slurm | SLURM : A Highly Scalable Resource Manager

I am currently trying to write a bash script which runs my executable with some input parameters. Most of the input parameters are set inside the script, some of them are passed to the bash script and evaluated. What I need now is to generalise the script so if I want to set other inputs known by my executable then I would want to write them in the bash script input. In other words my bash script executes at the end the command:

I'm relatively new to working with bash. I've inherited this bit of code to run a command via SLURM on an HPC system:

I am trying to run many smaller SLURM job steps within one big multi-node allocation, but am struggling with how the tasks of the job steps are assigned to the different nodes. In general I would like to keep the tasks of one job step as local as possible (same node, same socket) and only spill over to the next node when not all tasks can be placed on a single node.

The following example shows a case where I allocate 2 nodes with 4 tasks each and launch a job step asking for 4 tasks:

I have a job script called testjob.sh which I submit as

When trying to create a bash script (.sh file) in Java, random characters are added to the beginning of the file.

As a result, the script is rejected by SLURM when submitted using the sbatch command.

My Code:

I need to submit a slurm job that needs to have a core count divisible by 7 on a cluster with 64 core nodes. One solution is to run a 7 node/16 core job, which works well because the parallelization works extremely well between these 7 groups of cores (very little communication between the 7 groups).

Scheduling of this job becomes difficult however since its hard for 7 nodes to open up 16 cores at one time. Are there any ways to submit jobs in the following configurations?

• Explicitly request 2 nodes, one uses 64 cores and one uses 48 cores.

• Allow the job to combine the 7 node job to place multiple node allocations on a single node, allowing it to simply find 7 groups of 16 cores.

The only thing I cannot allow is the groups of 16 cores to be split over 2 nodes, as this will dramatically hurt performance.

This is running on slurm 20.11.8

I am using slurm to submit jobs to the university supercomputer. My matlab function has one parameter:

function test(variable_1)

and my slurm file is (I am not sure if it is correct. I know how to define the value of the parameter in the slurm file, but I would like to pass the value to the slurm file as I need to run the matlab function many times with different values for the parameter):

I have a SLURM job script as follows:

When submitting jobs with sbatch, is a copy of my executable taken to the compute node? Or does it just execute the file from /home/user/? Sometimes when I am unorganised I will submit a job, then change the source and re-compile to submit another job. This does not seem like a good idea, especially if the job is still in the queue. At the same time it seems like it should be allowed, and it would be much safer if at the moment of calling sbatch a copy of the source was made.

I ran some tests which confirmed (unsurprisingly) that once a job is running, recompiling the source code has no effect. But when the job is in the queue, I am not sure. It is difficult to test.

edit: man sbatch does not seem to give much insight, other than to say that the job is submitted to the Slurm controller "immediately".