Bioinformatics Center

User Tools

Site Tools

You are here: home » guides » slurm » basics
guides:slurm:basics

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
guides:slurm:basics [27.09.2019 10:21]
Juha Kekäläinen 		guides:slurm:basics [18.10.2024 14:09] (current)
Administrator
Line 8: Line 8:
   * Optional plugins can be used for accounting, advanced reservation, gang scheduling (time sharing for parallel jobs), backfill scheduling, topology optimized resource selection, resource limits by user or bank account, and sophisticated multifactor job prioritization algorithms.   * Optional plugins can be used for accounting, advanced reservation, gang scheduling (time sharing for parallel jobs), backfill scheduling, topology optimized resource selection, resource limits by user or bank account, and sophisticated multifactor job prioritization algorithms.
  
-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 Slurm on kudos.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)
 ``` ```
Line 17: Line 25:
 ``` ```
 #### 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 small # Partition to submit
  
-module load matlab/R2018b # load modules+module load matlab/R2022b # load modules
  
 matlab -nodisplay < matlab.m # Execute the script matlab -nodisplay < matlab.m # Execute the script
Line 32: Line 47:
 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 small   # 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.1569568893.txt.gz · Last modified: 29.10.2019 15:10 (external edit)

Page Tools