Table of Contents
Scheduling a Job using the SLURM job scheduler
The Computer Science Department uses a “job scheduler” called SLURM. The purpose of a job scheduler is to allocate computational resources (servers) to users who submit “jobs” to a queue. The job scheduler looks at the requirements stated in the job's script and allocates to the job a server (or servers) which matches the requirements specified in the job script. For example, if the job script specifies that a job needs 192GB of memory, the job scheduler will find a server with at least that much memory free.
The job scheduler supports a direct login option (see below) that allows direct interactive logins to servers controlled by the scheduler, without the need for a job script.
As of 10-Jan-2022, the SLURM job scheduler was updated to the latest revision which enforces memory limits. As a result, jobs that exceed their requested memory size will be terminated by the scheduler.
As of 02-Apr-2022, the time limit enforcement policy within SLURM has changed. All jobs submitted with time limits are extended 60 minutes past the user-submitted time limit. E.g. If the user submits a job with a time limit of 10 minutes using parameter “-t 10”, SLURM will kill the job after 70 minutes.
As of 23-Aug-2023, jobs on certain nodes are now preemptable. When using the
sinfo command, any nodes within a partition named 'hipri' have preemption enabled. If you submit a job to one of these nodes, it may be suspended if the owner or research group submits a job to it as well.
The SLURM commands below are ONLY available on the portal cluster of servers. They are not installed on the gpusrv* or the SLURM controlled nodes themselves.
To view information about compute nodes in the SLURM system, use the command
[abc1de@portal04 ~]$ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST main* up infinite 3 drain falcon[3-5] main* up infinite 27 idle cortado[01-10],falcon[1-2,6-10],lynx[08-12],slurm[1-5] gpu up infinite 4 mix ai[02-03,05],lynx07 gpu up infinite 1 alloc ai04 gpu up infinite 12 idle ai[01,06],lynx[01-06],ristretto[01-04]
sinfo we can see a listing of the job queues or “partitions” and a list of nodes associated with these partitions. A partition is a grouping of nodes, for example our main partition is a group of all general purpose nodes, and the gpu partition is a group of nodes that each contain GPUs. Sometimes hosts can be listed in two or more partitions.
To view jobs running on the queue, we can use the command
squeue. Say we have submitted one job to the main partition, running
squeue will look like this:
abc1de@portal01 ~ $ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 467039 main my_job abc1de R 0:06 1 artemis1
and now that a node has been allocated, that node
artemis1 will show as alloc in
abc1de@portal01 ~ $ sinfo PARTITION AVAIL TIMELIMIT NODES STATE NODELIST main* up infinite 37 idle hermes[1-4],artemis[2-7],slurm[1-5],nibbler[1-4],trillian[1-3],granger[1-6],granger[7-8],ai0[1-6] main* up infinite 1 alloc artemis1 qdata up infinite 8 idle qdata[1-8] qdata-preempt up infinite 8 idle qdata[1-8] falcon up infinite 10 idle falcon[1-10] intel up infinite 24 idle artemis7,slurm[1-5],granger[1-6],granger[7-8],nibbler[1-4],ai0[1-6] amd up infinite 13 idle hermes[1-4],artemis[1-6],trillian[1-3]
You can also see what resources (such as GPUs) that a node has available by running the command
scontrol show node <nodename>.
abc1de@portal01 ~$ scontrol show node ai10 NodeName=ai10 Arch=x86_64 CoresPerSocket=8 CPUAlloc=0 CPUTot=32 CPULoad=0.01 AvailableFeatures=(null) ActiveFeatures=(null) Gres=gpu:nvidia_geforce_gtx_1080:4 NodeAddr=ai10 NodeHostName=ai10 Version=20.11.9 OS=Linux 3.10.0-957.5.1.el7.x86_64 #1 SMP Fri Feb 1 14:54:57 UTC 2019 RealMemory=128000 AllocMem=0 FreeMem=120054 Sockets=2 Boards=1 State=IDLE ThreadsPerCore=2 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A Partitions=gnolim BootTime=2023-02-15T10:01:04 SlurmdStartTime=2023-03-14T12:29:33 CfgTRES=cpu=32,mem=125G,billing=32 AllocTRES= CapWatts=n/a CurrentWatts=0 AveWatts=0 ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s Comment=(null)
To use SLURM resources, you must submit your jobs (program/script/etc.) to the SLURM controller. The controller will then send your job to compute nodes for execution, after which time your results will be returned. There is also an direct login option (see below) that doesn't require a job script.
Here is our script, all it does is print the hostname of the server running the script. We must add
SBATCH options to our script to handle various SLURM options.
#!/bin/bash # --- this job will be run on any available node # and simply output the node's hostname to # my_job.output #SBATCH --job-name="Slurm Simple Test Job" #SBATCH --error="my_job.err" #SBATCH --output="my_job.output" echo "$HOSTNAME"
We run the script with
sbatch and the results will be put in the file we specified with
--output. If no output file is specified, output will be saved to a file with the same name as the SLURM jobid.
[abc1de@portal04 ~]$ sbatch slurm.test Submitted batch job 640768 [abc1de@portal04 ~]$ more my_job.output cortado06
Here is a similar example using
srun running on multiple nodes:
abc1de@portal01 ~ $ srun -w slurm[1-5] -N5 hostname slurm4 slurm1 slurm2 slurm3 slurm5
If the node to be used is NOT in the main (default) “partition” (or queue), then you must specify the partition in your job script:
#!/bin/bash # --- this job will be run on any available node in the "gpu" partition # and simply output the node's hostname to # my_job.output #SBATCH --job-name="Slurm Simple Test Job" #SBATCH --error="my_job.err" #SBATCH --output="my_job.output" # --- specify the partition (queue) name #SBATCH --partition="gpu" echo "$HOSTNAME"
If you are trying to use a node that is not in the default partition, and you don't specify the partition in your job script, you will get a message from
srun saying “queued and waiting for resources”, but the job will not start.
Direct login to servers (without a job script)
You can use
srun to login directly to a server controlled by the SLURM job scheduler. This can be useful for debugging purposes as well as running your applications without using a job script.
We must pass the
--pty option to
srun so output is directed to a pseudo-terminal.
For example, to open a direct login job on the node “cortado04”, use:
abc1de@portal ~$ srun -w cortado04 --pty bash -i -l - abc1de@cortado04 ~$ hostname cortado04 abc1de@cortado04 ~$
-w argument selects the server into which to login. The
-i argument tells
bash to run as an interactive shell. The
-l argument instructs bash that this is a login shell, this, along with the final
- are important to reset environment variables that otherwise might cause issues using Environment Modules
If a node is in a partition (see below for partition information) other than the default “main” partition (for example, the “gpu” partition), then you must specify the partition in your command, for example:
abc1de@portal ~$ srun -w lynx05 -p gpu --pty bash -i -l -
If you are using a reservation, you must specify the “–reservation=<reservationname>” option to srun.
Please be aware of jobs you start and make sure that they finish executing. If your job does not exit gracefully, it will continue running on the server, taking up resources and preventing others from running their jobs.
To cancel a running job, use the
scancel [jobid] command
abc1de@portal01 ~ $ squeue JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) 467039 main sleep abc1de R 0:06 1 artemis1 <-- Running job abc1de@portal01 ~ $ scancel 467039
The default signal sent to a running job is SIGTERM (terminate). If you wish to send a different signal to the job's processes (for example, a SIGKILL which is often needed if a SIGTERM doesn't terminate the process), use the
--signal argument to scancel, i.e.:
abc1de@portal01 ~ $ scancel --signal=KILL 467039
Slurm refers to job queues as partitions. We group similar systems into separate queues. For example, there is a “main” queue for general purpose systems, and a “gpu” queue for systems with GPUs. These queues can have unique constraints such as compute nodes, max runtime, resource limits, etc.
If no partition is specified in your job script or when using the 'srun' command, it will go to the default partition “main”.
The “main” and “gpu” partitions have a time limit set, so jobs will terminate after a specified number of days, as shown in the output of the 'sinfo' command. However, there are two additional partitions, “nolim” and “gnolim”, that have a time limit of 20 days, which is effectively unlimited time.
Partition is indicated by
-p partname or
To specify a partition with
Or from the command line with
An example running the command
hostname on the main partition, this will run on any node in the partition:
srun -p main hostname
Long Running Jobs
If a job is expected to run longer than the default for a given partition, two other paritions with unlimited runtime named
gnolim exist for jobs that have long runtimes.
nolim is for long running jobs that do not require a GPU, and
gnolim is for long running jobs that require a GPU.
To utilize these partitions, simply specify the name of the partition in
Slurm handles GPUs and other non-CPU computing resources using what are called GRES Resources (Generic Resource). To use the GPU(s) on a system using Slurm, either using
srun, you must request the GPUs using the
--gres:x option. You must specify the
gres flag followed by
: and the quantity of resources
Say we want to use 4 GPUs on a system, we would use the following
Or from the command line
The SLURM scheduler implements the Accounting features of slurm. So users can execute the
sacct command to find job accounting information, like job ids, job names, partition run upon, allocated CPUs, job state, and exit codes. There are numerous other options supported. Type
man sacct on portal to see all the options.
Using "module" to load software in a job
Due to the way
sbatch spawns a bash session as a no-login session, initialization files are not loaded from
/etc/profile.d. This prevents the initialization of the Environment Modules system and will prevent you from loading software modules.
To fix this, simply include the following line in your sbatch scripts:
The SLURM scheduler allows for preemption on certain nodes within the cluster. To view which nodes that have preemption enabled, execute the
sinfo --format="%P %N" | grep hipri. Any nodes within a partition with
hipri for high priority in its name, have preemption enabled.
If you submit a job to a node in a high prioirty partition, it is possible it will be suspended if the owner of the node or their research group submits to it while your job is running.
This does not apply if a node is reserved.
To use a high priority partition, simply specify the partition name in your
srun commands or
sbatch scripts. This is done using the partition flag
-p <partition name> or