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4. Ejemplo básico 3
Este es un ejemplo de un script (ejemplo3.sh) con los elementos minimos para ejecutar el programa R-3.6.1 a través de slurm:
#!/bin/bash
#SBATCH -J R-NOMBRE-SIMULACION # reemplazar por el nombre de tu simulacion
#SBATCH -a 1-11%3
#SBATCH --nodes=1 #numero de nodos a utilizar
#SBATCH --tasks-per-node=1 " numero de tareas por nodo
#SBATCH --mem=100G #cantidad de memoria requerida para la simulacion
#SBATCH --partition=intel #particion o cola donde enviaras el trabajo/simulacion
module load R/3.6.1 #modulo o programa que necesitas para tu simulación
cmds=(
'sleep 10;echo 10'
'sleep 20;echo 20'
'sleep 30;echo 30'
'sleep 40;echo 40'
'sleep 50;echo 50'
)
eval ${cmds[$SLURM_ARRAY_TASK_ID - 1]}
Para enviar este script a slurm, crear un job, y comenzar el procesamiento se requiere lo siguiente:
chmod x ejemplo3.sh
sbatch ejemplo3.sh
List of available clusters and partitions
List of available clusters
List of available partitions
FAQ (Frequently Asked Questions)
Q. What is the difference of cluster and particion?
Q. I always use only one cluster. Is there any way to omit –clusters=[cluster_name] when I check/delete jobs by scontrol/scancel?
Further information
Use 'man' command after login to servers
man sbatch
SLURM commands
- sacct
- salloc
- sbatch
- scancel
- scontrol
- sinfo
- squeue
- sreport
Useful reference pages
About job array
https://slurm.schedmd.com/job_array.html
https://rcc.uchicago.edu/docs/running-jobs/array/index.html
https://www.accre.vanderbilt.edu/wp-content/uploads/2016/04/UsingArrayJobs.pdf
How to rewrite PBSPro/SGE script to SLURM script
Common command
| PBS command | SGE command | SLURM command | |
| Job submission | qsub [scriptfile] | qsub [scriptfile] | sbatch [scriptfile] |
| Job deletion | qdel [job_id] | qdel [job_id] | scancel –clusters=[cluster_name] [job_id] |
| Job status (for user) | qstat -u [username] | qstat -u [username] | squeue -u [username] |
| Extended job status | qstat -f [job_id] | qstat -f -j [job_id] | scontrol –clusters=[cluster_name] show jobid=[job_id] |
| Hold a job temporarily | qhold [job_id] | qhold [job_id] | scontrol hold [job_id] |
| Release job hold | qrls [job_id] | qrls [job_id] | scontrol release [job_id] |
| List of usable queues | qstat -Q | qconf -sql | sinfo, squeue |
Resource speciation
| PBS command | SGE command | SLURM command | |
| Queue | #PBS -q [queue] | #$ -q [queue] | #SBATCH -M=[queue] / #SBATCH –clusters=[queue] |
| Processors (Single host) | #PBS -l select=1:ncpus=[#] | #$ -pe smp [#] | #SBATCH -c=[#]? |
| Wall clock limit | #PBS -l walltime=[hh:mm:ss] | #$ -l time=[hh:mm:ss] | #SBATCH -t=[#] (“minutes”, “minutes:seconds”, “hours:minutes:seconds”, “days-hours”, “days-hours:minutes” and “days-hours:minutes:seconds”) |
| Memory requirement | #PBS -l mem=XXXXmb | #$ -mem [#]G | #SBATCH –mem=[#][unit;K/M/G/T]? |
| Standard output file | #PBS -o [file] | #$ -o [path] | #SBATCH -o [path] |
| Standard error | #PBS -e [file] | #$ -e [path] | #SBATCH -e [path] |
| Array job | #PBS -J [#-#] | #$ -t [#-#] | #SBATCH -a=[#-#] |
| Array number Variable name | ${PBS_ARRAY_INDEX} | ${SGE_TASK_ID} | ${SLURM_ARRAY_TASK_ID} |
| Max simulaneously running tasks for an array job | n/a? | #$ -tc [#] | #SBATCH -a=[#-#]%[#] (e.g. -a=0-15%4) |
| Copy environment | #PBS -V | #$ -V | #SBATCH –get-user-env |
| Notification event | #PBS -m abe | #$ -m abe | ? |
| Email address | #PBS -M [email] | #$ -M [email] | #SBATCH -M [email] |
| Job name | #PBS -N [name] | #$ -N [name] | #SBATCH -J [name] |
| Job restart | #PBS -r [y/n] | #$ -r [yes/no] | #SBATCH –requeue / #SBATCH –no-requeue? |
| Move current directory | n/a | #$ -cwd | ? |
| Move working directory | n/a (in the main part of script, add cd ${PBS_O_WORKDIR}) | #$ -wd | #SBATCH -D [working_dirpath] |
| Use BASH | #PBS -S /bin/bash | ? | shebang line (At the first line of the script, add #!/usr/bin/bash |