SPDX-License-Identifier: CC-BY-SA-3.0
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-h2. Install Docker
+h2(#cgroups). Configure Linux cgroups accounting
-Compute nodes must have Docker installed to run containers. This requires a relatively recent version of Linux (at least upstream version 3.10, or a distribution version with the appropriate patches backported). Follow the "Docker Engine installation documentation":https://docs.docker.com/ for your distribution.
+Linux can report what compute resources are used by processes in a specific cgroup or Docker container. Crunch can use these reports to share that information with users running compute work. This can help workflow authors debug and optimize their workflows.
-h2(#configure_docker_daemon). Configure the Docker daemon
-
-Crunch runs Docker containers with relatively little configuration. You may need to start the Docker daemon with specific options to make sure these jobs run smoothly in your environment. This section highlights options that are useful to most installations. Refer to the "Docker daemon reference":https://docs.docker.com/reference/commandline/daemon/ for complete information about all available options.
-
-The best way to configure these options varies by distribution.
-
-* If you're using the Debian package, you can list these options in the @DOCKER_OPTS@ setting in @/etc/default/docker@.
-* On Red Hat-based distributions, you can list these options in the @other_args@ setting in @/etc/sysconfig/docker@.
+To enable cgroups accounting, you must boot Linux with the command line parameters @cgroup_enable=memory swapaccount=1@.
-h3. Default ulimits
+Currently Arvados is not compatible with the new cgroups accounting, also known as cgroups v2. Currently, all supported GNU/Linux distributions don't use cgroups v2 as default
+If you are using a distribution in the compute nodes that ships with cgroups v2 enabled, make sure to disable it by booting Linux with the command line parameters @systemd.unified_cgroup_hierarchy=0@.
-Docker containers inherit ulimits from the Docker daemon. However, the ulimits for a single Unix daemon may not accommodate a long-running Crunch job. You may want to increase default limits for compute containers by passing @--default-ulimit@ options to the Docker daemon. For example, to allow containers to open 10,000 files, set @--default-ulimit nofile=10000:10000@.
+After making changes, reboot the system to make these changes effective.
-h3. DNS
+h3. Red Hat and CentOS
-Your containers must be able to resolve the hostname of your API server and any hostnames returned in Keep service records. If these names are not in public DNS records, you may need to specify a DNS resolver for the containers by setting the @--dns@ address to an IP address of an appropriate nameserver. You may specify this option more than once to use multiple nameservers.
-
-h2. Configure Linux cgroups accounting
+<notextile>
+<pre><code>~$ <span class="userinput">sudo grubby --update-kernel=ALL --args='cgroup_enable=memory swapaccount=1 systemd.unified_cgroup_hierarchy=0'</span>
+</code></pre>
+</notextile>
-Linux can report what compute resources are used by processes in a specific cgroup or Docker container. Crunch can use these reports to share that information with users running compute work. This can help pipeline authors debug and optimize their workflows.
+h3. Debian and Ubuntu
-To enable cgroups accounting, you must boot Linux with the command line parameters @cgroup_enable=memory swapaccount=1@.
-
-On Debian-based systems, open the file @/etc/default/grub@ in an editor. Find where the string @GRUB_CMDLINE_LINUX@ is set. Add @cgroup_enable=memory swapaccount=1@ to that string. Save the file and exit the editor. Then run:
+Open the file @/etc/default/grub@ in an editor. Find where the string @GRUB_CMDLINE_LINUX@ is set. Add @cgroup_enable=memory swapaccount=1 systemd.unified_cgroup_hierarchy=0@ to that string. Save the file and exit the editor. Then run:
<notextile>
<pre><code>~$ <span class="userinput">sudo update-grub</span>
</code></pre>
</notextile>
-On Red Hat-based systems, run:
+h2(#install_docker). Install Docker
+
+Compute nodes must have Docker installed to run containers. This requires a relatively recent version of Linux (at least upstream version 3.10, or a distribution version with the appropriate patches backported). Follow the "Docker Engine installation documentation":https://docs.docker.com/install/ for your distribution.
+
+Make sure Docker is enabled to start on boot:
<notextile>
-<pre><code>~$ <span class="userinput">sudo grubby --update-kernel=ALL --args='cgroup_enable=memory swapaccount=1'</span>
+<pre><code># <span class="userinput">systemctl enable --now docker</span>
</code></pre>
</notextile>
-Finally, reboot the system to make these changes effective.
+h2(#configure_docker_daemon). Configure the Docker daemon
-h2. Create a project for Docker images
+Depending on your anticipated workload or cluster configuration, you may need to tweak Docker options.
-Here we create a default project for the standard Arvados Docker images, and give all users read access to it. The project is owned by the system user.
+For information about how to set configuration options for the Docker daemon, see https://docs.docker.com/config/daemon/systemd/
-<notextile>
-<pre><code>~$ <span class="userinput">uuid_prefix=`arv --format=uuid user current | cut -d- -f1`</span>
-~$ <span class="userinput">project_uuid=`arv --format=uuid group create --group "{\"owner_uuid\":\"$uuid_prefix-tpzed-000000000000000\", \"group_class\":\"project\", \"name\":\"Arvados Standard Docker Images\"}"`</span>
-~$ <span class="userinput">echo "Arvados project uuid is '$project_uuid'"</span>
-~$ <span class="userinput">read -rd $'\000' newlink <<EOF; arv link create --link "$newlink"</span>
-<span class="userinput">{
- "tail_uuid":"$all_users_group_uuid",
- "head_uuid":"$project_uuid",
- "link_class":"permission",
- "name":"can_read"
-}
-EOF</span>
-</code></pre></notextile>
-
-h2. Download and tag the latest arvados/jobs docker image
-
-In order to start workflows from workbench, there needs to be Docker image tagged @arvados/jobs:latest@. The following command downloads the latest arvados/jobs image from Docker Hub, loads it into Keep, and tags it as 'latest'. In this example @$project_uuid@ should be the UUID of the "Arvados Standard Docker Images" project.
+h3. Changing ulimits
-<notextile>
-<pre><code>~$ <span class="userinput">arv-keepdocker --pull arvados/jobs latest --project-uuid $project_uuid</span>
-</code></pre></notextile>
+Docker containers inherit ulimits from the Docker daemon. However, the ulimits for a single Unix daemon may not accommodate a long-running Crunch job. You may want to increase default limits for compute containers by passing @--default-ulimit@ options to the Docker daemon. For example, to allow containers to open 10,000 files, set @--default-ulimit nofile=10000:10000@.
+
+h2. Troubleshooting
+
+h3. Workflows fail with @ValidationException: Not found: '/var/lib/cwl/workflow.json#main'@
+
+A possible configuration error is having Docker installed as a @snap@ package rather than a @deb@ package. This is a problem because @snap@ packages are partially containerized and may have a different view of the filesystem than @crunch-run@. This will produce confusing problems, for example, directory bind mounts sent to Docker that are empty (instead of containing the intended files) and resulting in unexpected "file not found" errors.
-If the image needs to be downloaded from Docker Hub, the command can take a few minutes to complete, depending on available network bandwidth.
+To check for this situation, run @snap list@ and look for @docker@. If found, run @snap remove docker@ and follow the instructions to above to "install Docker Engine":#install_docker .
projects / arvados.git / blobdiff