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guides:slurm:basics [16.10.2020 10:47]
Juha Kekäläinen 		guides:slurm:basics [18.10.2024 14:09] (current)
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   * 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 |}} {{ :guides:slurm:slurm.png |}}
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 #SBATCH --time 5 # Runtime in minutes. #SBATCH --time 5 # Runtime in minutes.
 #SBATCH --mem=2000 # Reserve 2 GB RAM for the job #SBATCH --mem=2000 # Reserve 2 GB RAM for the job
-#SBATCH --partition serial # Partition to submit +#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
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 ``` ```
 **[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)**.  **[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
 +```
  
  
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 ``` ```
 scontrol show job <jobid> scontrol show job <jobid>
-``` 
- 
-#### Extend runtime of given jobid 
- 
-``` 
-scontrol update jobid=<job_id> TimeLimit=<new_timelimit> 
 ``` ```
  
guides/slurm/basics.1602834429.txt.gz · Last modified: 16.10.2020 10:47 by Juha Kekäläinen

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