Customizing Crunch environment using Docker

This page describes how to customize the runtime environment (e.g., the programs, libraries, and other dependencies needed to run a job) that a crunch script will be run in using Docker. Docker is a tool for building and running containers that isolate applications from other applications running on the same node. For detailed information about Docker, see the Docker User Guide.

This page will demonstrate how to:

Fetch the arvados/jobs Docker image
Manually install additional software into the container
Create a new custom image
Upload that image to Arvados for use by Crunch jobs
Share your image with others

Note:

This tutorial assumes that you have installed the Arvados Command line SDK and Python SDK on your workstation and have a working environment.

You also need ensure that Docker is installed, the Docker daemon is running, and you have permission to access Docker. You can test this by running docker version. If you receive a permission denied error, your user account may need to be added to the docker group. If you have root access, you can add yourself to the docker group using $ sudo addgroup $USER docker then log out and log back in again; otherwise consult your local sysadmin.

Fetch a starting image

The easiest way to begin is to start from the “arvados/jobs” image which already has the Arvados SDK installed along with other configuration required for use with Crunch.

Download the latest “arvados/jobs” image from the Docker registry:

$ docker pull arvados/jobs:latest
Pulling repository arvados/jobs
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Install new packages

Next, enter the container using docker run, providing the arvados/jobs image and the program you want to run (in this case the bash shell).

$ docker run --interactive --tty --user root arvados/jobs /bin/bash
root@fbf1d0f529d5:/#

Next, update the package list using apt-get update.

root@fbf1d0f529d5:/# apt-get update
Get:2 http://apt.arvados.org stretch-dev InRelease [3260 B]
Get:1 http://security-cdn.debian.org/debian-security stretch/updates InRelease [94.3 kB]
Ign:3 http://cdn-fastly.deb.debian.org/debian stretch InRelease
Get:4 http://cdn-fastly.deb.debian.org/debian stretch-updates InRelease [91.0 kB]
Get:5 http://apt.arvados.org stretch-dev/main amd64 Packages [208 kB]
Get:6 http://cdn-fastly.deb.debian.org/debian stretch Release [118 kB]
Get:7 http://security-cdn.debian.org/debian-security stretch/updates/main amd64 Packages [499 kB]
Get:8 http://cdn-fastly.deb.debian.org/debian stretch Release.gpg [2434 B]
Get:9 http://cdn-fastly.deb.debian.org/debian stretch-updates/main amd64 Packages.diff/Index [10.6 kB]
Get:10 http://cdn-fastly.deb.debian.org/debian stretch-updates/main amd64 Packages 2019-07-08-0821.07.pdiff [445 B]
Get:10 http://cdn-fastly.deb.debian.org/debian stretch-updates/main amd64 Packages 2019-07-08-0821.07.pdiff [445 B]
Fetched 1026 kB in 0s (1384 kB/s)
Reading package lists... Done

In this example, we will install the “R” statistical language Debian package “r-base-core”. Use apt-get install:

root@fbf1d0f529d5:/# apt-get install r-base-core
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following additional packages will be installed:
[...]
done.

Now we can verify that “R” is installed:

root@fbf1d0f529d5:/# R

R version 3.3.3 (2017-03-06) -- "Another Canoe"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

Note that you are not limited to installing Debian packages. You may compile programs or libraries from source and install them, edit systemwide configuration files, use other package managers such as pip or gem, and perform any other customization necessary to run your program.

Create a new image

We’re now ready to create a new Docker image. First, quit the container, then use docker commit to create a new image from the stopped container. The container id can be found in the default hostname of the container displayed in the prompt, in this case fbf1d0f529d5:

root@fbf1d0f529d5:/# exit
$ docker commit fbf1d0f529d5 arvados/jobs-with-r
sha256:2818853ff9f9af5d7f77979803baac9c4710790ad2b84c1a754b02728fdff205
$ docker images
$ docker images |head
REPOSITORY            TAG                 IMAGE ID            CREATED             SIZE
arvados/jobs-with-r   latest              2818853ff9f9        9 seconds ago       703.1 MB
arvados/jobs          latest              12b9f859d48c        4 days ago          362 MB

Upload your image

Finally, we are ready to upload the new Docker image to Arvados. Use arv-keepdocker with the image repository name to upload the image. Without arguments, arv-keepdocker will print out the list of Docker images in Arvados that are available to you.

$ arv-keepdocker arvados/jobs-with-r
703M / 703M 100.0%
Collection saved as 'Docker image arvados/jobs-with-r:latest 2818853ff9f9'
qr1hi-4zz18-abcdefghijklmno
$ arv-keepdocker
REPOSITORY                      TAG         IMAGE ID      COLLECTION                     CREATED
arvados/jobs-with-r             latest      2818853ff9f9  qr1hi-4zz18-abcdefghijklmno    Tue Jan 17 20:35:53 2017

You are now able to specify the runtime environment for your program using DockerRequirement in your workflow:

hints:
  DockerRequirement:
    dockerPull: arvados/jobs-with-r

Share Docker images

Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others (or wish to share a pipeline template that uses your Docker image) you will need to use arv-keepdocker with the --project-uuid option to upload the image to a shared project.

$ arv-keepdocker arvados/jobs-with-r --project-uuid qr1hi-j7d0g-xxxxxxxxxxxxxxx

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