Slurm F.A.Q¶

Q01 Is there a generic submission script I can use?¶

See the Slurm Script Generation Wizard.

First, make sure you only request the resources you need. The more you ask, the longer you will wait. Then, try and make your job flexible in terms of resources. If your program is able to work through the network, do not ask for all tasks on the same node. Use the Slurm options cleverly. For instance, the --nnodes option allows specifying a range of number of nodes, e.g. --nnodes=2-4, meaning that your job will start as soon as at least two nodes are available, but if, by then, four nodes are available, you will be allocated four nodes. Another example is –time-min, which allows you to specify a minimum running time which you are willing to set for your job if it makes it possible to start it earlier (through backfilling). Note that you can get, at any moment, the remaining time for your job in your script with the squeue -h -j $SLURM\_JOBID -o %L and that the --signal option can be used to be warned before the job is killed. Of course, it is always easier to get a job running when there are few jobs waiting in the queue. Try to plan ahead your work and submit your jobs when people usually do not work on the cluster: holidays, exam periods, etc. Q03 How do I cancel a job?¶ Use the scancel jobid command with the jobid of the job you want cancelled. In the case you want to cancel all your jobs, type scancel -u login. You can also cancel all your pending jobs for instance with scancel -t PD. Q04 How do I submit a job to a specific queue?¶ Slurm uses the term partition rather than queue. To submit a job to a given partition, use the --partition option of the sbatch, srun, or salloc commands. Queues can also appear under the form of qualities of service (QOS). To use a particular QOS, use the --qos option of the above-listed commands. To view all partitions on a cluster, use sinfo, while qualities of service can be listed with sacctmgr list qos. Q05 How do I create a parallel environment?¶ Slurm ignores the concept of parallel environment as such. Slurm simply requires that the number of nodes, or number of cores be specified. But you can have the control on how the cores are allocated; on a single node, on several nodes, etc. using the --cpus-per-task and --ntasks-per-node options for instance. With those options, there are several ways to get the same allocation. For instance, the following : --nodes=4 --ntasks=4 --cpus-per-task=4 is equivalent in terms of resource allocation to --ntasks=16 --ntasks-per-node=4. But each one will lead to environment variables being set, and understood, differently by srun and mpirun: in the first case 4 processes are launched while in the second one 16 processes will be launched. Suppose you need 16 cores, these are some possible scenarios: • you use mpi and do not care about where those cores are distributed: --ntasks=16 • you want to launch 16 independent processes (no communication): --ntasks=16 • you want those cores to spread across distinct nodes: --ntasks=16 --ntasks-per-node=1 or --ntasks=16 --nodes=16 • you want those cores to spread across distinct nodes and no interference from other jobs: --ntasks=16 --nodes=16 --exclusive • you want 16 processes to spread across 8 nodes to have two processes per node: --ntasks=16 --ntasks-per-node=2 • you want 16 processes to stay on the same node: --ntasks=16 --ntasks-per-node=16 • you want one process that can use 16 cores for multithreading: --ntasks=1 --cpus-per-task=16 • you want 4 processes that can use 4 cores each for multithreading: --ntasks=4 --cpus-per-task=4 Q06 How do I choose a node with certain features (e.g. CPU, GPU, etc.) ?¶ Slurm associates to each node a set of Features and a set of Generic resources. Features are immutable characteristics of the node (e.g. network connection type) while generic resources are consumable resources, meaning that as users reserve them, they become unavailable for the others (e.g. compute accelerators). Features are requested with --constraint="feature1&feature2" or --constraint="feature1|feature2". The former requests both, while the latter, as one would expect, requests at least one of feature1 or feature2. More complex expressions can be constructed. Type man sbatch for details. Generic resources are requested with --gres="resource:2" to request 2 resources. Generic resources and features can be listed with the command scontrol show nodes. Q07 How do I get the list of features and resources of each node ?¶ The command sinfo gives such information. You need to run it with specific output parameters though: sinfo -o "%15N %10c %10m %25f %10G"  It will output something like: dfr@manneback:~$ sinfo -o "%15N %10c %10m  %25f %10G"
NODELIST        CPUS       MEMORY      FEATURES                  GRES
mback[01-02]    8          31860+      Opteron,875,InfiniBand    (null)
mback[03-04]    4          31482+      Opteron,852,InfiniBand    (null)
mback05         8          64559       Opteron,2356              (null)
mback06         16         64052       Opteron,885               (null)
mback07         8          24150       Xeon,X5550                TeslaC1060
mback[08-19]    8          24151       Xeon,L5520,InfiniBand     (null)
mback[20-32,34] 8          16077       Xeon,L5420                (null)


In the above screen capture, we see that some compute nodes have Infiniband connections, some have Intel processors, while others have AMD processors. The node mback07 furthermore has one GPU, which is a generic resource in the sense that once requested by a job, it becomes unavailable for the others.

Q08 Is OpenMP ‘slurm-aware’ ?¶

No, you need to set export OMP_NUM_THREADS=... in your submission script.

For instance, if you requested several cores with the --cpus-per-task option, you can write:

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK  Q09 Is MPI ‘slurm-aware’ ?¶ Yes, you do not need to specify the -np nor the -host, or hostfile options to mpirun or mpiexec. Simply go with mpirun ./a.out  assuming you requested several cores with --ntasks Do not forget to set the environment correctly with something like module load openmpi/gcc if necessary. Q10 How do I know how much memory my job is using/has used ?¶ If your job is still running, you can have memory information with sstat. If your job is done, the information is provided by sacct. Both support the --format option so you can run, for instance: sacct --format JobID,jobname,NTasks,nodelist,MaxRSS,MaxVMSize,AveRSS,AveVMSize  See the manpages for both utilities: man sstat man sacct  Q11 How do I use the local scratch space ?¶ Slurm offers the sbcast command that propagates a file to the local file systems of the nodes that were allocated to the job. However, sbcast works one file at a time. It is therefore unsuited for copying entire data directories. One neat way to deal with several files is to use the srun cp construction. For instance, in the script below: #!/bin/bash #SBATCH --nodes=2 #SBATCH --output=output.txt SCRATCH=$LOCALSCRATCH/$SLURM_JOB_ID echo Creating temp dir$SCRATCH
srun mkdir -p $SCRATCH || exit$?
echo Copying files. srun cp is equivalent to loop over each node + scp
srun cp -r $SLURM_SUBMIT_DIR/*$SCRATCH || exit $?  a temporary SCRATCH directory is created with the jobid. Afterwards, the data is copied from the home to the local scratch (assuming the home directory is mounted on each compute node). The environment variables used in the script provided by Slurm are: • SLURM_JOB_ID: jobid • SLURM_SUBMIT_DIR: the directory you were when you launched the script with sbatch The variable$LOCALSCRATCH is provided by the CECI environment (see Local scratch).

If each output file had a different name from the input ones, we could simply srun cp from the scratch to the home after the code run.

echo Copying back output files to home submit directory
srun cp -r  $SCRATCH/*$SLURM_SUBMIT_DIR/*  || exit $?  At the end, make sure to clean the scratch space. echo Removing$SCRATCH
srun rm -rf $SCRATCH || exit$?


Q12 How do I get the node list in full rather than in compressed format ?¶

Slurm describes node lists with notations like hmem[05-07,09-17]. To get the full list, use the scontrol command:

dfr@hmem00:~ \$ scontrol show hostname hmem[05-07,09-17] | paste -d, -s
hmem05,hmem06,hmem07,hmem09,hmem10,hmem11,hmem12,hmem13,hmem14,hmem15,hmem16,hmem17


Q13 How do I know which slots exactly are assigned to my job ?¶

The command scontrol show -d job jobid gives very detailed information about jobs.

Q14 How do I translate a script from another job scheduler into Slurm ?¶

The Slurm developers maintain a ‘Rosetta stone of Workload manager‘ which gives the correspondences between the options of several job schedulers. [Direct link - pdf 156kb].

Q15 When will my job start ?¶

A job starts either when it has the highest priority and the required resources are available, or when it has an opportunity to backfill (See the document Slurm priorities for details). The squeue --start command gives an estimation of the date and time a job is supposed to start but beware that the estimation is based on the situation at a given time. Slurm cannot anticipate higher-priority jobs being submitted after yours, or machine downtimes which lead to fewer resources for the jobs, or job crashes which can lead to large jobs starting earlier than expected thus making smaller jobs scheduled for backfilling to lose that backfilling opportunity.

Q16 How do I know to which partition I should submit my job so that it starts as early as possible?¶

Simply submit the job to all the partitions you are considering, by listing them with the --partition option:

#SBATCH --partition=partition1,partition2


The job will be submitted to the partition which offers the earliest allocation according to your job parameters and priority.

Q17 What are the queue settings and cpu resources available per user on each CÉCI cluster?¶

The default settings are summarized on the cluster description page. These settings are indicative only, and may change depending on the load on the clusters. To obtain current settings on a given queue, see Question 4.