jl_isa {:doc "Return 1 if 't' isa 'x'" 88 | :rettype :int32 89 | ['x :pointer] 90 | ['t :pointer]} 91 | :jl_call {:rettype :pointer 92 | :argtypes [['f :pointer] 93 | ['args :pointer] 94 | ['nargs :int32]] 95 | :doc "Call a julia function with a variable number of arguments"} 96 | :jl_call0 {:rettype :pointer 97 | :argtypes [['f :pointer]] 98 | :doc "Call a julia function with no arguments"} 99 | :jl_call1 {:rettype :pointer 100 | :argtypes [['f :pointer] 101 | ['arg0 :pointer]] 102 | :doc "Call a julia function with 1 argument"} 103 | :jl_call2 {:doc "Call a julia function with 2 arguments" 104 | :rettype :pointer 105 | :argtypes [['f :pointer] 106 | ['a0 :pointer] 107 | ['a1 :pointer]]} 108 | :jl_call3 {:doc "Call a julia function with 3 arguments" 109 | :rettype :pointer 110 | :argtypes [['f :pointer] 111 | ['a0 :pointer] 112 | ['a1 :pointer] 113 | ['a2 :pointer]]} 114 | :jl_box_bool {:doc "Box a boolean value" 115 | :rettype :pointer 116 | :argtypes [['x :int8]]} 117 | 118 | :jl_box_uint8 {:doc "Box a uint8 value" 119 | :rettype :pointer 120 | :argtypes [['x :int8]]} 121 | :jl_box_int8 {:doc "Box a int8 value" 122 | :rettype :pointer 123 | :argtypes [['x :int8]]} 124 | 125 | :jl_box_uint16 {:doc "Box a uint16 value" 126 | :rettype :pointer 127 | :argtypes [['x :int16]]} 128 | :jl_box_int16 {:doc "Box a int16 value" 129 | :rettype :pointer 130 | :argtypes [['x :int16]]} 131 | 132 | :jl_box_uint32 {:doc "Box a uint32 value" 133 | :rettype :pointer 134 | :argtypes [['x :int32]]} 135 | :jl_box_int32 {:doc "Box a int32 value" 136 | :rettype :pointer 137 | :argtypes [['x :int32]]} 138 | 139 | :jl_box_uint64 {:doc "Box a uint64 value" 140 | :rettype :pointer 141 | :argtypes [['x :int64]]} 142 | :jl_box_int64 {:doc "Box a int64 value" 143 | :rettype :pointer 144 | :argtypes [['x :int64]]} 145 | 146 | :jl_box_float32 {:doc "Box a float32 value" 147 | :rettype :pointer 148 | :argtypes [['x :float32]]} 149 | :jl_box_float64 {:doc "Box a float64 value" 150 | :rettype :pointer 151 | :argtypes [['x :float64]]} 152 | 153 | :jl_box_voidpointer {:doc "Box a pointer value to a julia voidptr value" 154 | :rettype :pointer 155 | :argtypes [['x :pointer]]} 156 | 157 | :jl_unbox_bool {:doc "Unbox a boolean" 158 | :rettype :int32 159 | :argtypes [['x :pointer]]} 160 | 161 | :jl_unbox_uint8 {:doc "Unbox a uint8 value" 162 | :rettype :int8 163 | :argtypes [['x :pointer]]} 164 | :jl_unbox_int8 {:doc "Unbox a int8 value" 165 | :rettype :int8 166 | :argtypes [['x :pointer]]} 167 | 168 | :jl_unbox_uint16 {:doc "Unbox a uint16 value" 169 | :rettype :int16 170 | :argtypes [['x :pointer]]} 171 | :jl_unbox_int16 {:doc "Unbox a int16 value" 172 | :rettype :int16 173 | :argtypes [['x :pointer]]} 174 | 175 | :jl_unbox_uint32 {:doc "Unbox a uint32 value" 176 | :rettype :int32 177 | :argtypes [['x :pointer]]} 178 | :jl_unbox_int32 {:doc "Unbox a int32 value" 179 | :rettype :int32 180 | :argtypes [['x :pointer]]} 181 | 182 | :jl_unbox_uint64 {:doc "Unbox a uint64 value" 183 | :rettype :int64 184 | :argtypes [['x :pointer]]} 185 | :jl_unbox_int64 {:doc "Unbox a int64 value" 186 | :rettype :int64 187 | :argtypes [['x :pointer]]} 188 | 189 | :jl_unbox_float32 {:doc "Unbox a float32 value" 190 | :rettype :float32 191 | :argtypes [['x :pointer]]} 192 | :jl_unbox_float64 {:doc "Unbox a float64 value" 193 | :rettype :float64 194 | :argtypes [['x :pointer]]} 195 | 196 | :jl_cstr_to_string {:doc "Convert a jvm string to a julia string" 197 | :rettype :pointer 198 | :argtypes [['arg :string]]} 199 | 200 | :jl_string_ptr {:doc "Convert a julia string to the jvm" 201 | :rettype :string 202 | :argtypes [['arg :pointer]]} 203 | 204 | :jl_array_size {:doc "Return the size of this dimension of the array" 205 | :rettype :size-t 206 | :argtypes [['ary :pointer] 207 | ['d :int32]]} 208 | 209 | :jl_array_rank {:doc "Return the rank of the array" 210 | :rettype :int32 211 | :argtypes [['ary :pointer]]} 212 | 213 | :jl_array_eltype {:doc "Return elemwise datatype of the array" 214 | :rettype :pointer 215 | :argtypes [['ary :pointer]]} 216 | 217 | :jl_array_ptr {:doc "Return a pointer to the elemwise data of the array" 218 | :rettype :pointer 219 | :argtypes [['ary :pointer]]} 220 | 221 | :jl_arrayref {:doc "Return the rank of the array" 222 | :rettype :pointer 223 | :argtypes [['ary :pointer] 224 | ['d :int32]]} 225 | 226 | :jl_apply_tuple_type_v {:doc "Create a new tuple type." 227 | :rettype :pointer 228 | :argtypes [['ary :pointer?] 229 | ['d :size-t]]} 230 | 231 | :jl_apply_type {:doc "Apply a julia type" 232 | :rettype :pointer 233 | :argtypes [['tc :pointer] 234 | ['params :pointer] 235 | ['n :size-t]]} 236 | 237 | :jl_apply_type1 {:doc "Apply a julia type to 1 argument" 238 | :rettype :pointer 239 | :argtypes [['tc :pointer] 240 | ['p1 :pointer]]} 241 | 242 | :jl_apply_type2 {:doc "Apply julia type to 2 arguments" 243 | :rettype :pointer 244 | :argtypes [['tc :pointer] 245 | ['p1 :pointer] 246 | ['p2 :pointer]]} 247 | 248 | :jl_new_structv {:doc "Create a new julia struct from some values" 249 | :rettype :pointer 250 | :argtypes [['datatype :pointer] 251 | ['args :pointer?] 252 | ['n-args :int32]]} 253 | 254 | 255 | :jl_gc_collect {:doc "Force a GC run" 256 | :rettype :void} 257 | 258 | :jl_gc_enable {:doc "Enable/disable the gc - 1 is enabled, 0 is disabled" 259 | :rettype :int32 260 | :argtypes [['enable :int32]]} 261 | 262 | :jl_gc_is_enabled {:doc "Return 1 if the julia gc is enabled" 263 | :rettype :int32} 264 | 265 | }) 266 | 267 | 268 | ;;The symbols we need from the shared library 269 | (def julia-symbols-def ["jl_core_module" 270 | "jl_base_module" 271 | "jl_bool_type" 272 | "jl_symbol_type" 273 | "jl_string_type" 274 | "jl_bool_type" 275 | "jl_int8_type" 276 | "jl_uint8_type" 277 | "jl_int16_type" 278 | "jl_uint16_type" 279 | "jl_int32_type" 280 | "jl_uint32_type" 281 | "jl_int64_type" 282 | "jl_uint64_type" 283 | "jl_float32_type" 284 | "jl_float64_type"]) 285 | 286 | 287 | (defonce julia (dt-ffi/library-singleton #'julia-fns-def #'julia-symbols-def nil)) 288 | (dt-ffi/library-singleton-reset! julia) 289 | (defn set-library-instance! 290 | [lib-instance] 291 | (dt-ffi/library-singleton-set-instance! julia lib-instance)) 292 | 293 | 294 | (defn- windows-os? 295 | [] 296 | (-> (System/getProperty "os.name") 297 | (.toLowerCase) 298 | (.contains "windows"))) 299 | 300 | 301 | (defn initialize! 302 | "Load the libjulia library. This does no further initialization, so it is necessary 303 | to the call 'init-process-options' and then 'jl_init__threading' at which point 304 | 'jl_is_initialized' should be true." 305 | [& [options]] 306 | (let [jh (or (:julia-home options) (System/getenv "JULIA_HOME")) 307 | _ (errors/when-not-errorf jh "JULIA_HOME is unset") 308 | jdirs ["lib" "bin"] 309 | jpaths (map #(-> (java.nio.file.Paths/get 310 | jh (into-array String [% (System/mapLibraryName 311 | (if (windows-os?) 312 | ;;julia is libXXX nomenclature on 313 | ;;all operating systems. 314 | "libjulia" 315 | "julia"))])) 316 | (.toString)) 317 | jdirs) 318 | found-dir (-> (filter #(.exists (java.io.File. ^String %)) jpaths) 319 | first)] 320 | (errors/when-not-errorf found-dir 321 | "Julia shared library not found at paths\n%s 322 | - is JULIA_HOME set incorrectly?", (interpose jpaths "\n")) 323 | (dt-ffi/library-singleton-set! julia found-dir) 324 | :ok)) 325 | 326 | 327 | (defn find-fn [fn-name] (dt-ffi/library-singleton-find-fn julia fn-name)) 328 | 329 | (dt-ffi/define-library-functions libjulia-clj.impl.ffi/julia-fns-def find-fn nil) 330 | 331 | (defn jl_symbol_name 332 | ^String [ptr] 333 | (dt-ffi/c->string ptr)) 334 | 335 | 336 | (defn jl_get_function 337 | "Find a julia function in a julia module" 338 | [module fn-name] 339 | (jl_get_global module (jl_symbol fn-name))) 340 | 341 | 342 | (defn native-addr 343 | ^long [data] 344 | (-> (dt/as-native-buffer data) 345 | (.address))) 346 | 347 | 348 | (defn init-process-options 349 | "Must be called before jl_init__threading. 350 | 351 | Options are: 352 | * `:enable-signals?` - true to enable julia signal handling. If false you must disable 353 | threads (set n-threads to 1). If using signals you must preload libjsig.so - see 354 | documentation. Defaults to false. 355 | * `:n-threads` - Set the number of threads to use with julia. Defaults to nil which means 356 | unless JULIA_NUM_THREADS is set signals are disabled." 357 | [& [{:keys [enable-signals? n-threads] 358 | :or {enable-signals? false}}]] 359 | (resource/stack-resource-context 360 | (let [n-threads (cond 361 | (= n-threads -1) (.availableProcessors (Runtime/getRuntime)) 362 | (nil? n-threads) (when-let [env-val (System/getenv "JULIA_NUM_THREADS")] 363 | (Integer/parseInt env-val)) 364 | (= n-threads :auto) :auto 365 | :else (int n-threads)) 366 | enable-signals? (if (boolean? enable-signals?) 367 | enable-signals? 368 | (or enable-signals? (not (nil? n-threads)))) 369 | opt-strs [(format "--handle-signals=%s" (if enable-signals? "yes" "no")) 370 | "--threads" (str (or n-threads 1))] 371 | ptr-type (ffi-size-t/lower-ptr-type :pointer) 372 | str-ptrs (mapv (comp native-addr dt-ffi/string->c) opt-strs) 373 | argv (dt/make-container :native-heap ptr-type str-ptrs) 374 | argvp (dt/make-container :native-heap ptr-type [(native-addr argv)]) 375 | argcp (dt/make-container :native-heap ptr-type [(count opt-strs)])] 376 | (log/infof "julia library arguments: %s" opt-strs) 377 | (jl_parse_opts argcp argvp) 378 | (argcp 0)))) 379 | 380 | (defonce julia-symbols (jvm-map/concurrent-hash-map)) 381 | 382 | (defn find-julia-symbol 383 | ^tech.v3.datatype.ffi.Pointer [sym-name] 384 | (jvm-map/compute-if-absent! julia-symbols sym-name 385 | (fn [& args] 386 | (-> (dt-ffi/library-singleton-find-symbol julia sym-name) 387 | (dt-ffi/->pointer))))) 388 | 389 | 390 | (defn find-deref-julia-symbol 391 | ^tech.v3.datatype.ffi.Pointer [sym-name] 392 | (let [ptr-ptr (-> (find-julia-symbol sym-name) 393 | (.address)) 394 | buf-dtype (ffi-size-t/lower-ptr-type :pointer) 395 | nbuf (native-buffer/wrap-address ptr-ptr (casting/numeric-byte-width buf-dtype) 396 | buf-dtype :little-endian nil)] 397 | ;;deref the ptr 398 | (tech.v3.datatype.ffi.Pointer. (nbuf 0)))) 399 | 400 | 401 | (defn jl_main_module 402 | [] 403 | (find-deref-julia-symbol "jl_main_module")) 404 | 405 | (defn jl_core_module 406 | [] 407 | (find-deref-julia-symbol "jl_core_module")) 408 | 409 | (defn jl_base_module 410 | [] 411 | (find-deref-julia-symbol "jl_base_module")) 412 | 413 | (defn jl_top_module 414 | [] 415 | (find-deref-julia-symbol "jl_top_module")) 416 | 417 | (defn jl_nothing 418 | [] 419 | (find-deref-julia-symbol "jl_nothing")) 420 | 421 | 422 | (def jl-type->datatype 423 | {:jl-bool-type :boolean 424 | :jl-int8-type :int8 425 | :jl-uint8-type :uint8 426 | :jl-int16-type :int16 427 | :jl-uint16-type :uint16 428 | :jl-int32-type :int32 429 | :jl-uint32-type :uint32 430 | :jl-int64-type :int64 431 | :jl-uint64-type :uint64 432 | :jl-float32-type :float32 433 | :jl-float64-type :float64 434 | :jl-string-type :string 435 | :jl-symbol-type :symbol}) 436 | 437 | 438 | (def datatype->jl-type 439 | (set/map-invert jl-type->datatype)) 440 | 441 | (defonce type-ptr->kwd (jvm-map/concurrent-hash-map)) 442 | (defonce kwd->type-ptr (jvm-map/concurrent-hash-map)) 443 | 444 | (defn add-library-julia-type! 445 | ([type-symbol-name clj-kwd] 446 | (let [type-ptr (find-deref-julia-symbol type-symbol-name)] 447 | (jvm-map/compute-if-absent! type-ptr->kwd type-ptr (constantly clj-kwd)) 448 | (jvm-map/compute-if-absent! kwd->type-ptr clj-kwd (constantly type-ptr)) 449 | type-ptr)) 450 | ([type-symbol-name] 451 | (add-library-julia-type! type-symbol-name (keyword type-symbol-name)))) 452 | 453 | 454 | (defn initialize-type-map! 455 | [] 456 | (doseq [[typename clj-kwd] jl-type->datatype] 457 | (add-library-julia-type! (.replace (name typename) "-" "_") clj-kwd)) 458 | :ok) 459 | 460 | 461 | (defn lookup-library-type 462 | [type-kwd] 463 | (if-let [retval (get kwd->type-ptr type-kwd)] 464 | retval 465 | (add-library-julia-type! (.replace (name (get datatype->jl-type type-kwd type-kwd)) 466 | "-" "_") type-kwd))) 467 | 468 | 469 | (defn jl-ptr->typename 470 | "If the typename is a known typename, return the keyword typename. 471 | Else return typeof_str." 472 | [item-ptr] 473 | (when (not= 0 (ffi-ptr-value/ptr-value? item-ptr)) 474 | (if-let [retval (get type-ptr->kwd (jl_typeof item-ptr))] 475 | retval 476 | (let [^String type-str (jl_typeof_str item-ptr)] 477 | (if (.startsWith type-str "#") 478 | :jl-function 479 | type-str))))) 480 | 481 | 482 | (defn julia-eltype->datatype 483 | [eltype] 484 | (get type-ptr->kwd eltype :object)) 485 | 486 | 487 | (defmacro with-disabled-julia-gc 488 | "Run a block of code with the julia garbage collector temporarily disabled." 489 | [& body] 490 | `(let [cur-enabled# (jl_gc_is_enabled)] 491 | (jl_gc_enable 0) 492 | (try 493 | ~@body 494 | (finally 495 | (jl_gc_enable cur-enabled#))))) 496 | -------------------------------------------------------------------------------- /src/libjulia_clj/impl/gc.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.impl.gc 2 | "Binding of various sort of gc semantics optimized specifically for 3 | libpython-clj. For general bindings, see tech.resource" 4 | (:import [java.util.concurrent ConcurrentHashMap ConcurrentLinkedDeque] 5 | [java.lang.ref ReferenceQueue] 6 | [tech.resource GCReference])) 7 | 8 | 9 | (set! *warn-on-reflection* true) 10 | 11 | 12 | (defonce ^:dynamic *stack-gc-context* nil) 13 | (defn stack-context 14 | ^ConcurrentLinkedDeque [] 15 | *stack-gc-context*) 16 | 17 | 18 | (defonce reference-queue-var (ReferenceQueue.)) 19 | (defn reference-queue 20 | ^ReferenceQueue [] 21 | reference-queue-var) 22 | 23 | 24 | (defonce ptr-set-var (ConcurrentHashMap/newKeySet)) 25 | (defn ptr-set 26 | ^java.util.Set [] 27 | ptr-set-var) 28 | 29 | 30 | (defn track 31 | [item dispose-fn] 32 | (let [ptr-val (GCReference. item (reference-queue) (fn [ptr-val] 33 | (.remove (ptr-set) ptr-val) 34 | (dispose-fn))) 35 | ^ConcurrentLinkedDeque stack-context (stack-context)] 36 | ;;We have to keep track of the pointer. If we do not the pointer gets gc'd then 37 | ;;it will not be put on the reference queue when the object itself is gc'd. 38 | ;;Nice little gotcha there. 39 | (if stack-context 40 | (.add stack-context ptr-val) 41 | ;;Ensure we don't lose track of the weak reference. If it gets cleaned up 42 | ;;the gc system will fail. 43 | (.add (ptr-set) ptr-val)) 44 | item)) 45 | 46 | 47 | (defn clear-reference-queue 48 | [] 49 | (when-let [next-ref (.poll (reference-queue))] 50 | (.run ^Runnable next-ref) 51 | (recur))) 52 | 53 | 54 | (defn clear-stack-context 55 | [] 56 | (when-let [next-ref (.pollLast (stack-context))] 57 | (.run ^Runnable next-ref) 58 | (recur))) 59 | 60 | 61 | (defmacro with-stack-context 62 | [& body] 63 | `(with-bindings {#'*stack-gc-context* (ConcurrentLinkedDeque.)} 64 | (try 65 | ~@body 66 | (finally 67 | (clear-stack-context))))) 68 | -------------------------------------------------------------------------------- /src/libjulia_clj/impl/protocols.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.impl.protocols 2 | "Protocols and multimethod definitions for the base julia binding. 3 | Protocols get completely rebound (thus loosing all older bindings) 4 | when recompiled so it is often a good idea to separate them out into 5 | their own file." 6 | (:require [libjulia-clj.impl.ffi :as julia-ffi])) 7 | 8 | 9 | (defprotocol PToJulia 10 | (->julia [item])) 11 | 12 | 13 | (defprotocol PJuliaKWFn 14 | "Implementation protocol to get the julia kw fn for a given fn." 15 | (kw-fn [item])) 16 | 17 | 18 | (defmulti julia->jvm 19 | "Convert a julia value to the JVM. 20 | 21 | Options: 22 | 23 | * `:unrooted?` - defaults to false. When true, value is not rooted and thus the 24 | julia GC may remove the value any point in your program's execution most 25 | likely resulting in a crash. 26 | * `:log-level` - When anything at all, jvm-gc<->julia-gc bindings will emit messages 27 | when an object is bound or unbound. 28 | * `:gc-obj` - Have the new julia object maintain a reference to this object. Only 29 | used for very special cases." 30 | (fn [julia-val options] 31 | (let [dispatch (julia-ffi/jl-ptr->typename julia-val)] 32 | dispatch))) 33 | -------------------------------------------------------------------------------- /src/libjulia_clj/java_api.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.java-api 2 | "Java Users - Use the -aot postfixed version of the jar on clojars. Then import 3 | `libjulia_clj.java_api`. Each method in this namespace is exposed as a public static 4 | method on the java_api class so for instance `-initialize` is exposed as: 5 | 6 | ```java 7 | java_api.initialize(options); 8 | ```" 9 | (:import [clojure.java.api Clojure] 10 | [java.util Map Map$Entry] 11 | [java.util.function Supplier]) 12 | (:gen-class 13 | :name libjulia_clj.java_api 14 | :main false 15 | :methods [#^{:static true} [initialize [java.util.Map] Object] 16 | #^{:static true} [runString [String] Object] 17 | #^{:static true} [inJlContext [java.util.function.Supplier] Object] 18 | #^{:static true} [namedTuple [java.util.Map] Object] 19 | #^{:static true} [createArray [String Object Object] Object] 20 | #^{:static true} [arrayToJVM [Object] java.util.Map]])) 21 | 22 | 23 | (set! *warn-on-reflection* true) 24 | 25 | 26 | (defonce requires* (delay 27 | (let [require (Clojure/var "clojure.core" "require")] 28 | (require (Clojure/read "tech.v3.datatype")) 29 | (require (Clojure/read "libjulia-clj.julia")) 30 | (require (Clojure/read "tech.v3.tensor"))))) 31 | 32 | 33 | (defn -initialize 34 | "Initialize the julia interpreter. See documentation for [[libjulia-clj.julia/initialize!]]. 35 | Options may be null or must be a map of string->value for one of the supported initialization 36 | values. JULIA_HOME can be set by the user by setting the key \"julia-home\" in the 37 | options map to the desired value and this will supercede the environment variable 38 | version. 39 | 40 | Example: 41 | 42 | ```clojure 43 | (japi/-initialize (jvm-map/hash-map {\"n-threads\" 8})) 44 | ```" 45 | [options] 46 | @requires* 47 | ((Clojure/var "libjulia-clj.julia" "initialize!") 48 | (->> options 49 | (map (fn [^Map$Entry entry] 50 | [(keyword (.getKey entry)) 51 | (.getValue entry)])) 52 | (into {})))) 53 | 54 | 55 | (defn -runString 56 | "Run a string in Julia returning a jvm object if the return value is simple or 57 | a julia object if not. The returned object will have a property overloaded 58 | toString method for introspection." 59 | [^String data] 60 | ((Clojure/var "libjulia-clj.julia" "jl") data)) 61 | 62 | 63 | (defn -inJlContext 64 | "Execute a function in a context where all julia objects created will be released 65 | just after the function returns. The function must return pure JVM data - it cannot 66 | return a reference to a julia object." 67 | [^Supplier fn] 68 | ((Clojure/var "libjulia-clj.julia" "in-jl-ctx") fn)) 69 | 70 | 71 | (defn -namedTuple 72 | "Create a julia named tuple. This is required for calling keyword functions. The 73 | path for calling keyword functions looks something like: 74 | 75 | * `data` - must be an implementation of java.util.Map with strings as keys. 76 | 77 | ```clojure 78 | (let [add-fn (jl \"function teste(a;c = 1.0, b = 2.0) 79 | a+b+c 80 | end\") 81 | kwfunc (jl \"Core.kwfunc\") 82 | add-kwf (kwfunc add-fn)] 83 | (is (= 38.0 (add-kwf (jl/named-tuple {'b 10 'c 20}) 84 | add-fn 85 | 8.0))) 86 | (is (= 19.0 (add-kwf (jl/named-tuple {'b 10}) 87 | add-fn 88 | 8.0))) 89 | (is (= 11.0 (add-kwf (jl/named-tuple) 90 | add-fn 91 | 8.0))) 92 | 93 | (is (= 38.0 (add-fn 8.0 :b 10 :c 20))) 94 | (is (= 19.0 (add-fn 8 :b 10))) 95 | (is (= 11.0 (add-fn 8)))) 96 | ```" 97 | [^Map data] 98 | ((Clojure/var "libjulia-clj.julia" "named-tuple") data)) 99 | 100 | 101 | (defn -createArray 102 | "Return julia array out of the tuple of datatype, shape, and data. 103 | 104 | * `datatype` - must be one of the strings `[\"int8\" \"uint8\" \"int16\" \"uin16\" 105 | \"int32\" \"uint32\" \"int64\" \"uint64\" \"float32\" \"float64\"]. 106 | * `shape` - an array or implementation of java.util.List that specifies the row-major 107 | shape intended of the data. Note that Julia is column-major so this data will appear 108 | transposed when printed via Julia. 109 | * `data` may be a java array or an implementation of java.util.List. Ideally data is 110 | of the same datatype as data." 111 | [datatype shape data] 112 | (let [datatype (keyword datatype) 113 | reshape (Clojure/var "tech.v3.tensor" "reshape") 114 | ->array (Clojure/var "libjulia-clj.julia" "->array")] 115 | (-> ((Clojure/var "tech.v3.tensor" "->tensor") data :datatype (keyword datatype)) 116 | (reshape shape) 117 | (->array)))) 118 | 119 | 120 | (defn -arrayToJVM 121 | "Returns a map with three keys - shape, datatype, and data. Shape is an integer array 122 | that is the reverse of the julia shape, datatype is a string denoting one of the supported 123 | datatypes, and data is a primitive array of data." 124 | [jlary] 125 | (let [tens-data ((Clojure/var "tech.v3.tensor" "as-tensor") jlary) 126 | tens-shape ((Clojure/var "tech.v3.datatype" "shape") tens-data) 127 | n-dims (count tens-shape)] 128 | {"shape" ((Clojure/var "tech.v3.datatype" "->int-array") tens-shape) 129 | "datatype" (name ((Clojure/var "tech.v3.datatype" "elemwise-datatype") tens-data)) 130 | "data" ((Clojure/var "tech.v3.datatype" "->array") tens-data)})) 131 | -------------------------------------------------------------------------------- /src/libjulia_clj/julia.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.julia 2 | "Public API for Julia functionality. Initialize! must be called before any other functions 3 | and there are a choice of garbgage collection mechanisms (see topic in docs). 4 | is probably a bad idea to call Julia from multiple threads so access to julia 5 | should be from one thread or protected via a mutex. 6 | 7 | Example: 8 | 9 | ```clojure 10 | user> (require '[libjulia-clj.julia :as julia]) 11 | nil 12 | user> (julia/initialize!) 13 | :ok 14 | user> (def ones-fn (julia/jl \"Base.ones\")) 15 | Nov 27, 2020 12:39:39 PM clojure.tools.logging$eval6611$fn__6614 invoke 16 | INFO: Rooting address 0x00007F3E092D6E40 17 | #'user/ones-fn 18 | user> (def jl-ary (ones-fn 3 4)) 19 | 20 | Nov 27, 2020 12:40:02 PM clojure.tools.logging$eval6611$fn__6614 invoke 21 | INFO: Rooting address 0x00007F3DFF9C92A0 22 | #'user/jl-ary 23 | user> jl-ary 24 | [1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0] 25 | user> (type jl-ary) 26 | libjulia_clj.impl.base.JuliaArray 27 | user> (require '[tech.v3.tensor :as dtt]) 28 | nil 29 | user> ;;zero-copy 30 | user> (def tens (dtt/as-tensor jl-ary)) 31 | #'user/tens 32 | user> tens 33 | #tech.v3.tensor[3 4] 34 | [[1.000 1.000 1.000 1.000] 35 | [1.000 1.000 1.000 1.000] 36 | [1.000 1.000 1.000 1.000]] 37 | user> (dtt/mset! tens 0 25) 38 | #tech.v3.tensor[3 4] 39 | [[25.00 25.00 25.00 25.00] 40 | [1.000 1.000 1.000 1.000] 41 | [1.000 1.000 1.000 1.000]] 42 | user> jl-ary 43 | [25.0 25.0 25.0 25.0; 1.0 1.0 1.0 1.0; 1.0 1.0 1.0 1.0] 44 | ```" 45 | (:require [libjulia-clj.impl.base :as base] 46 | [libjulia-clj.impl.protocols :as julia-proto] 47 | [libjulia-clj.impl.ffi :as julia-ffi] 48 | [libjulia-clj.impl.gc :as julia-gc] 49 | ;;pure language extensions for now. 50 | [libjulia-clj.impl.collections] 51 | [tech.v3.datatype :as dtype] 52 | [tech.v3.tensor :as dtt] 53 | [tech.v3.datatype.export-symbols :refer [export-symbols]] 54 | [tech.v3.datatype.errors :as errors]) 55 | (:refer-clojure :exclude [struct])) 56 | 57 | 58 | (export-symbols libjulia-clj.impl.base 59 | initialize! 60 | apply-tuple-type 61 | apply-type 62 | struct 63 | tuple 64 | named-tuple 65 | call-function 66 | call-function-kw) 67 | 68 | 69 | (defn jl 70 | "Eval a string in julia returning the result. If the result is callable in Julia, 71 | the result will be callable in Clojure." 72 | ([str-data options] 73 | (let [retval (julia-ffi/jl_eval_string str-data)] 74 | (base/check-last-error) 75 | (julia-proto/julia->jvm retval nil))) 76 | ([str-data] 77 | (jl str-data nil))) 78 | 79 | 80 | (defn typeof 81 | "Get the julia type of an item." 82 | [item] 83 | (when item 84 | (let [retval (julia-ffi/jl_typeof item)] 85 | (base/check-last-error) 86 | (julia-proto/julia->jvm retval nil)))) 87 | 88 | 89 | (defn ^{:doc (:doc (meta #'base/apply-tuple-type))} 90 | apply-tuple-type 91 | [& args] 92 | (base/apply-tuple-type args)) 93 | 94 | 95 | (defn ^{:doc (:doc (meta #'base/apply-type))} apply-type 96 | [jl-type & args] 97 | (base/apply-type jl-type args)) 98 | 99 | 100 | (defn ^{:doc (:doc (meta #'base/struct))} struct 101 | [struct-type & args] 102 | (base/struct struct-type args)) 103 | 104 | 105 | (defn ^{:doc (:doc (meta #'base/tuple))} tuple 106 | [& args] 107 | (base/tuple args)) 108 | 109 | 110 | (defn cycle-gc! 111 | "Call periodically to release rooted Julia objects. We root return values if they 112 | aren't primitives and then hook them to the jvm GC such that they get put in a queue 113 | once they aren't reachable by the program. This call clears that queue and unroots 114 | them thus notifying the Julia GC that they aren't reachable any more. 115 | 116 | In the future point this may be done for you." 117 | [] 118 | (julia-gc/clear-reference-queue)) 119 | 120 | 121 | (defmacro with-stack-context 122 | "Run code in which all objects created within this context will be released once 123 | the stack unwinds where released means unrooted and thus potentially available to 124 | the next julia garbage collection run." 125 | [& body] 126 | `(julia-gc/with-stack-context 127 | ~@body)) 128 | 129 | 130 | (defn ^:no-doc in-jl-ctx 131 | [^java.util.function.Supplier supplier] 132 | (with-stack-context 133 | (-> (.get supplier) 134 | (julia-proto/julia->jvm nil)))) 135 | 136 | 137 | (defn set-julia-gc-root-log-level! 138 | "Set the log level to use when rooting/unrooting julia objects. We automatically 139 | root julia objects in a julia id dictionary that we expose to JVM objects. 140 | This code isn't yet perfect, so sometimes it is worthwhile to log all 141 | root/unroot operations. 142 | 143 | Valid log levels are valid log levels for 144 | [`clojure/tools.logging`](http://clojure.github.io/tools.logging/)." 145 | [log-level] 146 | (reset! base/julia-gc-root-log-level* log-level)) 147 | 148 | 149 | (defonce ^{:doc "Resolves to the base julia array datatype"} 150 | base-ary-type* (delay (jl "Base.Array"))) 151 | 152 | (defonce ^{:doc "Resolves to the julia undef type"} 153 | jl-undef* (delay (jl "Base.undef"))) 154 | 155 | 156 | (defonce zeros* (delay (jl "zeros"))) 157 | 158 | 159 | (defn new-array 160 | "Create a new, uninitialized dense julia array. Because Julia is column major 161 | while tech.v3.datatype is row major, the returned array's size will be the 162 | reverse of dtype/shape as that keeps the same in memory alignment of data." 163 | ([shape datatype] 164 | (let [jl-dtype (julia-ffi/lookup-library-type datatype)] 165 | (apply @zeros* jl-dtype shape))) 166 | ([shape] 167 | (new-array shape :float64))) 168 | 169 | 170 | (defn ->array 171 | "Create a new dense julia array that is the 'transpose' of the input tensor. 172 | Transposing ensures the memory alignment matches as Julia is column-major 173 | while datatype is row-major." 174 | [tens] 175 | (let [dtype (dtype/elemwise-datatype tens) 176 | tens-shape (dtype/shape tens) 177 | retval (new-array (reverse tens-shape) dtype)] 178 | (dtype/copy! tens retval) 179 | retval)) 180 | -------------------------------------------------------------------------------- /src/libjulia_clj/modules/Base.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.modules.Base 2 | (:require [libjulia-clj.impl.base :as base]) 3 | (:refer-clojure :exclude [* + - < <= == > >= 4 | cat conj conj! count denominator empty first filter float flush gensym hash 5 | keys last map max merge iterate macroexpand methods min mod numerator 6 | peek pop! print println rand range rationalize read reduce rem repeat 7 | replace reverse sort time vec get identity])) 8 | 9 | (base/initialize!) 10 | 11 | 12 | (base/define-module-publics 13 | "Base" 14 | ;;Remap names to avoid compilation errors 15 | {"def" "jl-def" 16 | "'" "quote" 17 | ":" "colon" 18 | "/" "div" 19 | "//" "divdiv" 20 | "div" "divv" 21 | "Enum" "jl-Enum"}) 22 | -------------------------------------------------------------------------------- /src/libjulia_clj/modules/Core.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.modules.Core 2 | (:require [libjulia-clj.impl.base :as base]) 3 | (:refer-clojure :exclude [eval])) 4 | 5 | 6 | (base/initialize!) 7 | 8 | 9 | (base/define-module-publics 10 | "Core" 11 | {"AssertionError" "jl-AssertionError" 12 | "Exception" "jl-Exception" 13 | "Integer" "jl-Integer" 14 | "Number" "jl-Number" 15 | "OutOfMemoryError" "jl-OutOfMemoryError" 16 | "StackOverflowError" "jl-StackOverflowError" 17 | "String" "jl-String"}) 18 | -------------------------------------------------------------------------------- /src/libjulia_clj/modules/LinearAlgebra.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.modules.LinearAlgebra 2 | (:require [libjulia-clj.impl.base :as base]) 3 | (:refer-clojure :exclude [/ cond])) 4 | 5 | 6 | (base/initialize!) 7 | 8 | 9 | (base/define-module-publics 10 | "import LinearAlgebra;LinearAlgebra" 11 | ;;Remap names to avoid compilation errors 12 | {}) 13 | -------------------------------------------------------------------------------- /test/libjulia_clj/api_test.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.api-test 2 | (:require [libjulia-clj.java-api :as japi] 3 | [tech.v3.datatype.jvm-map :as jvm-map] 4 | [clojure.test :refer [deftest is]])) 5 | 6 | 7 | (deftest java-api-test 8 | (japi/-initialize (jvm-map/hash-map {"n-threads" 8})) 9 | (is (= 4 (japi/-runString "2 + 2"))) 10 | (let [tuple (japi/-namedTuple {"a" 1 "b" 2}) 11 | getindex (japi/-runString "getindex")] 12 | (is (instance? clojure.lang.IFn getindex)) 13 | (is (= 1 (getindex tuple 1))) 14 | (is (= 2 (getindex tuple 2)))) 15 | (let [ary (japi/-createArray "int32" [2 3] (range 6))] 16 | (japi/-arrayToJVM ary))) 17 | -------------------------------------------------------------------------------- /test/libjulia_clj/julia_test.clj: -------------------------------------------------------------------------------- 1 | (ns libjulia-clj.julia-test 2 | (:require [libjulia-clj.julia :refer [jl] :as jl] 3 | [libjulia-clj.impl.base :as jl-base] 4 | [tech.v3.datatype :as dtype] 5 | [tech.v3.tensor :as dtt] 6 | [clojure.test :refer [deftest is]])) 7 | 8 | ;;init only once 9 | 10 | (defonce init* (delay (jl/initialize!))) 11 | 12 | @init* 13 | 14 | (jl/set-julia-gc-root-log-level! :info) 15 | 16 | 17 | (deftest julia-test 18 | (let [ones-fn (jl "Base.ones") 19 | jl-ary (ones-fn 3 4) 20 | tens-data (dtt/as-tensor jl-ary)] 21 | (dtt/mset! tens-data 0 25) 22 | ;;Make sure the both gc's are playing nice 23 | ;;with each other. 24 | (System/gc) 25 | (jl/cycle-gc!) 26 | ;;datatype is transpose of julia 27 | (is (= [4 3] (dtype/shape jl-ary))) 28 | (is (= [[25.0 25.0 25.0] 29 | [1.0 1.0 1.0] 30 | [1.0 1.0 1.0] 31 | [1.0 1.0 1.0]] 32 | (mapv vec (dtt/as-tensor jl-ary))))) 33 | (System/gc) 34 | (jl/cycle-gc!)) 35 | 36 | 37 | (deftest kw-manual-args-test 38 | (jl/with-stack-context 39 | (let [add-fn (jl "function teste(a;c = 1.0, b = 2.0) 40 | a+b+c 41 | end") 42 | kwfunc (jl "Core.kwfunc") 43 | add-kwf (kwfunc add-fn)] 44 | (is (= 38.0 (add-kwf (jl/named-tuple {'b 10 'c 20}) 45 | add-fn 46 | 8.0))) 47 | (is (= 19.0 (add-kwf (jl/named-tuple {'b 10}) 48 | add-fn 49 | 8.0))) 50 | (is (= 11.0 (add-kwf (jl/named-tuple) 51 | add-fn 52 | 8.0))) 53 | 54 | (is (= 38.0 (add-fn 8.0 :b 10 :c 20))) 55 | (is (= 19.0 (add-fn 8 :b 10))) 56 | (is (= 11.0 (add-fn 8)))))) 57 | 58 | 59 | (deftest stack-context 60 | (jl/with-stack-context 61 | (let [jl-data (jl/new-array [2 2] :float32) 62 | size (jl "size")] 63 | (= [2 2] (vec (size jl-data))))) 64 | (jl/with-stack-context 65 | (let [tdata (dtt/->tensor (partition 3 (range 9)) :datatype :int32) 66 | jl-ary (jl/->array tdata) 67 | ary-data (dtype/make-container :int32 jl-ary)] 68 | (is (= (vec (range 9)) 69 | (vec ary-data))))) 70 | (jl/with-stack-context 71 | (let [tdata (dtt/->tensor (partition 3 (range 9)) :datatype :int32) 72 | jl-ary (jl/->array tdata) 73 | id-fn (jl "identity") 74 | ;;This one should not get rooted 75 | jl-ary2 (id-fn jl-ary)] 76 | (is (= (vec (range 9)) 77 | (vec (dtype/make-container :int64 jl-ary2))))))) 78 | -------------------------------------------------------------------------------- /topics/gc.md: -------------------------------------------------------------------------------- 1 | # JVM/Julia Garbage Collection Integration 2 | 3 | Both the JVM and julia rely on garbage collection in order to decided 4 | when and how to cleanup objects. This means that we need a mechanism 5 | to ensure that objects visible across language boundaries are not cleaned 6 | up prematurely. 7 | 8 | 9 | ## Julia Objects in the JVM 10 | 11 | 12 | When a new julia object is returned from a function we first check 13 | if this is a primitive or atomic type - numbers, symbols, strings. 14 | If so, we convert the value into the JVM immediately. Else we 15 | return a JVM object and `root` the julia object in a datastructure 16 | we declared to julia. 17 | 18 | 19 | The user has a choice to link the Julia object to the JVM's GC mechanism 20 | such that when the JVM decided the object is no longer reachable we will 21 | then unroot the Julia object. This is default and requires the user 22 | to periodically call 23 | [`cycle-gc!`](https://github.com/cnuernber/libjulia-clj/blob/4bf826aa9651c848985e8e13c5d392db4da26d69/src/libjulia_clj/julia.clj#L112) 24 | in order to unroot objects as the JVM's callback happens in another thread and 25 | thus we can only mark objects that should be unrooted automatically. The 26 | gc based unrooting needs to be cooperative at this point to ensure it happens 27 | in whichever thread is currently using Julia. 28 | 29 | 30 | There is also a stack based mechanism, 31 | [`with-stack-context`](https://github.com/cnuernber/libjulia-clj/blob/4bf826aa9651c848985e8e13c5d392db4da26d69/src/libjulia_clj/julia.clj#L123) 32 | by which we can ensure that Julia objects rooted within a given stack 33 | scope are unrooted when programmatic flow exits that scope either 34 | normally or via an exception. 35 | 36 | 37 | ## JVM Objects in Julia 38 | 39 | 40 | - TODO - not sure if this is very necessary or the best way to handle this. 41 | Currently you can pass functions to Julia but this isn't very fleshed 42 | out and it is most likely not bullet-proof. If they are called from tasks 43 | then there is a decent chance they will be silently ignored. Most likely 44 | you, from the JVM side, will need to ensure they do not leave JVM scope 45 | while you think they are in scope in Julia. 46 | -------------------------------------------------------------------------------- /topics/images/julia.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cnuernber/libjulia-clj/42685f6bc13d141522783efbf827d70c4d895336/topics/images/julia.png -------------------------------------------------------------------------------- /topics/signals.md: -------------------------------------------------------------------------------- 1 | # Julia, The JVM, and Signals 2 | 3 | Julia and the JVM both rely on an operating concept called signals 4 | which are a simple method of IPC. If you aren't familiar with them 5 | it probably isn't necessary to get familiar right now but it is necessary 6 | in order to use libjulia-clj for you to understand how the signal mechanism 7 | in these two systems interact and what happens when they interact poorly. 8 | 9 | 10 | ## Two Worlds Collide 11 | 12 | When using both Julia and the JVM in the same process you are likely to run into 13 | instances where, during their normal course of operation their respective usage of 14 | signals conflict. For instance, the JVM uses `SIGSEGV` during it's normal course of 15 | operation and if the Julia handler for `SIGSEGV` is installed then things like a 16 | normal JVM garbage collection run can cause the process to unceremoniously exit: 17 | 18 | ```clojure 19 | user> (require '[libjulia-clj.julia :as julia]) 20 | nil 21 | user> (julia/initialize! {:signals-enabled? true}) 22 | 16:14:40.838 [nRepl-session-926e4a65-853b-40b4-a182-0f4b8a0cdfa3] INFO libjulia-clj.impl.base - Attempting to initialize Julia at /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so 23 | 16:14:40.875 [nRepl-session-926e4a65-853b-40b4-a182-0f4b8a0cdfa3] INFO tech.v3.jna.base - Library /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so found at [:system "/home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so"] 24 | 16:14:40.881 [nRepl-session-926e4a65-853b-40b4-a182-0f4b8a0cdfa3] INFO libjulia-clj.impl.jna - Julia startup options: n-threads null, signals? true 25 | :ok 26 | user> (System/gc) 27 | 28 | *** Closed on Mon Dec 14 16:14:45 2020 *** 29 | ``` 30 | 31 | Julia has an option to disable its use of signals but this results in a crash as it 32 | requires the use of at least `SIGINT` in order to manage garbage collection in 33 | multithreaded code. 34 | 35 | If we simply disable Julia's use of signals then single-threaded code works fine. 36 | Multithreaded code, however, will eventually crash without warning: 37 | 38 | ```clojure 39 | user> (require '[libjulia-clj.julia :as julia]) 40 | nil 41 | user> (julia/initialize! {:n-threads 8 :signals-enabled? false}) 42 | 16:28:10.854 [nRepl-session-a6713b61-bf94-4492-bcbb-7cc7e44c2a4f] INFO libjulia-clj.impl.base - Attempting to initialize Julia at /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so 43 | 16:28:10.908 [nRepl-session-a6713b61-bf94-4492-bcbb-7cc7e44c2a4f] INFO tech.v3.jna.base - Library /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so found at [:system "/home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so"] 44 | 16:28:10.925 [nRepl-session-a6713b61-bf94-4492-bcbb-7cc7e44c2a4f] INFO libjulia-clj.impl.jna - Julia startup options: n-threads 8, signals? false 45 | :ok 46 | user> (System/gc) 47 | nil 48 | user> (julia/eval-string "Threads.@threads for i in 1:1000; zeros(1024, 1024) .+ zeros(1024, 1024); end") 49 | 50 | *** Closed on Mon Dec 14 16:28:25 2020 *** 51 | ``` 52 | 53 | ## The Work-Around For Now 54 | 55 | The JVM has a facility for [signal chaining](https://docs.oracle.com/javase/10/troubleshoot/handle-signals-and-exceptions.htm#JSTGD356). This allows us to launch the JVM 56 | in a particular way where installs a handler that listens for entities attempting 57 | to install a signal handler and it records these handlers. When a signal occurse, 58 | it can detect whether it came from the JVM or from an outside entity and thus route 59 | the correct signal to the correct handler as required. 60 | 61 | Using this facility is fairly simple, setup an environment variable LD_PRELOAD that 62 | forces the operating system to load a shared library that exports functions that 63 | allow the JVM to chain signals as opposed to simply handling them. 64 | 65 | 66 | If we modify our example from before with this pathway we can successfully run 67 | our example: 68 | 69 | ```console 70 | chrisn@chrisn-lt-01:~/dev/cnuernber/libjulia-clj$ find /usr -name "*jsig*" 71 | /usr/lib/jvm/java-11-openjdk-amd64/lib/server/libjsig.so 72 | /usr/lib/jvm/java-11-openjdk-amd64/lib/libjsig.so 73 | /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server/libjsig.so 74 | /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/libjsig.so 75 | chrisn@chrisn-lt-01:~/dev/cnuernber/libjulia-clj$ export LD_PRELOAD=/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/libjsig.so 76 | ``` 77 | 78 | ```clojure 79 | user> (require '[libjulia-clj.julia :as julia]) 80 | nil 81 | user> ;;Signals are automatically enabled if n-threads has a value 82 | user> (julia/initialize! {:n-threads 8}) 83 | 16:37:40.695 [nRepl-session-447a06c6-bf23-4338-9618-34e0f841c82b] INFO libjulia-clj.impl.base - Attempting to initialize Julia at /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so 84 | 16:37:40.741 [nRepl-session-447a06c6-bf23-4338-9618-34e0f841c82b] INFO tech.v3.jna.base - Library /home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so found at [:system "/home/chrisn/dev/cnuernber/libjulia-clj/julia-1.5.3/lib/libjulia.so"] 85 | 16:37:40.747 [nRepl-session-447a06c6-bf23-4338-9618-34e0f841c82b] INFO libjulia-clj.impl.jna - Julia startup options: n-threads 8, signals? true 86 | :ok 87 | user> (julia/eval-string "Threads.@threads for i in 1:1000; zeros(1024, 1024) .+ zeros(1024, 1024); end") 88 | nil 89 | ``` 90 | 91 | So, for now, we have to setup some nonstandard JVM state in order to use Julia to 92 | it's full potential. Still, it is pretty amazing that the chaining facility exists 93 | and that it works as advertised and at least we have a solid pathway forward in 94 | order to using Julia from the JVM or vice versa. 95 | --------------------------------------------------------------------------------