in docker. - Githubissues

etherny commented 6 years ago

Hello i try to use the lib in docker container and i receive this error :

OpenJDK 64-Bit Server VM warning: You have loaded library /tmp/nativelib-loader_341152294144260927/libopencv_java400.so which might have disabled stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c <libfile>', or link it with '-z noexecstack'.

Here the docker file

FROM openjdk:jdk
RUN apt update && apt install -y libcglib-java
COPY indexation.jar indexation.jar

Command line :

docker run backend java -jar indexation.jar

PS: the indexation.jar works ouside of docker

blackholegalaxy commented 6 years ago

to add more information on that, we tried two thing to get similar thing done with no success:

find the .so file then use execstack on it but since the /tmp/xxx/libopencv_java400.so file is made accessible at build time and not run time, then in the docker running the jar we cannot reach this .so file.

Also please note the warning is blocking the execution since we then encounter:

Exception in thread "main" java.lang.ExceptionInInitializerError
        at java.base/java.lang.Class.forName0(Native Method)
        at java.base/java.lang.Class.forName(Class.java:398)
        at clojure.lang.RT.classForName(RT.java:2168)
        at clojure.lang.RT.classForName(RT.java:2177)
        at clojure.lang.RT.loadClassForName(RT.java:2196)
        at clojure.lang.RT.load(RT.java:443)
        at clojure.lang.RT.load(RT.java:419)
        at clojure.core$load$fn__5677.invoke(core.clj:5893)
        at clojure.core$load.invokeStatic(core.clj:5892)
        at clojure.core$load.doInvoke(core.clj:5876)
        at clojure.lang.RestFn.invoke(RestFn.java:408)
        at clojure.core$load_one.invokeStatic(core.clj:5697)
        at clojure.core$load_one.invoke(core.clj:5692)
        at clojure.core$load_lib$fn__5626.invoke(core.clj:5737)
        at clojure.core$load_lib.invokeStatic(core.clj:5736)
        at clojure.core$load_lib.doInvoke(core.clj:5717)
        at clojure.lang.RestFn.applyTo(RestFn.java:142)
        at clojure.core$apply.invokeStatic(core.clj:648)
        at clojure.core$load_libs.invokeStatic(core.clj:5774)
        at clojure.core$load_libs.doInvoke(core.clj:5758)
        at clojure.lang.RestFn.applyTo(RestFn.java:137)
        at clojure.core$apply.invokeStatic(core.clj:648)
        at clojure.core$require.invokeStatic(core.clj:5796)
        at clojure.core$require.doInvoke(core.clj:5796)
        at clojure.lang.RestFn.invoke(RestFn.java:457)
        at indexation.image_processing$loading__5569__auto____36.invoke(image_processing.clj:1)
        at indexation.image_processing__init.load(Unknown Source)
        at indexation.image_processing__init.<clinit>(Unknown Source)
        at java.base/java.lang.Class.forName0(Native Method)
        at java.base/java.lang.Class.forName(Class.java:398)
        at clojure.lang.RT.classForName(RT.java:2168)
        at clojure.lang.RT.classForName(RT.java:2177)
        at clojure.lang.RT.loadClassForName(RT.java:2196)
        at clojure.lang.RT.load(RT.java:443)
        at clojure.lang.RT.load(RT.java:419)
        at clojure.core$load$fn__5677.invoke(core.clj:5893)
        at clojure.core$load.invokeStatic(core.clj:5892)
        at clojure.core$load.doInvoke(core.clj:5876)
        at clojure.lang.RestFn.invoke(RestFn.java:408)
        at clojure.lang.Var.invoke(Var.java:379)
        at clojure.lang.Util.loadWithClass(Util.java:250)
        at indexation.image_processing.<clinit>(Unknown Source)
Caused by: java.io.IOException: Couldn't load library library opencv_java400
        at org.scijava.nativelib.NativeLoader.loadLibrary(NativeLoader.java:141)
        at opencv4.core__init.load(Unknown Source)
        at opencv4.core__init.<clinit>(Unknown Source)
        ... 42 more

Please also note we tried to run with CMD java -jar backend-standalone.jar -z noexecstack with not more success

hellonico commented 6 years ago

Hi there,

not sure how you are creating your fat jar, there is a sample Dockerfile in the sibling test project: https://github.com/hellonico/origami_samples_libc2_19/

It uses a more compatible native jar, so with leiningen:

[opencv/opencv-native-ubuntu16-noffmpeg "4.0.0-beta"]

or maven:

<dependency>
<groupId>opencv</groupId>
<artifactId>opencv-native-ubuntu16-noffmpeg</artifactId>
<version>4.0.0-beta</version>
</dependency>

hellonico commented 6 years ago

I just deployed a new version of origami (4.0.0-beta7) making that opencv-native version the default.

I took the opportunity to deprecate the above project, so you can just have a look at the samples project.

Some docker instructions are here: https://github.com/hellonico/origami_samples#docker

hellonico commented 6 years ago

by the way, I'd be super happy if there were any examples you could share ;)

etherny commented 6 years ago

Same issue

Hello, i m using embaded jar, not lein command in docker image.

Here my project file :

(defproject indexation "0.1.0-SNAPSHOT"
  :description "FIXME: write description"
  :url "http://example.com/FIXME"
  :license {:name "Eclipse Public License"
            :url  "http://www.eclipse.org/legal/epl-v10.html"}
  :repositories [["vendredi" "https://repository.hellonico.info/repository/hellonico/"]]
  :dependencies [[org.clojure/clojure "1.9.0"]
                 [origami "4.0.0-beta7"]
                 [opencv/opencv-native-libc_2_19 "4.0.0-beta"]
                 [org.clojure/clojure "1.9.0"]]
  :main indexation.image-processing)

Here the code

(ns indexation.image-processing
  (:gen-class)
  (:require [opencv4.core :refer [imread resize! new-size imwrite]]))

(defn resize-keep-ratio! [mat new-width]
  (let [size (.size mat)
        width (.width size)
        height (.height size)
        ratio (/ width height)
        new-height (/ new-width ratio)]
    (println "Image from" width "x" height "to" new-width "x" new-height)
    (resize! mat (new-size new-width new-height))))
;
(defn -main [& args]
  (time (-> "resources/photo.jpg"
            (imread)
            (resize-keep-ratio! 300)
            (imwrite "resources/output.png"))))

Dockerfile

FROM openjdk:jdk

COPY indexation-0.1.0-SNAPSHOT-standalone.jar indexation.jar
COPY resources resources

Docker image building :

Uberjar in lein project folder (indexation.jar)
Copy jar in dockerfile folder.
copy resources used by the test
docker build --no-cache -t local/indexation .
docker run --rm local/indexation java -jar indexation.jar

OpenJDK 64-Bit Server VM warning: You have loaded library /tmp/nativelib-loader_8297043941214514255/libopencv_java400.so which might have disabled stack guard. The VM will try to fix the stack guard now.
It's highly recommended that you fix the library with 'execstack -c <libfile>', or link it with '-z noexecstack'.
Exception in thread "main" java.lang.ExceptionInInitializerError
        at java.base/java.lang.Class.forName0(Native Method)
        at java.base/java.lang.Class.forName(Class.java:398)
        at clojure.lang.RT.classForName(RT.java:2204)
        at clojure.lang.RT.classForName(RT.java:2213)
        at clojure.lang.RT.loadClassForName(RT.java:2232)
        at clojure.lang.RT.load(RT.java:450)
        at clojure.lang.RT.load(RT.java:426)
        at clojure.core$load$fn__6548.invoke(core.clj:6046)
        at clojure.core$load.invokeStatic(core.clj:6045)
        at clojure.core$load.doInvoke(core.clj:6029)
        at clojure.lang.RestFn.invoke(RestFn.java:408)
        at clojure.core$load_one.invokeStatic(core.clj:5848)
        at clojure.core$load_one.invoke(core.clj:5843)
        at clojure.core$load_lib$fn__6493.invoke(core.clj:5888)
        at clojure.core$load_lib.invokeStatic(core.clj:5887)
        at clojure.core$load_lib.doInvoke(core.clj:5868)
        at clojure.lang.RestFn.applyTo(RestFn.java:142)
        at clojure.core$apply.invokeStatic(core.clj:659)
        at clojure.core$load_libs.invokeStatic(core.clj:5925)
        at clojure.core$load_libs.doInvoke(core.clj:5909)
        at clojure.lang.RestFn.applyTo(RestFn.java:137)
        at clojure.core$apply.invokeStatic(core.clj:659)
        at clojure.core$require.invokeStatic(core.clj:5947)
        at clojure.core$require.doInvoke(core.clj:5947)
        at clojure.lang.RestFn.invoke(RestFn.java:408)
        at indexation.image_processing$loading__6434__auto____180.invoke(image_processing.clj:1)
        at indexation.image_processing__init.load(Unknown Source)
        at indexation.image_processing__init.<clinit>(Unknown Source)
        at java.base/java.lang.Class.forName0(Native Method)
        at java.base/java.lang.Class.forName(Class.java:398)
        at clojure.lang.RT.classForName(RT.java:2204)
        at clojure.lang.RT.classForName(RT.java:2213)
        at clojure.lang.RT.loadClassForName(RT.java:2232)
        at clojure.lang.RT.load(RT.java:450)
        at clojure.lang.RT.load(RT.java:426)
        at clojure.core$load$fn__6548.invoke(core.clj:6046)
        at clojure.core$load.invokeStatic(core.clj:6045)
        at clojure.core$load.doInvoke(core.clj:6029)
        at clojure.lang.RestFn.invoke(RestFn.java:408)
        at clojure.lang.Var.invoke(Var.java:381)
        at clojure.lang.Util.loadWithClass(Util.java:250)
        at indexation.image_processing.<clinit>(Unknown Source)
Caused by: java.io.IOException: Couldn't load library library opencv_java400
        at org.scijava.nativelib.NativeLoader.loadLibrary(NativeLoader.java:141)
        at opencv4.core__init.load(Unknown Source)
        at opencv4.core__init.<clinit>(Unknown Source)
        ... 42 more

hellonico commented 6 years ago

Thanks for the feedback.

Sorry my explanation was not clear. You don' t need to use this anymore:

 [opencv/opencv-native-libc_2_19 "4.0.0-beta"]

just remove it from your project.clj file.

I have created a repository with two docker files: https://github.com/hellonico/origami-indexation

Hope it works for you.

etherny commented 6 years ago

You are very responsive, i will try.

etherny commented 6 years ago

It's working, thank you for your job !

hellonico / origami

in docker. #9