slurm is albedo's job scheduling system. It is used to submit jobs from the login nodes to the compute nodes.

Jobs

Submitting jobs

• To work interactively on a compute node use salloc.
  You can use all options (more CPU, RAM, time, partition, qos, ...) described in the next section.
  To enable working with graphical interfaces (X forwarding) add the option --x11 .
  
• Job scripts are submitted via sbatch

• You can ssh to a node where a job of yours is running, if (and only if) you have a valid ssh-key pair. (e.g. on a login node: ssh-keygen -t ed25519;  ssh-copy-id albedo1)
  Make sure your key is secured with a password!

Specifying job resources

Job resources are defined at the header of your job script (or as command line arguments for sbatch or salloc). A full list see https://slurm.schedmd.com/sbatch.html#SECTION_OPTIONS. Here is a list of the most common ones:

#SBATCH --account=<account>          # Your account
#SBATCH --partition=<partition>      # Slurm Partition; Default: smp
#SBATCH --time=<time>                # time limit for job; Default: 0:30:00
#SBATCH --qos=<QOS>                  # Slurm QOS; Default: 30min
#SBATCH --nodes=<#Nodes>             # Number of nodes
#SBATCH --ntasks=<#Tasks>            # Number of tasks (MPI) tasks to be launched
#SBATCH --mem=<memory>               # If more than the default memory is needed;
                                     # Default: <#Cores> * <mem per node>/<cores per node>
#SBATCH --ntasks-per-node=<ntasks>   # Numer of tasks per node
#SBATCH --mail-user=<email adress>   # Your mail adress if you want to get notifications
#SBATCH --mail-type=<email type>     # Valid type values are NONE, BEGIN, END, FAIL, REQUEUE, ALL
#SBATCH --job-name=<jobname>         # Job name
#SBATCH --output=<filename_pattern>  # File where the standard output is written to(*)
#SBATCH --error=<filename_pattern>   # File where the error messages are written to(*)

 *) For filename patterns see: https://slurm.schedmd.com/sbatch.html#SECTION_%3CB%3Efilename-pattern%3C/B%3E

Details about specific parameters

Account (-A)

Compute resources are attributed to (primary)sections and projects at AWI. Therefore it is mandatory to specify an account.

The slurm accounts you may use are listed after login. You can change this setting on their own:

sacctmgr modify user <user> set DefaultAccount=<account>

Partitions (-p)

Identical compute nodes are combined in partitions. More information about the hardware specification of each node can be found in the System Overview.

Quality of service (--qos)

A higher priority means your job is scheduled before other jobs. In addition,  during working hours 10 nodes are reserved exclusively for jobs using qos=30min (to facilitate development and testing). For longer runs, another QOS (and walltime) has to be specified.  Note: long running jobs (longer than 12 hours, up to 48 hours) “cost” more in terms of fairshare (meaning you priority will decrease for further jobs).

Job Scheduling

Priority

For the job scheduling, Slurm assigns each job a priority, which is calculated based on several factors (Multifactor Priority Plugin). Jobs with higher priority, run first. (In principle – the backfill scheduling plugin helps making best use of available resources by filling up resources that are reserved (and thus idle) for large higher priority jobs with small (lower priority) jobs.)

On albedo,  the priority is mainly influenced by the

• the fairshare factor (which is based on the user’s recent use of resources) and
• the QOS' priority factor and
• the time your job waits in the queue

Job size (RAM, cores), partitions and/or associations have no influence.

Fairshare

On Albedo all users have the same share of resources, independent of the account used. … TODO…

Sebastian Hinck 

Accounting

TODO...

Sebastian Hinck 

Useful Slurm commands

• sinfo shows existing queues
• scontrol show job <JobID> shows information about specific job
• sstat <JobID> shows resources used by a specific job
• squeue shows information about queues and used nodes
• smap curses-graphic of queues and nodes
• sbatch <script> submits a batch job
• salloc <resources> requests access to compute nodes for interactive use
• scancel <JobID> cancels a batch job
• srun <ressources> <executable> starts a (parallel) code
• sshare and sprio give information on fair share value and job priority

Example Scripts

ToDO... Sebastian Hinck 

Job arrays

Job arrays in Slurm are an easy way to submit multiple similar jobs (e.g. executing the same script with multiple input data). See here for further details.

#!/bin/bash

#SBATCH --account=<account>          # Your account
#SBATCH --partition=smp
#SBATCH --time=0:10:00
#SBATCH --ntasks=1

# run 100 tasks, but only run 10 at a time
#SBATCH --array=1-100%10
#SBATCH --output=result_%A_%a.out    # gives result_<jobID>_<taskID>.out

echo "SLURM_JOBID:         $SLURM_JOBID"
echo "SLURM_ARRAY_TASK_ID: $SLURM_ARRAY_TASK_ID"
echo "SLURM_ARRAY_JOB_ID:  $SLURM_ARRAY_JOB_ID"

# Here we "translate" the $SLURM_ARRAY_TASK_ID (which takes values from 1-100)
# into an input file, that we want to analyze.
# Suppose 'input_files.txt' is a text file that has 100 lines, each containing
# the respective input file.

INPUT_LIST=input_files.txt

# Read the (SLURM_ARRAY_TASK_ID)th input file
INPUT_FILE=`sed -n "${SLURM_ARRAY_TASK_ID}p" < ${INPUT_LIST}`

srun my_executable $INPUT_FILE

OpenMP

Sebastian Hinck 

MPI

#!/bin/bash

#SBATCH --time 0:10:00
#SBATCH -p mpp
#SBATCH -N 2
#SBATCH --tasks-per-node 128
#SBATCH --cpus-per-task 1
#SBATCH --hint=nomultithread
#SBATCH --job-name=mpi
#SBATCH --output=out_%x.%j

module purge
module load    xthi/1.0-intel-oneapi-mpi2021.6.0-oneapi2022.1.0    intel-oneapi-mpi
# module load    xthi/1.0-openmpi4.1.3-gcc8.5.0   openmpi/4.1.3

# To be on the safe side, we emphasize that it is pure MPI, no OpenMP threads
export OMP_NUM_THREADS=1

srun  xthi | sort -g -k 4

Hybrid (MPI+OpenMP)

#!/bin/bash

#SBATCH --time 0:10:00
#SBATCH -p mpp
#SBATCH -N 2
#SBATCH --tasks-per-node 8
#SBATCH --cpus-per-task 16
#SBATCH --job-name=hybrid
#SBATCH --output=out_%x.%j

# disable hyperthreading
#SBATCH --hint=nomultithread

module purge
module load    xthi/1.0-intel-oneapi-mpi2021.6.0-oneapi2022.1.0   intel-oneapi-mpi
# module load    xthi/1.0-openmpi4.1.3-gcc8.5.0   openmpi/4.1.3


ulimit -s unlimited

# OpenMP and srun, both need to know the number of CPUs per task
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export SRUN_CPUS_PER_TASK=$SLURM_CPUS_PER_TASK

srun xthi | sort -g -k 4