Test Slurm dispatch

Test compute node setup

You should now be able to submit Slurm jobs that run in Docker containers. On the node where you’re running the dispatcher, you can test this by running:

~$ sudo -u crunch srun -N1 docker run busybox echo OK

If it works, this command should print OK (it may also show some status messages from Slurm and/or Docker). If it does not print OK, double-check your compute node setup, and that the crunch user can submit Slurm jobs.

Test the dispatcher

Make sure all of your compute nodes are set up with Docker or Singularity.

On the dispatch node, start monitoring the crunch-dispatch-slurm logs:

# journalctl -o cat -fu crunch-dispatch-slurm.service

In another terminal window, use the diagnostics tool to run a simple container.

# arvados-client sudo diagnostics
INFO       5: running health check (same as `arvados-server check`)
INFO      10: getting discovery document from https://zzzzz.arvadosapi.com/discovery/v1/apis/arvados/v1/rest
...
INFO     160: running a container
INFO      ... container request submitted, waiting up to 10m for container to run

Once crunch-dispatch-slurm polls the API server for new containers to run, you should see it dispatch the new container. It will log messages like:

2016/08/05 13:52:54 Monitoring container zzzzz-dz642-hdp2vpu9nq14tx0 started
2016/08/05 13:53:04 About to submit queued container zzzzz-dz642-hdp2vpu9nq14tx0
2016/08/05 13:53:04 sbatch succeeded: Submitted batch job 8102

Before the container finishes, Slurm’s squeue command will show the new job in the list of queued and running jobs. For example, you might see:

~$ squeue --long
Fri Aug  5 13:57:50 2016
  JOBID PARTITION     NAME     USER    STATE       TIME TIMELIMIT  NODES NODELIST(REASON)
   8103   compute zzzzz-dz   crunch  RUNNING       1:56 UNLIMITED      1 compute0

The job’s name corresponds to the container’s UUID. You can get more information about it by running, e.g., scontrol show job Name=UUID.

When the container finishes, the dispatcher will log that, with the final result:

2016/08/05 13:53:14 Container zzzzz-dz642-hdp2vpu9nq14tx0 now in state "Complete" with locked_by_uuid ""
2016/08/05 13:53:14 Monitoring container zzzzz-dz642-hdp2vpu9nq14tx0 finished

After the container finishes, you can get the container record by UUID from a shell server to see its results:

shell:~$ arv get zzzzz-dz642-hdp2vpu9nq14tx0
{
 ...
 "exit_code":0,
 "log":"a01df2f7e5bc1c2ad59c60a837e90dc6+166",
 "output":"d41d8cd98f00b204e9800998ecf8427e+0",
 "state":"Complete",
 ...
}

You can use standard Keep tools to view the container’s output and logs from their corresponding fields. For example, to see the logs from the collection referenced in the log field:

~$ arv keep ls a01df2f7e5bc1c2ad59c60a837e90dc6+166
./crunch-run.txt
./stderr.txt
./stdout.txt
~$ arv-get a01df2f7e5bc1c2ad59c60a837e90dc6+166/stdout.txt
2016-08-05T13:53:06.201011Z Hello, Crunch!

If the container does not dispatch successfully, refer to the crunch-dispatch-slurm logs for information about why it failed.

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