Is it being written to NFS? You say on your local dev cluster it's a
single node. Is it also the login node as well as compute? In that case
I guess there is no NFS. Larger cluster will be using some sort of
shared storage, so whichever shared file system you are using likely has
caching.
If you are able to connect directly to the node which is running the
job, you can try tailing from there. It'll likely update immediately if
what I said above is the case.
Cheers,
Aaron
On 9 February 2021 at 23:47 GMT, Maria Semple wrote:
> Hello all,
>
> I've noticed an odd behaviour with job steps in some Slurm environments.
> When a script is launched directly as a job, the output is written to file
> immediately. When the script is launched as a step in a job, output is
> written in ~30 second chunks. This doesn't happen in all Slurm
> environments, but if it happens in one, it seems to always happen. For
> example, on my local development cluster, which is a single node on Ubuntu
> 18, I don't experience this. On a large Centos 7 based cluster, I do.
>
> Below is a simple reproducible example:
>
> loop.sh:
> #!/bin/bash
> for i in {1..100}
> do
> echo $i
> sleep 1
> done
>
> withsteps.sh:
> #!/bin/bash
> srun ./loop.sh
>
> Then from the command line running sbatch loop.sh followed by tail -f
> slurm-<job #>.out prints the job output in smaller chunks, which appears to
> be related to file system buffering or the time it takes for the tail
> process to notice that the file has updated. Running cat on the file every
> second shows that the output is in the file immediately after it is emitted
> by the script.
>
> If you run sbatch withsteps.sh instead, tail-ing or repeatedly cat-ing the
> output file will show that the job output is written in a chunk of 30 - 35
> lines.
>
> I'm hoping this is something that is possible to work around, potentially
> related to an OS setting, the way Slurm was compiled, or a Slurm setting.
--
Research Fellow
School of Computer Science
University of Nottingham
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