Install the SLURM dispatcher

The SLURM dispatcher can run on any node that can submit requests to both the Arvados API server and the SLURM controller. It is not resource-intensive, so you can run it on the API server node.

Install the dispatcher

First, add the appropriate package repository for your distribution.

On Red Hat-based systems:

~$ sudo yum install crunch-dispatch-slurm
~$ sudo systemctl enable crunch-dispatch-slurm

On Debian-based systems:

~$ sudo apt-get install crunch-dispatch-slurm

Create a dispatcher token

Create an Arvados superuser token for use by the dispatcher. If you have multiple dispatch processes, you should give each one a different token.

On the API server, use the following commands:

~$ cd /var/www/arvados-api/current
$ sudo -u webserver-user RAILS_ENV=production bundle exec script/create_superuser_token.rb
zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz

Configure the dispatcher

Set up crunch-dispatch-slurm’s configuration directory:

~$ sudo mkdir -p /etc/arvados
~$ sudo install -d -o root -g crunch -m 0750 /etc/arvados/crunch-dispatch-slurm

Edit /etc/arvados/crunch-dispatch-slurm/crunch-dispatch-slurm.yml to authenticate to your Arvados API server, using the token you generated in the previous step. Follow this YAML format:

Client:
  APIHost: zzzzz.arvadosapi.com
  AuthToken: zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz

This is the only configuration required by crunch-dispatch-slurm. The subsections below describe optional configuration flags you can set inside the main configuration object.

Client::KeepServiceURIs

Override Keep service discovery with a predefined list of Keep URIs. This can be useful if the compute nodes run a local keepstore that should handle all Keep traffic. Example:

Client:
  APIHost: zzzzz.arvadosapi.com
  AuthToken: zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz
  KeepServiceURIs:
  - http://127.0.0.1:25107

PollPeriod

crunch-dispatch-slurm polls the API server periodically for new containers to run. The PollPeriod option controls how often this poll happens. Set this to a string of numbers suffixed with one of the time units ns, us, ms, s, m, or h. For example:

PollPeriod: 3m30s

PrioritySpread

crunch-dispatch-slurm adjusts the “nice” values of its SLURM jobs to ensure containers are prioritized correctly relative to one another. This option tunes the adjustment mechanism.

• If non-Arvados jobs run on your SLURM cluster, and your Arvados containers are waiting too long in the SLURM queue because their “nice” values are too high for them to compete with other SLURM jobs, you should use a smaller PrioritySpread value.
• If you have an older SLURM system that limits nice values to 10000, a smaller PrioritySpread can help avoid reaching that limit.
• In other cases, a larger value is beneficial because it reduces the total number of adjustments made by executing scontrol.

The smallest usable value is 1. The default value of 10 is used if this option is zero or negative. Example:

PrioritySpread: 1000

SbatchArguments

When crunch-dispatch-slurm invokes sbatch, you can add arguments to the command by specifying SbatchArguments. You can use this to send the jobs to specific cluster partitions or add resource requests. Set SbatchArguments to an array of strings. For example:

SbatchArguments:
- "--partition=PartitionName"

Note: If an argument is supplied multiple times, slurm uses the value of the last occurrence of the argument on the command line. Arguments specified through Arvados are added after the arguments listed in SbatchArguments. This means, for example, an Arvados container with that specifies partitions in scheduling_parameter will override an occurrence of --partition in SbatchArguments. As a result, for container parameters that can be specified through Arvados, SbatchArguments can be used to specify defaults but not enforce specific policy.

CrunchRunCommand: Dispatch to SLURM cgroups

If your SLURM cluster uses the task/cgroup TaskPlugin, you can configure Crunch’s Docker containers to be dispatched inside SLURM’s cgroups. This provides consistent enforcement of resource constraints. To do this, use a crunch-dispatch-slurm configuration like the following:

CrunchRunCommand:
- crunch-run
- "-cgroup-parent-subsystem=memory"

The choice of subsystem (“memory” in this example) must correspond to one of the resource types enabled in SLURM’s cgroup.conf. Limits for other resource types will also be respected. The specified subsystem is singled out only to let Crunch determine the name of the cgroup provided by SLURM. When doing this, you should also set ReserveExtraRAM .

CrunchRunCommand: Using host networking for containers

Older Linux kernels (prior to 3.18) have bugs in network namespace handling which can lead to compute node lockups. This by is indicated by blocked kernel tasks in “Workqueue: netns cleanup_net”. If you are experiencing this problem, as a workaround you can disable use of network namespaces by Docker across the cluster. Be aware this reduces container isolation, which may be a security risk.

CrunchRunCommand:
- crunch-run
- "-container-enable-networking=always"
- "-container-network-mode=host"

MinRetryPeriod: Rate-limit repeated attempts to start containers

If SLURM is unable to run a container, the dispatcher will submit it again after the next PollPeriod. If PollPeriod is very short, this can be excessive. If MinRetryPeriod is set, the dispatcher will avoid submitting the same container to SLURM more than once in the given time span.

MinRetryPeriod: 30s

ReserveExtraRAM: Extra RAM for jobs

Extra RAM to reserve (in bytes) on each SLURM job submitted by Arvados, which is added to the amount specified in the container’s runtime_constraints. If not provided, the default value is zero. Helpful when using -cgroup-parent-subsystem, where crunch-run and arv-mount share the control group memory limit with the user process. In this situation, at least 256MiB is recommended to accomodate each container’s crunch-run and arv-mount processes.

ReserveExtraRAM: 268435456

Restart the dispatcher

Restart the dispatcher to run with your new configuration:

~$ sudo systemctl restart crunch-dispatch-slurm

---

Previous: Set up a compute node Next: Test SLURM dispatch