Develop Reference

How to install tomcat native with oracle jdk 8

I'm trying to install oracle jdk 8 along with tomcat native with APR support on an Alpine linux docker image. I'm continually faced with the following error:
No such file or directory
#include <jni.h>
when trying to make install. I have tried using the '-I/$JAVA_HOME/ option added to the ./configure command to no avail.
This here below is my Dockerfile:
FROM alpine:latest
WORKDIR /tmp
# BASH
RUN apk add --no-cache --update-cache bash curl ca-certificates
ENV GLIBC_PKG_VERSION=2.23-r3
RUN curl -Lo /etc/apk/keys/sgerrand.rsa.pub https://raw.githubusercontent.com/sgerrand/alpine-pkg-glibc/master/sgerrand.rsa.pub
RUN curl -Lo glibc-${GLIBC_PKG_VERSION}.apk https://github.com/sgerrand/alpine-pkg-glibc/releases/download/${GLIBC_PKG_VERSION}/glibc-${GLIBC_PKG_VERSION}.apk
RUN curl -Lo glibc-bin-${GLIBC_PKG_VERSION}.apk https://github.com/sgerrand/alpine-pkg-glibc/releases/download/${GLIBC_PKG_VERSION}/glibc-bin-${GLIBC_PKG_VERSION}.apk
RUN curl -Lo glibc-i18n-${GLIBC_PKG_VERSION}.apk https://github.com/sgerrand/alpine-pkg-glibc/releases/download/${GLIBC_PKG_VERSION}/glibc-i18n-${GLIBC_PKG_VERSION}.apk
RUN apk add glibc-${GLIBC_PKG_VERSION}.apk glibc-bin-${GLIBC_PKG_VERSION}.apk glibc-i18n-${GLIBC_PKG_VERSION}.apk
RUN /usr/glibc-compat/bin/localedef -i en_US -f UTF-8 en_US.UTF-8
# DATE
RUN apk --update add --no-cache bash tzdata && \
cp /usr/share/zoneinfo/Asia/Shanghai /etc/localtime && \
echo "Asia/Shanghai" > /etc/timezone && \
apk del tzdata && \
rm -rf /var/cache
# ADD JAVA
ENV JAVA_VERSION_MAJOR=8 \
JAVA_VERSION_MINOR=73 \
JAVA_VERSION_BUILD=02 \
JAVA_PACKAGE=server-jre
# The JDK reference version / server-jre / jdk
# 8/73/02
# 7/80/15
RUN curl -jksSLH "Cookie: oraclelicense=accept-securebackup-cookie" \
"http://download.oracle.com/otn-pub/java/jdk/${JAVA_VERSION_MAJOR}u${JAVA_VERSION_MINOR}-b${JAVA_VERSION_BUILD}/${JAVA_PACKAGE}-${JAVA_VERSION_MAJOR}u${JAVA_VERSION_MINOR}-linux-x64.tar.gz" | gunzip -c - | tar -xf - && \
# apk del curl ca-certificates && \
mv jdk1.${JAVA_VERSION_MAJOR}.0_${JAVA_VERSION_MINOR}/jre /jre && \
mv jdk1.${JAVA_VERSION_MAJOR}.0_${JAVA_VERSION_MINOR}/include/linux /jre/linux && \
# rm /jre/bin/jjs && \
rm /jre/bin/keytool && \
rm /jre/bin/orbd && \
rm /jre/bin/pack200 && \
rm /jre/bin/policytool && \
rm /jre/bin/rmid && \
rm /jre/bin/rmiregistry && \
rm /jre/bin/servertool && \
rm /jre/bin/tnameserv && \
rm /jre/bin/unpack200 && \
# rm /jre/lib/ext/nashorn.jar && \
rm /jre/lib/jfr.jar && \
rm -rf /jre/lib/jfr && \
rm -rf /jre/lib/oblique-fonts && \
rm -rf /tmp/* && \
rm -rf /var/cache/* && \
echo 'hosts: files mdns4_minimal [NOTFOUND=return] dns mdns4' >> /etc/nsswitch.conf
ENV JAVA_HOME /jre
ENV PATH ${PATH}:${JAVA_HOME}/bin
ENV CATALINA_HOME /apache-tomcat
ENV PATH $CATALINA_HOME/bin:$PATH
RUN mkdir -p "$CATALINA_HOME"
WORKDIR $CATALINA_HOME
# let "Tomcat Native" live somewhere isolated
ENV TOMCAT_NATIVE_LIBDIR $CATALINA_HOME/native-jni-lib
ENV LD_LIBRARY_PATH ${LD_LIBRARY_PATH:+$LD_LIBRARY_PATH:}$TOMCAT_NATIVE_LIBDIR
RUN apk add --no-cache busybox
RUN apk add --no-cache libgcc
RUN apk add --no-cache pinentry-gtk
RUN apk add --no-cache gnupg
# see https://www.apache.org/dist/tomcat/tomcat-8/KEYS
RUN set -ex \
&& for key in \
05AB33110949707C93A279E3D3EFE6B686867BA6 \
07E48665A34DCAFAE522E5E6266191C37C037D42 \
47309207D818FFD8DCD3F83F1931D684307A10A5 \
541FBE7D8F78B25E055DDEE13C370389288584E7 \
61B832AC2F1C5A90F0F9B00A1C506407564C17A3 \
713DA88BE50911535FE716F5208B0AB1D63011C7 \
79F7026C690BAA50B92CD8B66A3AD3F4F22C4FED \
9BA44C2621385CB966EBA586F72C284D731FABEE \
A27677289986DB50844682F8ACB77FC2E86E29AC \
A9C5DF4D22E99998D9875A5110C01C5A2F6059E7 \
DCFD35E0BF8CA7344752DE8B6FB21E8933C60243 \
F3A04C595DB5B6A5F1ECA43E3B7BBB100D811BBE \
F7DA48BB64BCB84ECBA7EE6935CD23C10D498E23 \
; do \
gpg --keyserver ha.pool.sks-keyservers.net --recv-keys "$key"; \
done
ENV TOMCAT_MAJOR 8
ENV TOMCAT_VERSION 8.5.6
ENV TOMCAT_TGZ_URL http://archive.apache.org/dist/tomcat/tomcat-$TOMCAT_MAJOR/v$TOMCAT_VERSION/bin/apache-tomcat-$TOMCAT_VERSION.tar.gz
ENV TOMCAT_ASC_URL http://archive.apache.org/dist/tomcat/tomcat-$TOMCAT_MAJOR/v$TOMCAT_VERSION/bin/apache-tomcat-$TOMCAT_VERSION.tar.gz.asc
RUN set -x \
\
&& apk add --no-cache --virtual .fetch-deps \
ca-certificates \
tar \
openssl \
&& wget -O tomcat.tar.gz "$TOMCAT_TGZ_URL" \
&& wget -O tomcat.tar.gz.asc "$TOMCAT_ASC_URL" \
&& gpg --batch --verify tomcat.tar.gz.asc tomcat.tar.gz \
&& tar -xvf tomcat.tar.gz --strip-components=1 \
\
&& nativeBuildDir="$(mktemp -d)" \
&& tar -xvf bin/tomcat-native.tar.gz -C "$nativeBuildDir" --strip-components=1 \
&& ls -l $nativeBuildDir \
&& apk add --no-cache --virtual .native-build-deps \
apr-dev \
gcc \
libc-dev \
make \
openssl-dev \
&& ( \
export CATALINA_HOME=$PWD \
&& cd $nativeBuildDir/native \
&& ./configure \
--libdir=$TOMCAT_NATIVE_LIBDIR \
--prefix=$CATALINA_HOME \
--with-apr="$(which apr-1-config)" \
--with-java-home=$JAVA_HOME \
--with-ssl=yes \
--with-os-type=linux \
&& make -j$(getconf _NPROCESSORS_ONLN) \
&& make install \
) \
&& runDeps="$( \
scanelf --needed --nobanner --recursive "$TOMCAT_NATIVE_LIBDIR" \
| awk '{ gsub(/,/, "\nso:", $2); print "so:" $2 }' \
| sort -u \
| xargs -r apk info --installed \
| sort -u \
)" \
&& apk add --virtual .tomcat-native-rundeps $runDeps \
&& apk del .fetch-deps .native-build-deps \
&& rm -rf "$nativeBuildDir" \
&& rm bin/tomcat-native.tar.gz
# verify Tomcat Native is working properly
RUN set -e \
&& nativeLines="$(catalina.sh configtest 2>&1)" \
&& nativeLines="$(echo "$nativeLines" | grep 'Apache Tomcat Native')" \
&& nativeLines="$(echo "$nativeLines" | sort -u)" \
&& if ! echo "$nativeLines" | grep 'INFO: Loaded APR based Apache Tomcat Native library' >&2; then \
echo >&2 "$nativeLines"; \
exit 1; \
fi
# Delete tomcat files
RUN rm -rf /apache-tomcat/bin/*.bat \
&& rm -rf /apache-tomcat/webapps/docs \
&& rm -rf /apache-tomcat/webapps/examples \
&& rm -rf /apache-tomcat/webapps/manager \
&& rm -rf /apache-tomcat/webapps/host-manager \
&& rm -rf /apache-tomcat/webapps/ROOT/* \
&& rm -rf /tmp/* \
&& rm -rf /var/cache/*
RUN cat /apache-tomcat/conf/server.xml
RUN echo "TEST" > /apache-tomcat/webapps/ROOT/readme.txt
# WORKDIR
WORKDIR /apache-tomcat/webapps
EXPOSE 8080 8443
#ENTRYPOINT /apache-tomcat/bin/catalina.sh run
CMD ["/bin/bash"]

How do you disable "$HOME/.java_usagetracker" from being created?

According to Java's documentation:
https://docs.oracle.com/javacomponents/usage-tracker/overview/toc.htm#JSUTO-GUID-6642AAD5-85A1-462F-9D77-09A52DF72404
Java Usage Tracker should be disabled by default. But that is not the case for Java 8u161 or greater.

Setting com.oracle.usagetracker.track.last.usage=false in /etc/oracle/java/usagetracker.properties does the trick.
Dockerfile example:
FROM centos:7
ARG JAVA_VERSION=8u171
ARG JAVA_BUILD=b11
ARG JAVA_HASH=512cd62ec5174c3487ac17c61aaa89e8
ENV JAVA_HOME=/usr/java/default
RUN mkdir /usr/java \
&& curl --create-dirs -L --retry 2 --retry-delay 2 --connect-timeout 30 \
--cookie "oraclelicense=accept-securebackup-cookie;gpw_e24=http://edelivery.oracle.com" \
http://download.oracle.com/otn-pub/java/jdk/${JAVA_VERSION}-${JAVA_BUILD}/${JAVA_HASH}/jdk-${JAVA_VERSION}-linux-x64.rpm \
-o /tmp/jdk-linux-x64.rpm \
&& rpm -ivh /tmp/jdk-linux-x64.rpm \
&& rm -f /tmp/jdk-linux-x64.rpm \
&& mkdir -p /etc/oracle/java/ \
&& echo "com.oracle.usagetracker.track.last.usage=false" > /etc/oracle/java/usagetracker.properties

Jersey Grizzly HTTP Server shutdown inside container docker

I am trying to execute a Grizzly HTTP Server inside a container.
My problem is that when I am running the container (using docker-compose) the container shuts down after a few seconds.
Here is my server Dockerfile:
FROM alpine:3.5
MAINTAINER Maybe One <maybe#maybe.com>
# Java Version and other ENV
ENV JAVA_VERSION_MAJOR=8 \
JAVA_VERSION_MINOR=102 \
JAVA_VERSION_BUILD=14 \
JAVA_PACKAGE=jdk \
JAVA_JCE=standard \
JAVA_HOME=/opt/jdk \
PATH=${PATH}:/opt/jdk/bin \
GLIBC_VERSION=2.23-r3 \
LANG=C.UTF-8
RUN apk upgrade --update && \
apk add --update libstdc++ curl ca-certificates bash && \
for pkg in glibc-${GLIBC_VERSION} glibc-bin-${GLIBC_VERSION} glibc-i18n-${GLIBC_VERSION}; do curl -sSL https://github.com/andyshinn/alpine-pkg-glibc/releases/download/${GLIBC_VERSION}/${pkg}.apk -o /tmp/${pkg}.apk; done && \
apk add --allow-untrusted /tmp/*.apk && \
rm -v /tmp/*.apk && \
( /usr/glibc-compat/bin/localedef --force --inputfile POSIX --charmap UTF-8 C.UTF-8 || true ) && \
echo "export LANG=C.UTF-8" > /etc/profile.d/locale.sh && \
/usr/glibc-compat/sbin/ldconfig /lib /usr/glibc-compat/lib && \
mkdir /opt && \
curl -jksSLH "Cookie: oraclelicense=accept-securebackup-cookie" -o /tmp/java.tar.gz \
http://download.oracle.com/otn-pub/java/jdk/${JAVA_VERSION_MAJOR}u${JAVA_VERSION_MINOR}-b${JAVA_VERSION_BUILD}/${JAVA_PACKAGE}-${JAVA_VERSION_MAJOR}u${JAVA_VERSION_MINOR}-linux-x64.tar.gz && \
gunzip /tmp/java.tar.gz && \
tar -C /opt -xf /tmp/java.tar && \
ln -s /opt/jdk1.${JAVA_VERSION_MAJOR}.0_${JAVA_VERSION_MINOR} /opt/jdk && \
if [ "${JAVA_JCE}" == "unlimited" ]; then echo "Installing Unlimited JCE policy" >&2 && \
curl -jksSLH "Cookie: oraclelicense=accept-securebackup-cookie" -o /tmp/jce_policy-${JAVA_VERSION_MAJOR}.zip \
http://download.oracle.com/otn-pub/java/jce/${JAVA_VERSION_MAJOR}/jce_policy-${JAVA_VERSION_MAJOR}.zip && \
cd /tmp && unzip /tmp/jce_policy-${JAVA_VERSION_MAJOR}.zip && \
cp -v /tmp/UnlimitedJCEPolicyJDK8/*.jar /opt/jdk/jre/lib/security; \
fi && \
sed -i s/#networkaddress.cache.ttl=-1/networkaddress.cache.ttl=30/ $JAVA_HOME/jre/lib/security/java.security && \
apk del curl glibc-i18n && \
rm -rf /opt/jdk/*src.zip \
/opt/jdk/lib/missioncontrol \
/opt/jdk/lib/visualvm \
/opt/jdk/lib/*javafx* \
/opt/jdk/jre/plugin \
/opt/jdk/jre/bin/javaws \
/opt/jdk/jre/bin/jjs \
/opt/jdk/jre/bin/orbd \
/opt/jdk/jre/bin/pack200 \
/opt/jdk/jre/bin/policytool \
/opt/jdk/jre/bin/rmid \
/opt/jdk/jre/bin/rmiregistry \
/opt/jdk/jre/bin/servertool \
/opt/jdk/jre/bin/tnameserv \
/opt/jdk/jre/bin/unpack200 \
/opt/jdk/jre/lib/javaws.jar \
/opt/jdk/jre/lib/deploy* \
/opt/jdk/jre/lib/desktop \
/opt/jdk/jre/lib/*javafx* \
/opt/jdk/jre/lib/*jfx* \
/opt/jdk/jre/lib/amd64/libdecora_sse.so \
/opt/jdk/jre/lib/amd64/libprism_*.so \
/opt/jdk/jre/lib/amd64/libfxplugins.so \
/opt/jdk/jre/lib/amd64/libglass.so \
/opt/jdk/jre/lib/amd64/libgstreamer-lite.so \
/opt/jdk/jre/lib/amd64/libjavafx*.so \
/opt/jdk/jre/lib/amd64/libjfx*.so \
/opt/jdk/jre/lib/ext/jfxrt.jar \
/opt/jdk/jre/lib/ext/nashorn.jar \
/opt/jdk/jre/lib/oblique-fonts \
/opt/jdk/jre/lib/plugin.jar \
/tmp/* /var/cache/apk/*
# Maven
ENV MAVEN_VERSION 3.3.9
ENV MAVEN_HOME /usr/lib/mvn
ENV PATH $MAVEN_HOME/bin:$PATH
RUN wget http://ftp.fau.de/apache/maven/maven-3/$MAVEN_VERSION/binaries/apache-maven-$MAVEN_VERSION-bin.tar.gz && \
tar -zxvf apache-maven-$MAVEN_VERSION-bin.tar.gz && \
rm apache-maven-$MAVEN_VERSION-bin.tar.gz && \
mv apache-maven-$MAVEN_VERSION /usr/lib/mvn
# Workspace
ENV WORKSPACE /home/app/
RUN mkdir -p $WORKSPACE
WORKDIR $WORKSPACE
COPY . $WORKSPACE # Copy Server Project
RUN mvn clean install -DskipTests
ENTRYPOINT mvn exec:java
docker-compose.yml
version: '2.1'
services:
server:
build: ./server/
ports:
- "8080:8080"
server docker logs:
... maven...
[INFO] --- exec-maven-plugin:1.2.1:java (default-cli) # restful.littleapp ---
Jan 30, 2017 2:10:18 PM org.glassfish.grizzly.http.server.NetworkListener start
INFO: Started listener bound to [0.0.0.0:8080]
Jan 30, 2017 2:10:18 PM org.glassfish.grizzly.http.server.HttpServer start
INFO: [HttpServer] Started.
Jersey app started with WADL available at http://0.0.0.0:8080/littleapp/application.wadl
Hit enter to stop it...
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 5.507 s
[INFO] Finished at: 2017-01-30T14:10:18+00:00
Jan 30, 2017 2:10:18 PM org.glassfish.grizzly.http.server.NetworkListener shutdownNow
INFO: Stopped listener bound to [0.0.0.0:8080]
[INFO] Final Memory: 37M/90M
[INFO] ------------------------------------------------------------------------
Normally, the server has to listen...

The problem is probably that your main class is waiting for input before stopping the grizzly server. Since the docker container is not run in interactive mode it will never get input on command line and the System.in is terminated. The mvn exec process stops.
You should find a way to keep the grizzly server running without waiting for input.
Something like
server.start();
Thread.currentThread().join(); // instead of System.in.read();
edit: seems there is a solution like this already described on s.o. grizzly-http-server-should-keep-running which also incorporates a graceful shutdown by mean of a shutdownhook.

Docker - Running Apache and Multiple JARs

I need to Run Apache and Two JAR files on different ports(say 80 for apache, 8080 and 8070 for two JAR Tomcat's) in a Docker Image. The problem is, three of them are not starting in parallel. I have shared my DockerFile. What are the changes that need to be done here?
Dockerfile
FROM phusion/baseimage:0.9.17
CMD ["/sbin/my_init"] && ["service", "apache2", "start"]
RUN echo "deb http://archive.ubuntu.com/ubuntu trusty main universe" > /etc/apt/sources.list
RUN apt-get -y update
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y -q python-software-properties software-properties-common
ENV JAVA_VER 8
ENV JAVA_HOME /usr/lib/jvm/java-8-oracle
RUN echo 'deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main' >> /etc/apt/sources.list && \
echo 'deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main' >> /etc/apt/sources.list && \
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys C2518248EEA14886 && \
apt-get update && \
echo oracle-java${JAVA_VER}-installer shared/accepted-oracle-license-v1-1 select true | sudo /usr/bin/debconf-set-selections && \
apt-get install -y --force-yes --no-install-recommends oracle-java${JAVA_VER}-installer oracle-java${JAVA_VER}-set-default && \
apt-get clean && \
rm -rf /var/cache/oracle-jdk${JAVA_VER}-installer && \
apt-get -y install apache2
RUN update-java-alternatives -s java-8-oracle
RUN echo "export JAVA_HOME=/usr/lib/jvm/java-8-oracle" >> ~/.bashrc
RUN echo "ServerName localhost" | sudo tee /etc/apache2/conf-available/fqdn.conf
RUN sudo a2enconf fqdn
RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
ADD File1.jar /root/File1.jar
ADD File2.jar /root/File2.jar
# Add File1 service
RUN mkdir /etc/service/File1
ADD start-File1.sh /etc/service/File1/run
RUN chmod +x /etc/service/File1/run
# Add File2 service
RUN mkdir /etc/service/File2
ADD start-File2.sh /etc/service/File2/run
RUN chmod +x /etc/service/File2/run

Mahout CVB topics file

I can't understand the output, maybe someone can help
cvb command
bin/mahout cvb \
-i /work/matrix \
-o /work/cvb -k 10 -ow -x 20 \
-dict /work/sparseVectors/dictionary.file-* \
-dt /work/topics \
-mt /work/models
After cvb and vector dump
bin/mahout vectordump -i /work/topics \
-d /work/sparseVectors/dictionary.file-* \
-o /work/cvb-topic \
-dt sequencefile --vectorSize 10 \
-sort /work/topics \
-p TRUE
the file cvb-topic has something like
0 {0:0.5380152557598438,09:0.4619846630645179,10:1.541304295897372E-8,08:1.5405183424669223E-8,04:1.4964621316424798E-8,01:1.0302427985842305E-8,00:7.566567734425231E-9,1:7.394593812516846E-9,1.180:6.745071922943742E-9,07:3.3841292288528656E-9}
What do i do with it next ?

I had the same issue today, to get probabilities for words, use instead -i /work/cvb