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Overview

What is needed to be able to run at UPPMAX

  • SUPR
    • account
    • project

How to access the clusters?

  • login
    • ssh
    • ThinLinc

Where should you keep your data?

  • uquota

How to transfer files?

  • sftp
  • rsync
    • example: rsync -av /local/dir user@rackham.uppmax.uu.se:/proj/naiss2023-22-247/nobackup/private/user/.
  • SFTP graphical tools

The module system

  • built on LMOD

Some useful comamnds:

  • module avail <name>
  • module spider <name>
  • module load <module>/<version>
  • module list
  • module unload <module>/<version>
  • module purge

Slurm

How to submit a job to Slurm?

sbatch  -A naiss2023-22-247 -t 10:00  -p core  -n 10  my_job.sh

What should a jobscript contain?

  • project number
  • max time
  • partition
  • number or core and/or nodes
  • job name
  • special features

A typical job script:

#!/bin/bash
#SBATCH -A naiss2023-22-247
#SBATCH -p node
#SBATCH -N 1
#SBATCH -t 24:00:00

module load software/version

./my-script.sh

Useful SBATCH options:

  • --mail-type=BEGIN,END,FAIL,TIME_LIMIT_80
  • --output=slurm-%j.out
  • --error=slurm-%j.err

Useful commands:

  • jobinfo -p devel
  • sinfo -p node - M snowy
  • jobinfo -u username --state=running
  • jobinfo -u username --state=pending
  • salloc -A naiss2023-22-247 --begin=2023-03-24T08:00:00 starts an interactive job earliest tomorrow at 08:00

How to cancel jobs?

  • scancel <jobid>

Job dependencies

  • sbatch jobscript.sh submitted job with jobid1
  • sbatch anotherjobscript.sh submitted job with jobid2
  • --dependency=afterok:jobid1:jobid2 job will only start running after the successful end of jobs jobid1:jobid2
  • very handy for clearly defined workflows
  • One may also use --dependency=afternotok:jobid in case you’d like to resubmit a failed job, OOM for example, to a node with a higher memory: -C mem215GB or -C mem1TB
  • More in slurm documents.

GPU flags

#SBATCH -M snowy
#SBATCH --gres=gpu:1
#SBATCH --gpus-per-node=1
Example of a job running on part of a GPU node 
#!/bin/bash
#SBATCH -J GPUjob
#SBATCH -A snic2023-22-247
#SBATCH -t 03-00:00:00
#SBATCH -p core
#SBATCH -n 16
#SBATCH -M snowy
#SBATCH --gres=gpu:1
#SBATCH --gres=mps:50

module use /sw/EasyBuild/snowy/modules/all/
module load intelcuda/2019b

I/O intensive jobs: use the scratch local to the node

Example 
#!/bin/bash
#SBATCH -J jobname
#SBATCH -A naiss2023-22-247
#SBATCH -p core
#SBATCH -n 1
#SBATCH -t 10:00:00

module load bioinfo-tools
module load bwa/0.7.17 samtools/1.14

export SRCDIR=$HOME/path-to-input

cp $SRCDIR/foo.pl $SRCDIR/bar.txt $SNIC_TMP/.
cd $SNIC_TMP

./foo.pl bar.txt

cp *.out $SRCDIR/path-to-output/.

Job arrays

Example

Submit many jobs at once with the same or similar parameters Use $SLURM_ARRAY_TASK_ID in the script in order to find the correct path

#!/bin/bash
#SBATCH -A naiss2023-22-21
#SBATCH -p node
#SBATCH -N 2
#SBATCH -t 01:00:00
#SBATCH -J jobarray
#SBATCH --array=0-19
#SBATCH --mail-type=ALL,ARRAY_TASKS

# SLURM_ARRAY_TASK_ID tells the script which iteration to run
echo $SLURM_ARRAY_TASK_ID

cd /pathtomydirectory/dir_$SLURM_ARRAY_TASK_ID/

srun -n 40 my-program
env

You may use scontrol to modify some of the job arrays.

Profiling on the GPUs

  • nvidia-smi

    • nvidia-smi dmon -o DT
    • nvidia-smi --format=noheader,csv --query-compute-apps=timestamp,gpu_name,pid,name,used_memory --loop=1 -f sample_run.log
    • nvidia-smi --help or man nvidia-smi

  • module load nvtop

    • nvtop

Additional information