I have a simple startup script which looks like so:
#!/usr/bin/env bash
sudo apt update
sudo apt install -y ruby-full ruby-bundler build-essential
And create VM instance on GCP like so:
$ gcloud compute instances create test-app --boot-disk-size=10GB --image-family ubuntu-1604-lts --image-project=ubuntu-os-cloud --machine-type=g1-small --zone europe-west1-b --tags test-server --restart-on-failure --metadata-from-file startup-script=startup.sh
My startup.sh is executable. I set its rights like so:
$ chmod +x startup.sh
When however I enter the shell of my newly created instance and check bundler:
test-app:~$ bundle -v
I get these messages:
The program 'bundle' is currently not installed...
So, what is wrong with that and how can I fix it? PS. If I run all my commands just from inside the instance shell, it's all ok, so there is some problem with using startup script on GCP.
I tested with your use case, But the bundle package was installed without making any changes.
Output:
bundle -v
Bundler version 1.11.2
You can check VM serial console log output to verify if start-up script ran. Check the VM instance to verify if the package is installed using the commands below:
sudo apt list --installed | grep -i bundle
sudo egrep bundle /var/log/dpkg.log
In addition, check the gem list bundle
Related
I am trying to run MySQL in an R script running inside a Docker (actually Rocker) container, but am getting an error on the “install_packages(…” step. The only solution I found that was somewhat similar was specific to running RedHat Linux (I am running Mac OS X 10.15) and the solution included pointing to several directories that I do not have. Running under RStudio or from the command line, RMySQL loads without a problem.
Dockerfile:
FROM rocker/r-ver:latest
RUN mkdir /home/analysis
COPY install_packages.R /home/analysis/install_packages.R
COPY script_basic.R /home/analysis/script_basic.R
RUN Rscript /home/analysis/install_packages.R
CMD Rscript /home/analysis/script_basic.R
R files:
script_basic.R
library( RMySQL )
install_packages.R
install_packages(“RMySQL”)
Commands and responses:
$ docker build -t myapp .
…
Successfully tagged myapp:latest
$ docker run -it --rm myapp
Loading required package: DBI
Error: package or namespace load failed for ‘RMySQL’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/RMySQL/libs/RMySQL.so':
libmysqlclient.so.21: cannot open shared object file: No such file or directory
Execution halted
$
I believe that rocker/r-dev does not include the libraries you need to get this to run. Untested, but try something like this.
Dockerfile
FROM rocker/r-ver:latest
RUN mkdir /home/analysis
RUN apt-get update \
&& apt-get install -y --no-install-recommends libmariadbclient-dev
COPY install_packages.R /home/analysis/install_packages.R
COPY script_basic.R /home/analysis/script_basic.R
RUN Rscript /home/analysis/install_packages.R
CMD Rscript /home/analysis/script_basic.R
You can find the need for certain libraries on https://cran.r-project.org/web/packages/RMySQL/index.html, as
SystemRequirements: libmariadb-client-dev | libmariadb-client-lgpl-dev | libmysqlclient-dev (deb), mariadb-devel (rpm), mariadb | mysql-connector-c (brew), mysql56_dev (csw)
and a note on how to install them in RMySQL's github README.md's Installation section.
(The CRAN page references libmysqlclient-dev, but the github page suggests "the mariadb implementation is much better". I don't know the premise of the statement, just explaining why I suggested one and CRAN listed another.)
I was creating an own docker image based on the latest rakudo-star docker image. I wanted to use DBIish to connect to a mysql database. Unfortunately I am not able to get the DBDish::mysql to work.
I've installed default-libmysqlclient-dev as you can see in
# find / -name 'libmysqlclient*.so'
/usr/lib/x86_64-linux-gnu/libmysqlclient_r.so
/usr/lib/x86_64-linux-gnu/libmysqlclient.so
The error i am facing is:
# perl6 -Ilib -e 'use DBDish::mysql; DBDish::mysql.connect()'
Cannot locate native library 'mysqlclient': mysqlclient: cannot open shared object file: No such file or directory
in method setup at /usr/share/perl6/sources/24DD121B5B4774C04A7084827BFAD92199756E03 (NativeCall) line 289
in method CALL-ME at /usr/share/perl6/sources/24DD121B5B4774C04A7084827BFAD92199756E03 (NativeCall) line 539
in method connect at /root/DBIish/lib/DBDish/mysql.pm6 (DBDish::mysql) line 12
in block <unit> at -e line 1
Short answer: you need the package libmysqlclient20 (I added the documentation request to a similar DBIish issue). Debian 9 (stable at the moment) uses and older version than Ubuntu 18.04 (stable at the moment) and Debian Unstable. It also refers to mariadb instead of mysql. Pick libmariadbclient18 on images based on Debian Stable and create a link with the mysql name (see below).
On Debian Testing/Unstable and recent derivatives:
$ sudo apt-get install libmysqlclient20
$ dpkg -L libmysqlclient20
/.
/usr
/usr/lib
/usr/lib/x86_64-linux-gnu
/usr/lib/x86_64-linux-gnu/libmysqlclient.so.20.3.9
/usr/share
/usr/share/doc
/usr/share/doc/libmysqlclient20
/usr/share/doc/libmysqlclient20/NEWS.Debian.gz
/usr/share/doc/libmysqlclient20/changelog.Debian.gz
/usr/share/doc/libmysqlclient20/copyright
/usr/lib/x86_64-linux-gnu/libmysqlclient.so.20
On Debian 9 and derivatives:
$ dpkg -L libmariadbclient18
/.
/usr
/usr/lib
/usr/lib/x86_64-linux-gnu
/usr/lib/x86_64-linux-gnu/libmariadbclient.so.18.0.0
/usr/lib/x86_64-linux-gnu/mariadb18
/usr/lib/x86_64-linux-gnu/mariadb18/plugin
/usr/lib/x86_64-linux-gnu/mariadb18/plugin/client_ed25519.so
/usr/lib/x86_64-linux-gnu/mariadb18/plugin/dialog.so
/usr/lib/x86_64-linux-gnu/mariadb18/plugin/mysql_clear_password.so
/usr/share
/usr/share/doc
/usr/share/doc/libmariadbclient18
/usr/share/doc/libmariadbclient18/changelog.Debian.gz
/usr/share/doc/libmariadbclient18/copyright
/usr/lib/x86_64-linux-gnu/libmariadbclient.so.18
Create the link:
$ sudo ln -s /usr/lib/x86_64-linux-gnu/libmariadbclient.so.18 /usr/lib/x86_64-linux-gnu/libmysqlclient.so.18
In order to illustrate this, I created an Ubuntu 18.04 container for the occasion*:
docker run -ti --rm --entrypoint=bash rakudo/ubuntu-amd64-18.04
And the abbreviated commands and output:
# apt-get install -y libmysqlclient20 build-essential
# zef install DBIish
# perl6 -e 'use DBDish::mysql; DBDish::mysql.connect()'
Cannot look up attributes in a DBDish::mysql type object
[...]
The error is because I didn't pass the correct parameters for connect as I didn't have a db running. The important thing is that no .so file is missing.
*: I uploaded it to the Docker Hub, a normal run will put you right in the REPL:
$ docker run -ti --rm rakudo/ubuntu-amd64-18.04
To exit type 'exit' or '^D'
>
(I didn't use the Star image when debugging, but it does not matter because this is a more generic problem.)
I created a Dockerfile to create an image to run web based application. When I running that file and it tries to collect mysqlclient==1.3.7 ,following error is occured.
"mysql_config raise EnvironmentError("%s not found" %(mysql_config.path,))
EnvironmentError: mysql_config not found
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-ME9Fq7/mysqlclient/
You are using pip version 8.1.1, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command. "
This is Dockerfile
############################################################
# Dockerfile to build Python WSGI Application Containers
# Based on Ubuntu
############################################################
# Set the base image to Ubuntu
FROM ubuntu:latest
# File Author / Maintainer
MAINTAINER Brian
# Add the application resources URL
#RUN echo "deb http://archive.ubuntu.com/ubuntu/ $(lsb_release -sc) main universe" >> /etc/apt/sources.list
# Update the sources list
RUN apt-get update -y;
# Install basic applications
RUN apt-get install -y tar git curl nano wget dialog net-tools build-essential
# Install Python and Basic Python Tools
RUN apt-get install -y python python3-dev python-distribute python-pip libssl-dev
# Copy the application folder inside the container
ADD /WebApp /WebApp
#RUN pip install mysql
# Get pip to download and install requirements:
RUN pip install -r /WebApp/requirements.txt
# Expose ports
EXPOSE 80
# Set the default directory where CMD will execute
WORKDIR /WebApp
# Set the default command to execute
# when creating a new container
# i.e. using CherryPy to serve the application
CMD ./start.sh
How can I solve this problem?
I believe that you are trying to install the mysql driver for Python, but you don't have MySQL installed. Try to install MySQL before installing mysql driver:
RUN apt-get install mysql-server
Hope it helps!
I am creating a docker image with tomcat and mySql. I have a .war file that I can push to the Tomcat and the docker image is working as expected.
But the application also need a database on mySQL in the same docker image (as I do not want to run multiple images as this is fairly small and is for a demonstration only).
I am using a tomcat image as base and install mySql on it. The base OS is Ubuntu.
Here is my dockerfile:
#Get the base
FROM davidcaste/debian-tomcat:tomcat8
#Add mySql
RUN echo 'debconf debconf/frontend select Noninteractive' | debconf-set-selections
RUN apt-get -y update
RUN apt-get -y install wget zip gcc
RUN { \
echo mysql-community-server mysql-community-server/data-dir select ''; \
echo mysql-community-server mysql-community-server/root-pass password ''; \
echo mysql-community-server mysql-community-server/re-root-pass password ''; \
echo mysql-community-server mysql-community-server/remove-test-db select false; \
} | debconf-set-selections \
&& apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y mysql-server
RUN /etc/init.d/mysql start
RUN wget http://github.com/xxxx/xxxx/blob/master/xxxx/src/main/resources/sql/create-schema.sql
RUN cp create-schema.sql /usr/
RUN wget http://github.com/xxxx/xxxx/blob/master/xxxx/src/main/resources/sql/metadata.sql
RUN cp metadata.sql /usr/
#RUN mysql -- this gives error
#RUN create database test; -- this gives error
#Get the Web Application from Nexus
RUN wget "http://mynexus:8081/nexus/service/local/artifact/maven/redirect?g=org.my&a=my-app&r=repo&e=war&v=LATEST" --content-disposition -O app.war
#Copy the war file
RUN cp app.war /opt/tomcat/webapps/
EXPOSE 8080
CMD ["catalina.sh", "run"]
Without the mySql related items (create database etc) the docker build works and it runs well. But I am not able to understand how to create the database using my schema and metadata sql files.
You can run the SQL commands after container start up but not during you build it. One option would be to override the entrypoint and do it there. Another option would be to have a docker-compose first bringing up the plain mysql container and after that create db and schema with an additional container that runs the bash script.
See i.e. here to get an idea about it. Another option is to pass the SQL related stuff as ENV setting as depicted in one of the answers in above link.
EDIT: My goal is to be able to emit metrics from my spring-boot application and have them sent to a Graphite server. For that I am trying to set up statsd. If you can suggest a cleaner approach, that would be better.
I have a Beanstalk application which requires statsd to run as a background process. I was able to specify commands and packages through ebextensions config file as follows:
packages:
yum:
git: []
commands:
01_nodejs_install:
command: sudo yum -y install nodejs npm --enablerepo=epel
ignoreErrors: true
02_mkdir_statsd:
command: mkdir /home/ec2-user/statsd
03_fetch_statsd:
command: git clone https://github.com/etsy/statsd.git /home/ec2-user/statsd
ignoreErrors: true
04_run_statsd:
command: node stats.js exampleConfig.js
cwd: /home/ec2-user/statsd
When I try to deploy the application to a new environment, the EC2 node never comes up fully. I logged in to check what might be going on and noticed in /var/log/cfn-init.log that 01_nodejs_install, 02_mkdir_statsd and 03_fetch_statsd were executed successfully. So I guess the system was stuck on the fourth command (04_run_statsd).
2016-05-24 01:25:09,769 [INFO] Yum installed [u'git']
2016-05-24 01:25:37,751 [INFO] Command 01_nodejs_install succeeded
2016-05-24 01:25:37,755 [INFO] Command 02_mkdir_statsd succeeded
2016-05-24 01:25:38,700 [INFO] Command 03_fetch_statsd succeeded
cfn-init.log (END)
I need help with the following:
If there is a better way to install and run statsd while instantiating an environment, I would appreciate if you could provide details on that approach. This current scheme seems hacky.
If this is the approach I need to stick with, how can I run the fourth command so that statsd can be run as a background process?
Tried a few things and found that the following ebextensions configs work:
packages:
yum:
git: []
commands:
01_nodejs_install:
command: sudo yum -y install nodejs npm --enablerepo=epel
ignoreErrors: true
02_mkdir_statsd:
command: mkdir /home/ec2-user/statsd
03_fetch_statsd:
command: git clone https://github.com/etsy/statsd.git /home/ec2-user/statsd
ignoreErrors: true
04_change_config:
command: cat exampleConfig.js | sed 's/2003/<graphite server port>/g' | sed 's/graphite.example.com/my.graphite.server.hostname/g' > config.js
cwd: /home/ec2-user/statsd
05_run_statsd:
command: setsid node stats.js config.js >/dev/null 2>&1 < /dev/null &
cwd: /home/ec2-user/statsd
Note that I added another command (04_change_config) so that I may configure my own Graphite server and port in statsd configs. This change is not needed to address the original question, though.
The actual run command uses setsid to run the command as a daemon.