Can not install MariaDB through Docker and Vagrant - vagrant

When installing MariaDB through a Dockerfile and Vagrant I keep getting this error:
New password for the MariaDB "root" user:
Use of uninitialized value $_[1] in join or string at /usr/share/perl5/Debconf/DbDriver/Stack.pm line 111.
invoke-rc.d: policy-rc.d denied execution of stop.
Use of uninitialized value $val in substitution (s///) at /usr/share/perl5/Debconf/Format/822.pm line 83, <GEN6> line 1.
Use of uninitialized value $val in concatenation (.) or string at /usr/share/perl5/Debconf/Format/822.pm line 84, <GEN6> line 1.
dpkg: error processing mariadb-server-10.0 (--configure):
subprocess installed post-installation script returned error exit status 1
Setting up libhtml-template-perl (2.91-1) ...
dpkg: dependency problems prevent configuration of mariadb-server:
mariadb-server depends on mariadb-server-10.0 (= 10.0.15+maria-1~wheezy); however:
Package mariadb-server-10.0 is not configured yet.
dpkg: error processing mariadb-server (--configure):
dependency problems - leaving unconfigured
Errors were encountered while processing:
mariadb-server-10.0
mariadb-server
E: Sub-process /usr/bin/dpkg returned an error code (1)
This happens with every MariaDB that I have tried (10.0.15, 10.1.2).
My DockerFile:
# vim:set ft=dockerfile:
FROM debian:wheezy
# add our user and group first to make sure their IDs get assigned consistently, regardless of whatever dependencies get added
RUN groupadd -r mysql && useradd -r -g mysql mysql
# grab gosu for easy step-down from root
RUN gpg --keyserver pool.sks-keyservers.net --recv-keys B42F6819007F00F88E364FD4036A9C25BF357DD4
RUN apt-get update && apt-get install -y curl && rm -rf /var/lib/apt/lists/* \
&& curl -o /usr/local/bin/gosu -SL "https://github.com/tianon/gosu/releases/download/1.2/gosu-$(dpkg --print-architecture)" \
&& curl -o /usr/local/bin/gosu.asc -SL "https://github.com/tianon/gosu/releases/download/1.2/gosu-$(dpkg --print-architecture).asc" \
&& gpg --verify /usr/local/bin/gosu.asc \
&& rm /usr/local/bin/gosu.asc \
&& chmod +x /usr/local/bin/gosu \
&& apt-get purge -y --auto-remove curl
RUN apt-key adv --keyserver pool.sks-keyservers.net --recv-keys 199369E5404BD5FC7D2FE43BCBCB082A1BB943DB
ENV MARIADB_MAJOR 10.0
ENV MARIADB_VERSION 10.0.15+maria-1~wheezy
RUN echo "deb http://ftp.osuosl.org/pub/mariadb/repo/$MARIADB_MAJOR/debian wheezy main" > /etc/apt/sources.list.d/mariadb.list
RUN apt-get update \
&& apt-get install -y \
mariadb-server=$MARIADB_VERSION \
&& rm -rf /var/lib/apt/lists/* \
&& rm -rf /var/lib/mysql \
&& mkdir /var/lib/mysql \
&& sed -ri 's/^(bind-address|skip-networking)/;\1/' /etc/mysql/my.cnf
VOLUME /var/lib/mysql
COPY docker-entrypoint.sh /
ENTRYPOINT ["/docker-entrypoint.sh"]
EXPOSE 3306
CMD ["mysqld"]
I have been looking on Google after possible solutions but I could only find people having the same problem without any solution being posted.
My vagrant definition looks like this:
Vagrant.configure(VAGRANTFILE_API_VERSION) do |config|
config.vm.define "mariadb" do |v|
v.vm.provider "docker" do |d|
d.build_dir = "./docker/mariadb"
d.name = "mariadb"
d.ports = ["3306:3306"]
d.vagrant_vagrantfile = "#{DOCKER_HOST_VAGRANTFILE}"
d.env = {
MYSQL_ROOT_PASSWORD: "root",
MYSQL_USER: "root",
MYSQL_PASS: "root"
}
end
end
end
Also, when I try to install MySQL instead of MariaDB then it works. So my idea here is that there is an error when setting the Root Passwords for MariaDB. The thing that makes me think that is that this error pops up just after the line New password for the MariaDB "root" user: and on the end it then says it hasn't been configured yet.
Maybe the problem is in the VagrantFile then? However I tried changing the way the env variables were set and that didn't fixed my problem :(
I would be glad if someone could help me with this.
Update:
DockerFile used: https://github.com/docker-library/mariadb/blob/d06c367c4b199f91b36f5f6fabf8305282b8abac/10.0/Dockerfile (I corrected the permissions to 755)

The solution was adding more RAM to my VirtualMachine and completely recreating it (so opening virtualbox and removing the boot2docker machine too). (Thanks to user2915097 for point this out!)

Related

docker container nginx start but keeps hanging

my dockerfile:
FROM AWS_ECR_IMAGE
RUN apt-get update && apt-get install -y \
cron \
python-dev \
git \
zlib1g-dev \
libffi-dev \
libssl-dev \
autotools-dev \
automake \
libbz2-dev \
libaio-dev \
libsasl2-dev \
python-pip
RUN pip install boto boto3 awscli
# Install Nginx.
RUN \
add-apt-repository -y ppa:nginx/stable && \
apt-get update && \
apt-get install -y nginx && \
rm -rf /var/lib/apt/lists/* && \
echo "\ndaemon off;" >> /etc/nginx/nginx.conf && \
chown -R www-data:www-data /var/lib/nginx
# Define mountable directories.
VOLUME ["/etc/nginx/sites-enabled", "/etc/nginx/certs", "/etc/nginx/conf.d", "/var/log/nginx", "/var/www/html"]
# Define working directory.
WORKDIR /etc/nginx
# Define default command.
CMD ["nginx"]
COPY nginx_conf /etc/nginx/sites-available/default
# Start service, replace server name, update web ui
COPY main.sh /opt/annotation-pipeline-docs/main.sh
RUN chmod 0755 /opt/annotation-pipeline-docs/main.sh
ENTRYPOINT [ "sh", "-c", "/opt/annotation-pipeline-docs/main.sh" ]
# Expose ports.
EXPOSE 80
And my entrypoint bash file (I need to update the server name first when the container runs) is:
#!/bin/bash -e
/usr/local/bin/aws s3 sync s3://${S3_Bucket}/docs/${ENVIRONMENT}/HEAD/ /var/www/html/
if [ "$ENVIRONMENT" == "prod" ]
then
sed -i.bak "s/REPLACE_ME/example.com/g" /etc/nginx/sites-available/default
else
sed -i.bak "s/REPLACE_ME/example-$ENVIRONMENT.com/g" /etc/nginx/sites-available/default
fi
nginx
while true; do
sleep 60
echo "s3 sync again:"
/usr/local/bin/aws s3 sync s3://${S3_Bucket}/docs/${ENVIRONMENT}/HEAD/ /var/www/html/
done
The issue is when
nginx
runs, it will hanging forever in the terminal:
and the while loop will never get called. Anyone know why is hanging and how to resolve it? Please help, tks in advanced.
The reason for my issue is waiting for the traffic, the while loop will never get called until Nginx start free the bash. However, Nginx will be running in the foreground and not release the focus.
The solution I tried is instead of letting Nginx running as a foreground service, I changed it run in the background. Since this is the only service in my container, should have no problem to do it.
the code changed is simply removed below line in my dockerfile:
echo "\ndaemon off;" >> /etc/nginx/nginx.conf
which will make Nginx as a foreground service

Build failed while appending line in source of docker container

I'm working on https://github.com/audip/rpi-haproxy and get this error message when building the docker container:
Build failed: The command '/bin/sh -c echo "deb http://httpredir.debian.org/debian jessie-backports main" >> /etc/apt/sources.list' returned a non-zero code: 1
This can be viewed at https://hub.docker.com/r/audip/rpi-haproxy/builds/brxdkayq3g45jjhppndcwnb/
I tried to find answers, but the problem seems to be something off on Line 4 of the Dockerfile. Need help to fix this build from failing.
# Pull base image.
FROM resin/rpi-raspbian:latest
# Enable Jessie backports
RUN echo "deb http://httpredir.debian.org/debian jessie-backports main" >> /etc/apt/sources.list
# Setup GPG keys
RUN gpg --keyserver pgpkeys.mit.edu --recv-key 8B48AD6246925553 \
&& gpg -a --export 8B48AD6246925553 | sudo apt-key add - \
&& gpg --keyserver pgpkeys.mit.edu --recv-key 7638D0442B90D010 \
&& gpg -a --export 7638D0442B90D010 | sudo apt-key add -
# Install HAProxy
RUN apt-get update \
&& apt-get install haproxy -t jessie-backports
# Define working directory.
WORKDIR /usr/local/etc/haproxy/
# Copy config file to container
COPY haproxy.cfg .
COPY start.bash .
# Define mountable directories.
VOLUME ["/haproxy-override"]
# Run loadbalancer
# CMD ["haproxy", "-f", "/usr/local/etc/haproxy/haproxy.cfg"]
# Define default command.
CMD ["bash", "start.bash"]
# Expose ports.
EXPOSE 80
EXPOSE 443
From your logs:
standard_init_linux.go:178: exec user process caused "exec format error"
It's complaining about an invalid binary format. The image you are using is a Raspberry Pi image, which would be based on an ARM chipset. Your build is running on an AMD64 chipset. These are not binary compatible. I believe this image is designed to be built on a Pi itself.

Failed to Call Access Method Exception when Creating a MedicationOrder in FHIR

I am using this http://fhirtest.uhn.ca/baseDstu2 test FHIR server and it worked okay so far.
Now I am getting an HTTP-500 - Failed to Call Access Method exception.
Anyone has any idea on what has gone wrong?
This happens frequently. Probably because someone tested weird queries or similar that put the server in an unstable status.
I suggest posting a comment in https://chat.fhir.org/#narrow/stream/hapi to get the server restarted,
or install http://hapifhir.io/doc_cli.html which does basically the same but you have full control.
I built a Dockerfile:
FROM debian:sid
MAINTAINER Günter Zöchbauer <guenter#yyy.com>
ENV DEBIAN_FRONTEND noninteractive
RUN \
apt-get -q update && \
DEBIAN_FRONTEND=noninteractive && \
apt-get install --no-install-recommends -y -q \
apt-transport-https \
apt-utils \
wget \
bzip2 \
default-jdk
# net-tools sudo procps telnet
RUN \
apt-get update && \
rm -rf /var/lib/apt/lists/*
https://github.com/jamesagnew/hapi-fhir/releases/download/v2.0/hapi-fhir-2.0-cli.tar.bz2 && \
ADD hapi-* /hapi_fhir_cli/
RUN ls -la
RUN ls -la /hapi_fhir_cli
ADD prepare_server.sh /hapi_fhir_cli/
RUN \
cd /hapi_fhir_cli && \
bash -c /hapi_fhir_cli/prepare_server.sh
ADD start.sh /hapi_fhir_cli/
WORKDIR /hapi_fhir_cli
EXPOSE 5555
ENTRYPOINT ["/hapi_fhir_cli/start.sh"]
Which requires in the same directory as the Dockerfile
prepare_server.sh
#!/usr/bin/env bash
ls -la
./hapi-fhir-cli run-server --allow-external-refs &
while ! timeout 1 bash -c "echo > /dev/tcp/localhost/8080"; do sleep 10; done
./hapi-fhir-cli upload-definitions -t http://localhost:8080/baseDstu2
./hapi-fhir-cli upload-examples -c -t http://localhost:8080/baseDstu2
start.sh
#!/usr/bin/env bash
cd /hapi_fhir_cli
./hapi-fhir-cli run-server --allow-external-refs -p 5555
Build
docker build myname/hapi_fhir_cli_dstu2 -t . #--no-cache
Run
docker run -d -p 5555:5555 [image id from docker build]
Hope this helps.

How can I run elasticsearch on a docker container using supervisor?

I ran into some problems running elasticsearch on a debian-based container, a combination of not being able to find log files and not being able to run as root. But even symlinking the config files didn't work for me. I was able to get it running and thought it might be helpful for somebody.
I installed elasticsearch with this command:
wget -qO - https://packages.elastic.co/GPG-KEY-elasticsearch | apt-key add - \
&& echo "deb http://packages.elastic.co/elasticsearch/2.x/debian stable main" | tee -a /etc/apt/sources.list.d/elasticsearch-2.x.list \
&& apt-get update \
&& apt-get install -y elasticsearch \
&& update-rc.d elasticsearch defaults 95 10
Update: See comment about deprecation from #Morfie
Setting the es.insecure.allow.root flag has been removed: https://github.com/elastic/elasticsearch/commit/3ccd59592a46aa26b0675025248a69b4ade3d516
Previous Answer:
Dockerfile:
RUN mkdir /usr/share/elasticsearch/config \
&& ln /etc/elasticsearch/logging.yml /usr/share/elasticsearch/config/ \
&& ln /etc/elasticsearch/elasticsearch.yml /usr/share/elasticsearch/config/ \
&& chmod 774 /usr/share/elasticsearch/config
COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
CMD ["/usr/bin/supervisord"]
And elasticsearch entry in supervisord.conf
[program:elasticsearch]
command=/usr/share/elasticsearch/bin/elasticsearch -Des.insecure.allow.root=true

Why does "docker run" error with "no such file or directory"?

I am trying to run a container which runs an automated build. Here is the dockerfile:
FROM ubuntu:14.04
MAINTAINER pmandayam
# update dpkg repositories
RUN apt-get update
# install wget
RUN apt-get install -y wget
# get maven 3.2.2
RUN wget --no-verbose -O /tmp/apache-maven-3.2.2.tar.gz http://archive.apache.or
g/dist/maven/maven-3/3.2.2/binaries/apache-maven-3.2.2-bin.tar.gz
# verify checksum
RUN echo "87e5cc81bc4ab9b83986b3e77e6b3095 /tmp/apache-maven-3.2.2.tar.gz" | md5
sum -c
# install maven
RUN tar xzf /tmp/apache-maven-3.2.2.tar.gz -C /opt/
RUN ln -s /opt/apache-maven-3.2.2 /opt/maven
RUN ln -s /opt/maven/bin/mvn /usr/local/bin
RUN rm -f /tmp/apache-maven-3.2.2.tar.gz
ENV MAVEN_HOME /opt/maven
# remove download archive files
RUN apt-get clean
# set shell variables for java installation
ENV java_version 1.8.0_11
ENV filename jdk-8u11-linux-x64.tar.gz
ENV downloadlink http://download.oracle.com/otn-pub/java/jdk/8u11-b12/$filename
# download java, accepting the license agreement
RUN wget --no-cookies --header "Cookie: oraclelicense=accept-securebackup-cookie
" -O /tmp/$filename $downloadlink
# unpack java
RUN mkdir /opt/java-oracle && tar -zxf /tmp/$filename -C /opt/java-oracle/
ENV JAVA_HOME /opt/java-oracle/jdk$java_version
ENV PATH $JAVA_HOME/bin:$PATH
# configure symbolic links for the java and javac executables
RUN update-alternatives --install /usr/bin/java java $JAVA_HOME/bin/java 20000 &
& update-alternatives --install /usr/bin/javac javac $JAVA_HOME/bin/javac 20000
# install mongodb
RUN echo 'deb http://downloads-distro.mongodb.org/repo/ubuntu-upstart dist 10gen
' | sudo tee /etc/apt/sources.list.d/mongodb.list && \
apt-get update && \
apt-get --allow-unauthenticated install -y mongodb-org mongodb-org-s
erver mongodb-org-shell mongodb-org-mongos mongodb-org-tools && \
echo "mongodb-org hold" | dpkg --set-selections && \
echo "mongodb-org-server hold" | dpkg --set-selections && \
echo "mongodb-org-shell hold" | dpkg --set-selections &&
\
echo "mongodb-org-mongos hold" | dpkg --set-selectio
ns && \
echo "mongodb-org-tools hold" | dpkg --set-selec
tions
RUN mkdir -p /data/db
VOLUME /data/db
EXPOSE 27017
COPY build-script /build-script
CMD ["/build-script"]
I can build the image successfully but when I try to run the container I get this error:
$ docker run mybuild
no such file or directory
Error response from daemon: Cannot start container 3e8aa828909afcd8fb82b5a5ac894
97a537bef2b930b71a5d20a1b98d6cc1dd6: [8] System error: no such file or directory
what does it mean 'no such file or directory'?
Here is my simple script:
#!/bin/bash
sudo service mongod start
mvn clean verify
sudo service mongod stop
I copy it like this: COPY build-script /build-script
and run it like this: CMD ["/build-script"] not sure why its not working
Using service isn't going to fly - the Docker base images are minimal and don't support this. If you want to run multiple processes, you can use supervisor or runit etc.
In this case, it would be simplest just to start mongo manually in the script e.g. /usr/bin/mongod & or whatever the correct incantation is.
BTW the lines where you try to clean up don't have much effect:
RUN rm -f /tmp/apache-maven-3.2.2.tar.gz
...
# remove download archive files
RUN apt-get clean
These files have already been committed to a previous image layer, so doing this doesn't save any disk-space. Instead you have to delete the files in the same Dockerfile instruction in which they're added.
Also, I would consider changing the base image to a Java one, which would save a lot of work. However, you may have trouble finding one which bundles the official Oracle JDK rather than OpenJDK if that's a problem.

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