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Compute environment overview

Seqera Platform compute environments define the execution platform where a pipeline will run. Compute environments enable users to launch pipelines on a growing number of cloud and on-premises platforms.

Each compute environment must be configured to enable Seqera to submit tasks. See the individual compute environment pages below for platform-specific configuration steps.

Platforms​

Select default compute environment​

If you have more than one compute environment, you can select a workspace primary compute environment to be used as the default when launching pipelines in that workspace. In a workspace, select Compute Environments. Then select Make primary from the options menu next to the compute environment you wish to use as default.

Disable compute environment​

Users with Admin or Owner workspace permissions can disable and enable compute environments.

When you disable a compute environment:

  • Actions that use this compute environment will fail to run. Update actions to use a new compute environment.
  • New pipelines and Studio sessions will not run on the disabled compute environment. Update pipelines and Studios to use a new compute environment.
  • Running pipelines and Studio sessions are not terminated. Ongoing runs and Studio sessions will finish gracefully.
  • If the compute environment was set as primary, it will be unset. Until you select a new primary compute environment, new runs will default to the next available compute environment.

To disable a compute environment, select Disable from the options menu next to the compute environment in your workspace Compute Environments page.

To re-enable a disabled compute environment, select Enable from the options menu. Enabled compute environments can run new pipelines and Studio sessions.

Rename compute environment​

You can edit the names of compute environments in private and organization workspaces. Select Rename from the options menu next to the compute environment you wish to edit.

Select Update on the edit page to save your changes after you have updated the compute environment name.

GPU usage​

The process for provisioning GPU instances in your compute environment differs for each cloud provider.

AWS Batch​

The AWS Batch compute environment creation form in Seqera includes an Enable GPUs option. This enables you to run GPU-dependent workflows in the compute environment.

Some important considerations:

  • Seqera only supports NVIDIA GPUs. Select instances with NVIDIA GPUs for your GPU-dependent processes.
  • The Enable GPUs setting causes Batch Forge to specify the most current AWS-recommended GPU-optimized ECS AMI as the EC2 fleet AMI when creating the compute environment. This setting can be overridden by AMI ID in the advanced options.
  • The Enable GPUs setting alone does not deploy GPU instances in your compute environment. You must still specify GPU-enabled instance types in the Advanced options > Instance types field.
  • Your Nextflow script must include accelerator directives to use the provisioned GPUs.
  • The NVIDIA Container Runtime uses environment variables in container images to specify a GPU accelerated container. These variables should be included in the containerOptions directive for each GPU-dependent process in your Nextflow script. The containerOptions directive can be set inline in your process definition or via configuration. For example, to add the directive to a process named UseGPU via configuration:
process {
  withName: UseGPU {
    containerOptions '-e NVIDIA_DRIVER_CAPABILITIES=compute,utility -e NVIDIA_VISIBLE_DEVICES=all'
  }
}