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Version: 23.2

Grid Engine

Altair Grid Engine is a workload manager maintained by Altair Engineering, Inc.

Tower streamlines the deployment of Nextflow pipelines into both cloud-based and on-prem Grid Engine clusters.

Requirements​

To launch pipelines into a Grid Engine cluster from Tower, the following requirements must be satisfied:

  • The cluster should allow outbound connections to the Tower web service.
  • The cluster queue used to run the Nextflow head job must be able to submit cluster jobs.
  • The Nextflow runtime version 21.02.0-edge (or later) must be installed on the cluster.

Compute environment​

To create a new compute environment for Grid Engine in Tower:

  1. In a workspace, select Compute environments and then New environment.

  2. Enter a descriptive name for this environment, e.g., "Grid Engine".

  3. Select Altair Grid Engine as the target platform.

  4. Select your credentials, or select + and SSH or Tower Agent to add new credentials.

  5. Enter a name for the credentials.

  6. Enter the absolute path of the Work directory to be used on the cluster.

  7. Enter the absolute path of the Launch directory to be used on the cluster. If omitted, it will be the same as the work directory.

  8. Enter the Login hostname. This is usually the hostname or public IP address of the cluster's login node.

  9. Enter the Head queue name. This is the cluster queue to which the Nextflow job will be submitted.

  10. Enter the Compute queue name. This is the cluster queue to which the Nextflow job will submit tasks.

The compute queue can be overridden by the Nextflow pipeline configuration. See the Nextflow documentation for more details.

  1. Expand Staging options to include optional pre- or post-run Bash scripts that execute before or after the Nextflow pipeline execution in your environment.

  2. You can use the Environment variables option to specify custom environment variables for the Head job and/or Compute jobs.

  3. Configure any advanced options described below, as needed.

  4. Select Create to finalize the creation of the compute environment.

Jump to the documentation for launching pipelines.

Advanced options​

  • Use the Nextflow queue size to limit the number of jobs that Nextflow can submit to the scheduler at the same time.

  • Use the Head job submit options to specify Grid Engine options for the head job. You can optionally apply these options to compute jobs as well: