Triton is a large system that combines many different individual computers. At the same time, hundreds of people are using it. Thus, we must use a batch queuing system (slurm) in order to allocate resources.
The queue system takes computation requests from everyone, figures out the optimal use of resources, and allocates code to nodes. You have to start your code in a structured way in order for this to work. Our previous tutorial showed how to run things directly from the command line, without any scripting needed. Now let’s see how to put these into scripts for making things more automated and reproducible.
A basic script¶
Let’s say we want to run
echo 'hello world'. We have to tell the
system how to run it. Here is a simple submission script:
#!/bin/bash #SBATCH --time=0-00:05:00 # 5 mins #SBATCH --mem-per-cpu=500 # 500MB of memory # Defaults to directory of when submitted. Explicit cd if needed (slurm defaults # to submission directory). cd $WRKDIR/myproject/ # output goes into hello.out # If you use srun for each command, the mem/cpu usage of each step # can be seen individually with "slurm history" srun echo 'hello, world'
Then submit it with
$ sbatch hello.sh
This sends it to the queue to wait. Since the time requested is short, it will probably run on the debug partition, which is reserved for small test jobs (see below). Let’s see if it is in the queue:
Checking job status
$ slurm q JOBID PARTITION NAME TIME START_TIME STATE NODELIST(REASON) 13031249 debug hello.sh 0:00 N/A PENDING (None)
slurm q until you see it finish.
The output is then saved to
slurm-13031249.out in your current
directory (the number being the job ID).
As you can see, the above script is limited to 5 minutes and 500MB of
memory. All scripts have to have limits, otherwise they can’t be
efficiently scheduled. If you exceed the limits, the jobs will be
killed. At least you need to set
The same parameters can be used in
- The sbatch script, prefixed by
sbatchcommand line program directly (like
srunfrom the command line, which lets you run programs without a batch script.
It is important to note that slurm is a declarative system. You declare what you need, and slurm handles finding the resources without you having to worry about details. The more resources you request, the harder it will be to schedule and the longer you may have to wait. So, you should ask for what you need to ensure it runs, but after you get experience with your code reduce resources to just what is needed.
In general, you don’t want to go submitting too short jobs (under 5 minutes) because there is a lot of startup, accounting, and scheduling overhead. If you are testing, short things are fine, but once you get to bulk production try to have each job take at least 30 minutes if possible. If you have lots of things to run, combine them into fewer jobs.
Status of the jobs¶
Once you submit jobs, it goes into a queue. You need to be able to see the status of jobs. There are commands to do this.
|slurm j <jobid>||Status on single job (still running)|
|slurm history [2hours|5days|…]||Info on completed jobs, including mem/cpu usage.|
See the full list of status commands on the reference page
There are different partitions, which have different limits. The
“debug” partition is for short debugging, so is designed to always be
available. The “batch” partition is designed for all the normal long
jobs. There are also partitions for GPUs, huge memory nodes, interactive
shells, and so on. Most of the time, you should leave the partition off,
and slurm will use all possible partitions. You can specify your
-p PARTITION_NAME to whatever command you are
running, which is mainly needed if you want to force interactive or GPU
partitions. The available partitions are listed below and on the
reference page. For the fastest running, consider if you code can be
right below one of the limits you see here.
|Partition||Max job size||Mem/core (GB)||Tot mem (GB)||Cores/node||Limits||Use|
|<default>||If you leave off all possible partitions will be used (based on time/mem)|
|debug||2 nodes||2.66 - 12||32-256||12,20,24||15 min||testing and debugging short interactive. work. 1 node of each arch.|
|batch||16 nodes||2.66 - 12||32-256||12, 20,24||5d||primary partition, all serial & parallel jobs|
|short||8 nodes||4 - 12||48-256||12, 20,24||4h||short serial & parallel jobs, +96 dedicated CPU cores|
|hugemem||1 node||43||1024||24||3d||huge memory jobs, 1 node only|
|gpu||1 node, 2-8GPUs||2 - 10||24-128||12||5d||GPU computing|
|gpushort||4 nodes, 2-8 GPUs||2 - 10||24-128||12||4h||GPU computing|
slurm partitions to see more details.
- Submit a batch job
- Set time to 1 hour and 15 minutes, memory to 500MB.
- Change the job’s name and output file
- Monitor the job with
slurm watch queue
- Create a simple batch script with multiple job steps (
echo Hello, world!, and
date. How does this appear in
slurm history. When would you use extra
sruncommands, and when not?
- Create a batch script which does nothing (or some pointless
operation for a while), for example
sleep 300(wait for 300 seconds) in the
debugpartition. Check the queue to see when it starts running. Then, cancel the job. What output is produced?
- (Advanced) Create a batch script that runs in another language. Does it run? What are some of the advantages and problems here?