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guides:slurm:basics [27.09.2019 10:21]
Juha Kekäläinen 		guides:slurm:basics [06.04.2023 11:19]
Administrator
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 Bioinformatics Center uses unmodified version of Slurm on sampo.uef.fi computing cluster. This guarantees that the most of the tutorials and guides found from the Internet are applicable as-is. The most obvious starting place to search for usage information is documentation section of the Slurm own website [[https://slurm.schedmd.com|Slurm Workload Manager]]. Bioinformatics Center uses unmodified version of Slurm on sampo.uef.fi computing cluster. This guarantees that the most of the tutorials and guides found from the Internet are applicable as-is. The most obvious starting place to search for usage information is documentation section of the Slurm own website [[https://slurm.schedmd.com|Slurm Workload Manager]].
 +
 +{{ :guides:slurm:slurm.png |}}
 +
 +
 ### Example ### Example
 +
 +In this example we will run simple [MATLAB](https://www.mathworks.com/products/matlab.html) code on one computing node.
 +
 +
 #### Example MATLAB code (matlab.m) #### Example MATLAB code (matlab.m)
 ``` ```
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 ``` ```
 #### Example script (submit.sbatch) #### Example script (submit.sbatch)
 +
 +Here we have specified the [batch script](https://slurm.schedmd.com/sbatch.html) with few basic [options](https://slurm.schedmd.com/sbatch.html#lbAG). It is important to reserve the amount of RAM that you'll need and estimate the runtime of your code. Optionally you can give name for your job.
 +
 ``` ```
  
 #!/bin/bash #!/bin/bash
 +#SBATCH --ntasks 1 # Number of task
 +#SBATCH --time 5 # Runtime in minutes.
 +#SBATCH --mem=2000 # Reserve 2 GB RAM for the job
 +#SBATCH --partition serial # Partition to submit
  
 module load matlab/R2018b # load modules module load matlab/R2018b # load modules
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 sbatch submit.sbatch sbatch submit.sbatch
 ``` ```
 +**[sbatch](https://slurm.schedmd.com/sbatch.html)** command submits the job to the job queue and executes the **[bash script](https://en.wikipedia.org/wiki/Bash_(Unix_shell)**. 
 +
 +Here is an another example on how to analyze variants.
 +
 +```
 +#!/bin/bash
 +#SBATCH --ntasks 1          # Number of task
 +#SBATCH --time 00:30:00     # Runtime 30min
 +#SBATCH --mem 2000          # Reserve 2 GB RAM for the job
 +#SBATCH --partition serial  # Partition to submit
 +
 +module load bcftools # load modules
 +
 +# filter variants and calculate stats
 +bcftools filter --include'%QUAL>20' calls.vcf.gz | bcftools stats --output calls_filtered.stats 
 +```
 +
 +Submit the job to computing queue with the **[sbatch](https://slurm.schedmd.com/sbatch.html)** command.
 +
 +```
 +sbatch variants.sbatch
 +```
 +
 +
 +### Slurm job queue
 +User can monitor the state of the job with the **[squeue](https://slurm.schedmd.com/squeue.html)** command. JOBID is provided by the sbatch commmand when the job is submitted.
 +
 +```
 +squeue -j <jobid>
 +```
 +
 +### Output of the job is available in local output file.
 +
 +```
 +less slurm-<jobid>.out
 +```
 +
 +### Scontrol - View or modify Slurm configuration and state.
 +[Scontrol](https://slurm.schedmd.com/scontrol.html) command gives some information about the job, queue (partition) or the compute nodes. This tool can also modify various parameters of submitted job (runtime for example).
 +
 +#### List all compute nodes
 +```
 +scontrol show node
 +```
 +
 +#### List all compute nodes
 +```
 +scontrol show node
 +```
 +
 +#### List all queues/partitions
 +```
 +scontrol show partition
 +```
 +
 +#### List information of the given jobid
 +```
 +scontrol show job <jobid>
 +```
 +
 +
 +### Slurm job effiency report (seff)
 +Seff command will give the report of the completed job on how much resources it consumed. The reported information are CPU wall time, job runtime and memory usage.
 +
 +```
 +seff <jobid>
 +```
 +
  
guides/slurm/basics.txt · Last modified: 27.11.2023 12:40 by Administrator

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