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Submitting Jobs

The balsam launcher command starts running the launcher component inside of a scheduled job. The launcher automatically detects the allocated resources and begins executing your workflows.

However, you typically do not run balsam launcher yourself, unless you are working interactively to test and debug workflows. From a login node, there are two ways to submit jobs that run balsam launcher for you:

  1. balsam submit-launch -- manually submit a job using the specified resources
  2. balsam service -- start up the service daemon, which persists on the login node and submits launcher jobs on your behalf over time.

In either case, the following takes place when you submit with Balsam:

  • A bash script is generated from the Job Template
  • The script is named qlaunch{ID}.sh and saved in the qsubmit/ subdirectory
  • The script is submitted to the batch scheduler using the platform's scheduler interface (e.g. qsub)

Manually Submit with submit-launch

balsam submit-launch passes on most of its arguments to the local scheduler submission command (e.g. qsub). Hence, usage is straightforward:

$ balsam submit-launch -A Project -q Queue -t 15 -n 5 --job-mode=mpi

The only required argument that is unique to Balsam is the --job-mode, explained below.

MPI job mode

For --job-mode=mpi, the Balsam launcher runs as a pilot job on the head node of the allocated resources. From this head node, it issues MPI launch commands (mpirun or equivalent) to launch jobs against the available resources.

This job mode maps very closely to the traditional \"ensemble job\" script that you may be accustomed to thinking about and can run any kind of task, whether it actually uses MPI or not.

Note

The launcher continuously attempts to launch tasks on idle nodes. Tasks are prioritized in order of decreasing num_nodes and then decreasing wall_time_minutes (refer to BalsamJob fields) This means that bigger, longer jobs will start earlier than smaller, shorter jobs at the beginning. The wall_time_minutes is a completely optional field that defaults to 0. If you don't want to provide a runtime estimate, simply leave it blank and jobs will not be prioritized according to this value.

Serial job mode

For tasks that run on a single node and do not use MPI, you may wish to pack several tasks per node. You may also wish to run 4000 such tasks on 4000 nodes, without overburdening the head node with 4000 mpirun background processes.

The --job-mode=serial option solves both of these problems by launching a single forker process on each compute node. These processes then run isolated tasks on the single nodes. This job mode will not process any tasks that have specified the use of multiple MPI ranks.

Filtering jobs by workflow tag

By default, launchers will consume all runnable tasks from the database. If you want a launcher job to only run tasks with a specific workflow tag, you can provide the wf-filter option:

$ balsam submit-launch -A Project -q Queue -t 15 -n 5 --job-mode=mpi --wf-filter=Experiment3

Now, only tasks whose workflow field contains the substring "Experiment3" will be eligible to run inside this job. This is a useful way to limit what workflows are allowed to run in which job. Of course, if you are running a large campaign, it is useful to use the workflow tag merely for organization and omit the --wf-filter option, so that all jobs can get as much work done as possible.

Running many launchers concurrently

One of the big advantages of Balsam is that many launcher jobs can be scheduled to run concurrently.

If you have a lot of tasks to run, simply call submit-launch multiple times (up to the queue limit, if you like) to enqueue many launcher jobs. They may run one-after-another or simultaneously, depending on resource availability. When launchers run simultaneously, they cooperatively "check-out" idle runnable tasks from the database, ensuring that every task runs exactly once.

Monitoring and Killing Jobs

You can always use the scheduler utilities to monitor (e.g. qstat) and kill (e.g. qdel) Balsam jobs. Running launchers will intercept SIGINT or SIGTERM signals sent by the scheduler when a job is killed or timed out. In turn, they gracefully stop running your workflow and mark timed-out tasks accordingly.

Note

For Slurm, use scancel --batch --signal=TERM job_id (or INT) to kill a running Balsam launcher and allow it to gracefully exit. Unlike the Cobalt scheduler, Slurm signals the child processes of the batch shell process by default when canceling jobs, including the job steps invoked by srun. The --batch option prevents this behavior, and the --signal option overrides the default sending of SIGKILL to the batch step.

If you want to kill a particular task while it\'s running inside a launcher, you can use the balsam kill <jobid> command or update the job state to USER_KILLED with the Python API. The killed task will stop in near-realtime and be replaced by the next eligible task to run.