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Transition from SGE to SLURM

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Christian Kniep edited this page Jun 9, 2020 · 3 revisions

Introduction

When using a shared cluster resource access to utilize the compute nodes is guarded by a resource scheduler such as SLURM, Sun Grid Engine, PBS Pro et al. They line up jobs to be run suquentially, allow for prioritization and job placement within the cluster.

SLURM is one of the most popular open-source job schedulers and this document intends to help end-users transition off their current scheduler to SLURM. Transition to a new scheduler comes down to learn and practise new commands to handle the lifecycle of a job (submit/view/cancel/..), view resources like queues and compute nodes and adjust the way submit scripts are written. In some cases the last step can be made easier by using a compatibility mode to use existing submit scripts.

Sun Grid Engine

Sun Grid Engine (SGE) is commonly used amongst our users. Moving off SGE to SLURM needs some adjustments in how to interact with the scheduler by using SLURM commands and adjust the submission scripts.

Nomenclature

  • queue/partition SGE uses the term queues, while SLRUM calls them partitions
  • node-count SGE has no concept of node counts, SLURM has

Commands

Firstly, common commands used in SGE have an equivalent in the SLURM environment. The following table reviews the most common once.

User Command SGE SLURM
Interactive Login qlogin srun --pty [-p $partition_name] [--time=hh:mm:ss] bash
Job submission qsub $script_file sbatch $script_file
Job deletion qdel $job_id scancel $job_id
Job status by job qstat -u \* -j $job_id squeue $job_id
Job status by user qstat -u $user_name squeue -u $user_name
Job hold qhold $job_id scontrol hold $job_id
Job release qrls $job_id scontrol release $job_id
Queue list qconf -sql squeue
List nodes qhost sinfo -N OR scontrol show nodes
Cluster status qhost -q sinfo
GUI qmon sview

Environment Variables

Environment variables are used within a script to get access to information about the running job.

Information SGE SLURM
Job ID $JOB_ID $SLURM_JOBID
Submit directory $SGE_O_WORKDIR $SLURM_SUBMIT_DIR
Submit host $SGE_O_HOST $SLURM_SUBMIT_HOST
Node list $PE_HOSTFILE $SLURM_JOB_NODELIST
Job Array Index $SGE_TASK_ID $SLURM_ARRAY_TASK_ID

Job Specification

Submission scripts are able to inform the scheduler about certain parameters of the submission using a directive and options. The following table collects the most common specifications.

Information SGE SLURM
Script directive #$ #SBATCH
queue/partition -q $queue -p $partition
count of nodes N/A -N [min[-max]]
CPU count -pe smp <count> OR -pe orte <count> -n <count>
Wall clock limit -l h_rt=<seconds> -t <min> OR -t <days-hh:mm:ss>
stdout file -o <file_name> -o <file_name>
stderr file -e <file_name> -e <file_name>
combine stdout/stderr -j yes use -o without -e
copy environment -V --export=(ALL/NONE/<variables>)
event notification -m abe --mail-type=<events>
send notification email -M <address> --mail-user=<address>
job name -N <name> --job-name=<name>
Restart job `-r (yes no)`
set working directory -wd <dir_name> --workdir=<dir_name>
Resource sharing -l exclusive --exclusive OR —shared
Memory size `-l mem_free=(K M
Charge to an account -A <account> --account=<account>
Tasks per node fixed rule in parallel environment (PE) --tasks-per-node=<count>
Job dependency -hold_jid <job_id> OR -hold_jid=<job_name> --depend=[<state>:]<job_id>
Job project -P <name> --wckey=<name>
Job host preferences -q <queue>@<node> OR -q <queue>@@<hostgroup> --nodelist=<nodes> AND/OR —exclude=<nodes>
Quality of service N/A` --qos=<name>
Job arrays -t $array_spec --array=$array_spec
Generic Resources -l $resource=$value --gres=<resource_spec>
Licenses -l <license>=<count> --licenses=<license_spec>
Begin Time -a <YYMMDDhhmm> --begin=<YYYY-MM-DD[THH:MM[:SS]]>

Submit Scripts

SGE SLURM
Single-core application 
#!/bin/bash

#$ -N test
#$ -j y
#$ -o test.output
#$ -cwd
#$ -M $USER@stanford.edu
#$ -m bea
##Request 5 hours run time
#$ -l h_rt=5:0:0
#$ -P your_project_id_here
#$ -l mem=4G



#!/bin/bash -l
# NOTE the -l flag!

#SBATCH -J test
#SBATCH -o test."%j".out
#SBATCH -e test."%j".err
#Default in slurm
#SBATCH --mail-user $USER@stanford.edu
#SBATCH —mail-type=ALL
#Request 5 hours run time
#SBATCH -t 5:0:0
#SBATCH —mem=4000
#SBATCH -p normal


<load modules, call your app here>
MPI application w/o Hyperthreading 
#!/bin/bash -l

#Standard output and error:
#SBATCH -o ./tjob.out.%j
#SBATCH -e ./tjob.err.%j
#Initial working directory:
#SBATCH -D ./
#Job Name:
#SBATCH -J test_slurm
#Queue (Partition):
#SBATCH --partition=general
#Number of nodes and MPI tasks per node:
#SBATCH --nodes=8
#SBATCH --ntasks-per-node=32




#Wall clock limit:
#SBATCH --time=24:00:00
#Run the program:
srun ./myprog > prog.out
Hybrid MPI/OpenMP w/o hyperthreading 
#!/bin/bash -l
#Standard output and error:
#SBATCH -o ./tjob_hybrid.out.%j
#SBATCH -e ./tjob_hybrid.err.%j
#Initial working directory:
#SBATCH -D ./
#Job Name:
#SBATCH -J test_slurm
#Queue (Partition):
#SBATCH --partition=general
##Number of nodes and MPI tasks per node:
#SBATCH --nodes=8
#SBATCH --ntasks-per-node=4
##for OpenMP:
#SBATCH --cpus-per-task=8
#
##Wall clock limit:
#SBATCH --time=24:00:00
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
##For pinning threads correctly:
export OMP_PLACES=cores
##Run the program:
srun ./myprog > prog.out
Batch job using job steps 
#!/bin/bash
##Submit a chain of batch jobs with dependencies
#
##Number of jobs to submit:
NR_OF_JOBS=6
##Batch job script:
JOB_SCRIPT=./my_batch_script
echo "Submitting job chain of ${NR_OF_JOBS}"
echo "jobs for batch script ${JOB_SCRIPT}:"
JOBID=$(sbatch ${JOB_SCRIPT} 2>&1 | awk '{print $(NF)}')
echo "  " ${JOBID}
I=1
while [ ${I} -lt ${NR_OF_JOBS} ]; do
JOBID=$(sbatch --dependency=afterany:${JOBID} \
        ${JOB_SCRIPT} 2>&1 | awk '{print $(NF)}')
echo "  " ${JOBID}
let I=${I}+1
done
Batch job using job array 
#!/bin/bash -l
##specify the indexes of the job array elements
#SBATCH --array=1-20
##Standard output and error:
##Standard output, %A = job ID, %a = job array index
#SBATCH -o job_%A_%a.out
##Standard error, %A = job ID, %a = job array index
#SBATCH -e job_%A_%a.err
##Initial working directory:
#SBATCH -D ./
##Job Name:
#SBATCH -J test_array
##Queue (Partition):
#SBATCH --partition=general
##Number of nodes and MPI tasks per node:
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=40
#
##Wall clock limit:
#SBATCH --time=24:00:00

##Run the program:
srun ./myprog > prog.out
MPI Batch job using GPUs 
#!/bin/bash -l
##Standard output and error:
#SBATCH -o ./tjob.out.%j
#SBATCH -e ./tjob.err.%j
##Initial working directory:
#SBATCH -D ./
#
#SBATCH -J test_slurm
##Queue:
##If using both GPUs of a node
#SBATCH --partition=gpu
##If using only 1 GPU of a shared node
###SBATCH --partition=gpu:1
##Node feature:
#SBATCH --constraint="gpu"
##Specify number of GPUs to use:
# If using both GPUs of a node
#SBATCH --gres=gpu:2
### If using only 1 GPU of a shared node
###SBATCH --gres=gpu:1
### Memory is necessary if using only 1 GPU
###SBATCH --mem=61000
#
##Number of nodes and MPI tasks per node:
#SBATCH --nodes=1
##If using both GPUs of a node
#SBATCH --ntasks-per-node=32
##If using only 1 GPU of a shared node
###SBATCH --ntasks-per-node=16
#
##wall clock limit:
#SBATCH --time=24:00:00

module load cuda
##Run the program:
srun ./my_gpu_prog > prog.out

Tipps & Tricks

Requeuehold

To keep track which jobs are actually failed or not inside the script.

scontrol requeuehold ${SLURM_JOB_ID}

And for an array job.

scontrol requeuehold ${SLURM_ARRAY_JOB_ID}_${SLURM_ARRAY_TASK_ID})
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