Command settings

The Command settings tab includes all settings related to workload manager commands, i.e., job querying and removal commands.

The settings described here are the same for pre-configured and user-defined workload managers.

Define job commands

The first three commands will poll jobs from a host and will populate the corresponding tabs in the Cluster monitor window.

Job polling commands support the following aliases:

{project} – current project’s name

{author} – name of researcher from General settings page of Pirana settings

{username} – Grid user name from remote host settings (refer to the “Remote hosts” section). If not set, then the current user’s login is used.

Poll scheduled jobs — Command to retrieve jobs waiting to start execution.

Poll running jobs — Command to retrieve jobs that are currently executing.

Poll finished jobs — Command to retrieve finished jobs.

Job info — Command to retrieve information about a selected job. If this option is not set, only the Stop jobs option on the right-click menu in the Cluster Monitor window will be available.

Delete a job — Command to delete unfinished jobs related to a search that is stopped.

Job Info and Delete a job support the alias {job}, which is substituted with selected jobs IDs. Usually this is not necessary and, if the alias is not used, job IDs will be added as a space-separated list to the end of the command (e.g., for SGE: qdel will become qdel 101 102 103, qstat -j will be sent as qstat -j 104). But if the workload manager requires arguments of such commands to be enclosed, e.g., within quotes, it may be entered as: delete_job_command --job={job}

Delete all jobs — Command to delete all unfinished jobs. This is typically used to delete jobs submitted by the current user. It supports the aliases:

{project} – current project’s name

{author} – name of researcher from General settings page of Pirana settings

{username} – Grid user name from remote host settings (refer to the “Remote hosts” section). If not set, then the current user’s login is used.

Define commands for node and queue information

Get nodes — Command to retrieve information about grid nodes.

Get queues — Command to retrieve information about grid queues.

Define argument names for priority, job name, and PsN prepend flags

Run priority argument — Argument to use for the run priority.

The alias {val} can be used in cases where the priority cannot be set as a simple -p argument (e.g., for Slurm: --priority={val}).

Job name argument — Argument to use for the job name.

The aliases {val} and {refined_val} are supported. {refined_val} replaces all non-letters and non-digits in {val} with underscores. For example, if {val} is “Project 1-model2.2”, then {refined_val} is “Project_1_model2_2”.

PsN prepend flags argument — Argument to use when setting the PsN prepend flags (e.g., for SGI: -sge_prepend_flags).

Exclusive PsN arguments — Additional PsN arguments to use (e.g., for SGI: -run_on_sge).

These last two arguments will be deleted from the PsN command line when switching job schedulers. For example, if the PsN command for SGE is:

   custom_command1; execute -run_on_sge -sge_prepend_flags=’flag1; 
   flag2 -flag3’ run4.mod

switching to a different job scheduler, such as a custom grid, will change the PsN command to:

   execute run4.mod

Use the Defaults button to reload the command settings default values specific to the workload manager. All values are cleared, and, for pre-configured managers, the values shown in the following table are loaded.