Do you have a different machine to test on? Could also be a factor, alpine gave me a segfault (see attached) but slim works OK.
[john@toaster jni-inchi-docker]$ more Dockerfile > FROM openjdk:8u171-slim > COPY smi2inchi.jar . John On Tue, 11 Sep 2018 at 16:23, John Mayfield <[email protected]> wrote: > I'll have a poke around in an alpine container this evening, does seem odd. > > A third option is nested-vm version, we used this in JChemPaint when it > was an Applet - (see inchi-nestedvm in > https://github.com/JChemPaint/jchempaint). > > On Tue, 11 Sep 2018 at 16:03, Maria Sorokina <[email protected]> > wrote: > >> I am building my jar with Maven, but I don’t think that it is the >> problem, as I tried tu run the jar on a Centos7 VM having just Java and it >> worked without any problem. >> I also desperately tried the dirty solution of downloading the manifest >> and the jniinchi-1.03_1-LINUX-AMD64.so files the ini-inchi seems to >> search for and put them where it seems to search them within the container, >> but, of course it failed. >> >> I’ll try to search for a solution, but for now I’ll just do my thing >> without containerizing this part of my app. If I find a solution, I’ll post >> it here. Meanwhile, I’m still very open to any suggestion! >> >> Kind regards, >> >> Maria Sorokina, PhD >> Steinbeck Research Group >> Analytical Chemistry - Cheminformatics and Chemometrics >> Friedrich-Schiller-University Jena, Germany >> http://cheminf.uni-jena.de >> >> Le 11 sept. 2018 à 14:51, John Mayfield <[email protected]> a >> écrit : >> >> Right, alpine was probably a red herring. Looking again I presume you >> build app.jar yourself? It looks like you've removed the MANIFEST.xml that >> is needed by JNI InChI to locate the native dependency. How are you >> building the JAR? >> >> Unfortunately v1.03 of InChI is all we have for JNI ATM. My former >> colleague has been looking at JNA InChI version ( >> https://github.com/dan2097/jna-inchi) but this is very different to the >> JNI bindings and not a drop in replacement. >> >> John >> >> On Tue, 11 Sep 2018 at 09:48, Maria Sorokina <[email protected]> >> wrote: >> >>> I tried the ubuntu 16.04 based image with Java 8 added, I get exactly >>> the same error, only at the InChi generation. I have the feeling that >>> something is missing in this minimal linux images for the InChi generator >>> to run correctly, but I cannot find what. >>> >>> I also noticed that for an old version of ini-inchi (1.03, and the >>> latest and only available is 1.6): >>> npls-db-filler_1 | 2181 [main] INFO >>> net.sf.jnati.deploy.repository.RemoteRepository - Searching remote >>> repository for: jniinchi-1.03_1-LINUX-AMD64 ( >>> http://jnati.sourceforge.net/jnati-repo) >>> >>> What am I missing in my configuration ? Knowing that everything works >>> fine outside of Docker? >>> >>> The Dockerfile using Ubuntu: >>> >>> FROM ubuntu:16.04 >>> LABEL maintainer="[email protected]" >>> >>> >>> RUN apt-get update && \ >>> apt-get upgrade -y && \ >>> apt-get install -y software-properties-common && \ >>> add-apt-repository ppa:webupd8team/java -y && \ >>> apt-get update && \ >>> echo oracle-java7-installer shared/accepted-oracle-license-v1-1 select >>> true | /usr/bin/debconf-set-selections && \ >>> apt-get install -y oracle-java8-installer && \ >>> apt-get clean >>> >>> EXPOSE 8080 >>> VOLUME /tmp >>> ARG JAR_FILE >>> COPY ${JAR_FILE} app.jar >>> ENTRYPOINT >>> ["java","-Djava.security.egd=file:/dev/./urandom","-jar","/app.jar"] >>> >>> Thank you for your help! >>> >>> Kind regards, >>> >>> >>> Maria Sorokina, PhD >>> Steinbeck Research Group >>> Analytical Chemistry - Cheminformatics and Chemometrics >>> Friedrich-Schiller-University Jena, Germany >>> http://cheminf.uni-jena.de >>> >>> Le 11 sept. 2018 à 00:13, John Mayfield <[email protected]> a >>> écrit : >>> >>> Unlikely to work in alpine, have you tried ubuntu/debian slim? >>> >>> John >>> >>> On Mon, 10 Sep 2018 at 18:16, Maria Sorokina <[email protected]> >>> wrote: >>> >>>> Hi, >>>> >>>> I developed an app using CDK, and in particular it’s InChi Generator. >>>> It runs perfectly with IntelliJ, and as a jar on MacOS and on CentOS. I >>>> wanted to make it run within a Docker container (openjdk:8-jdk-alpine with >>>> additional installation of gcc), the image is created without any problem, >>>> but when I run the container, I get the following error just once: >>>> >>>> >>>> npls-db-filler_1 | 0 [main] INFO >>>> net.sf.jnati.deploy.artefact.ConfigManager - Loading global configuration >>>> npls-db-filler_1 | 4 [main] DEBUG >>>> net.sf.jnati.deploy.artefact.ConfigManager - Loading defaults: >>>> jar:file:/app.jar!/BOOT-INF/lib/jnati-deploy-0.3.jar!/META-INF/jnati/jnati.default-properties >>>> npls-db-filler_1 | 5 [main] INFO >>>> net.sf.jnati.deploy.artefact.ConfigManager - Loading artefact >>>> configuration: jniinchi-1.03_1 >>>> npls-db-filler_1 | 6 [main] DEBUG >>>> net.sf.jnati.deploy.artefact.ConfigManager - Loading instance defaults: >>>> jar:file:/app.jar!/BOOT-INF/lib/jnati-deploy-0.3.jar!/META-INF/jnati/jnati.instance.default-properties >>>> npls-db-filler_1 | 9 [main] INFO >>>> net.sf.jnati.deploy.repository.ClasspathRepository - Searching classpath >>>> for: jniinchi-1.03_1-LINUX-AMD64 >>>> npls-db-filler_1 | 14 [main] INFO >>>> net.sf.jnati.deploy.repository.LocalRepository - Searching local >>>> repository for: jniinchi-1.03_1-LINUX-AMD64 >>>> npls-db-filler_1 | 16 [main] DEBUG >>>> net.sf.jnati.deploy.repository.LocalRepository - Artefact path: >>>> /root/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64 >>>> npls-db-filler_1 | 16 [main] INFO >>>> net.sf.jnati.deploy.repository.LocalRepository - Creating artefact: >>>> /root/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64 >>>> npls-db-filler_1 | 18 [main] DEBUG >>>> net.sf.jnati.deploy.source.JarSource - Opening jar: /app.jar >>>> npls-db-filler_1 | 19 [main] WARN >>>> net.sf.jnati.deploy.NativeArtefactLocator - Error resolving artefact to >>>> local repository >>>> npls-db-filler_1 | java.io.FileNotFoundException: File not found: >>>> MANIFEST.xml >>>> npls-db-filler_1 | at >>>> net.sf.jnati.deploy.source.JarSource.openFile(JarSource.java:67) >>>> npls-db-filler_1 | at >>>> net.sf.jnati.deploy.source.ArtefactSource.loadManifest(ArtefactSource.java:41) >>>> >>>> >>>> And this every time the InChiGenerator is called in my code: >>>> >>>> >>>> Error loading JNI InChI native code. >>>> npls-db-filler_1 | You may need to compile the native code for your >>>> platform. >>>> npls-db-filler_1 | See http://jni-inchi.sourceforge.net for >>>> instructions. >>>> npls-db-filler_1 | >>>> npls-db-filler_1 | 1033 [main] INFO >>>> net.sf.jnati.deploy.artefact.ConfigManager - Loading artefact >>>> configuration: jniinchi-1.03_1 >>>> npls-db-filler_1 | 1037 [main] DEBUG >>>> net.sf.jnati.deploy.artefact.ConfigManager - Loading instance defaults: >>>> jar:file:/app.jar!/BOOT-INF/lib/jnati-deploy-0.3.jar!/META-INF/jnati/jnati.instance.default-properties >>>> npls-db-filler_1 | 1039 [main] INFO >>>> net.sf.jnati.deploy.repository.ClasspathRepository - Searching classpath >>>> for: jniinchi-1.03_1-LINUX-AMD64 >>>> npls-db-filler_1 | 1039 [main] INFO >>>> net.sf.jnati.deploy.repository.LocalRepository - Searching local >>>> repository for: jniinchi-1.03_1-LINUX-AMD64 >>>> npls-db-filler_1 | 1039 [main] DEBUG >>>> net.sf.jnati.deploy.repository.LocalRepository - Artefact path: >>>> /root/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64 >>>> npls-db-filler_1 | 1040 [main] INFO >>>> net.sf.jnati.deploy.repository.LocalRepository - Creating artefact: >>>> /root/.jnati/repo/jniinchi/1.03_1/LINUX-AMD64 >>>> npls-db-filler_1 | 1040 [main] DEBUG >>>> net.sf.jnati.deploy.source.JarSource - Opening jar: /app.jar >>>> npls-db-filler_1 | 1041 [main] WARN >>>> net.sf.jnati.deploy.NativeArtefactLocator - Error resolving artefact to >>>> local repository >>>> npls-db-filler_1 | java.io.FileNotFoundException: File not found: >>>> MANIFEST.xml >>>> npls-db-filler_1 | at >>>> net.sf.jnati.deploy.source.JarSource.openFile(JarSource.java:67) >>>> >>>> >>>> >>>> Have anybody tried and succeed using InChiGenerator within a Docker >>>> container? Which package/library/software I should add to either my Docker >>>> image, either to my Maven repo to make it work within this container? >>>> >>>> Thank you for your help! >>>> >>>> Kind regards, >>>> >>>> Maria Sorokina, PhD >>>> Steinbeck Research Group >>>> Analytical Chemistry - Cheminformatics and Chemometrics >>>> Friedrich-Schiller-University Jena, Germany >>>> http://cheminf.uni-jena.de >>>> >>>> _______________________________________________ >>>> Cdk-user mailing list >>>> [email protected] >>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>> >>> >>> >>
8u171-alpine.log
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8u171-slim.log
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