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SLURM offers a variety of ways to run jobs. It is important to understand the different options available and how to request the resources required for a job in order for it to run successfully. All job submission should be done from submit nodes; any computational code should be run in a job allocation on compute nodes. The following commands outline how to allocate resources on the compute nodes and submit processes to be run on the allocated nodes. | SLURM offers a variety of ways to run jobs. It is important to understand the different options available and how to request the resources required for a job in order for it to run successfully. All job submission should be done from submit nodes; any computational code should be run in a job allocation on compute nodes. The following commands outline how to allocate resources on the compute nodes and submit processes to be run on the allocated nodes. | ||
Please note that the hard maximum number of jobs that the SLURM scheduler can handle is 10000. It is best to limit your number of submitted jobs at any given time to less than half this amount in the case that another user also wants to submit a large number of jobs. | Please note that the hard maximum number of jobs that the SLURM scheduler can handle at once is 10000. It is best to limit your number of submitted jobs at any given time to less than half this amount in the case that another user also wants to submit a large number of jobs. | ||
'''Computational jobs run on submission nodes will be terminated. Please use compute nodes for running computational jobs.''' | '''Computational jobs run on submission nodes will be terminated. Please use compute nodes for running computational jobs.''' | ||
Revision as of 16:38, 14 August 2023
Job Submission
SLURM offers a variety of ways to run jobs. It is important to understand the different options available and how to request the resources required for a job in order for it to run successfully. All job submission should be done from submit nodes; any computational code should be run in a job allocation on compute nodes. The following commands outline how to allocate resources on the compute nodes and submit processes to be run on the allocated nodes.
Please note that the hard maximum number of jobs that the SLURM scheduler can handle at once is 10000. It is best to limit your number of submitted jobs at any given time to less than half this amount in the case that another user also wants to submit a large number of jobs.
Computational jobs run on submission nodes will be terminated. Please use compute nodes for running computational jobs.
For details on how SLURM decides how to schedule jobs when multiple jobs are waiting in a scheduler's queue, please see SLURM/Priority.
srun
srun is the command used to run a process on the compute nodes in the cluster. It works by passing it a command (this could be a script) which will be run on a compute node and then srun will return. srun accepts many command line options to specify the resources required by the command passed to it. Some common command line arguments are listed below and full documentation of all available options is available in the man page for srun, which can be accessed by running man srun.
username@nexuscml010:srun --qos=default --mem=100mb --time=1:00:00 bash -c 'echo "Hello World from" `hostname`' Hello World from tron33.umiacs.umd.edu
It is important to understand that srun is an interactive command. By default input to srun is broadcast to all compute nodes running your process and output from the compute nodes is redirected to srun. This behavior can be changed; however, srun will always wait for the command passed to finish before exiting, so if you start a long running process and end your terminal session, your process will stop running on the compute nodes and your job will end. To run a non-interactive submission that will remain running after you logout, you will need to wrap your srun commands in a batch script and submit it with sbatch.
Common srun arguments
--mem=1gbif no unit is given MB is assumed--nodes=2if passed to srun, the given command will be run concurrently on each node--qos=defaultto see the available QOS options on a cluster, runshow_qos--time=hh:mm:sstime needed to run your job--job-name=helloWorld--output=filenamefile to redirect stdout to--error=filenamefile to redirect stderr--partition=$PNAMErequest job run in the $PNAME partition--ntasks=2request 2 "tasks" which map to cores on a CPU, if passed to srun the given command will be run concurrently on each core--account=accountnameuse qos specific to an account
Interactive Shell Sessions
An interactive shell session on a compute node can be useful for debugging or developing code that isn't ready to be run as a batch job. To get an interactive shell on a node, use srun to invoke a shell:
username@nexuscml00:srun --pty --qos=default --mem 1gb --time=01:00:00 bash username@tron33:
Please do not leave interactive shells running for long periods of time when you are not working. This blocks resources from being used by everyone else.
salloc
The salloc command can also be used to request resources be allocated without needing a batch script. Running salloc with a list of resources will allocate the resources you requested, create a job, and drop you into a subshell with the environment variables necessary to run commands in the newly created job allocation. When your time is up or you exit the subshell, your job allocation will be relinquished.
username@nexuscml00:salloc --qos=default -N 1 --mem=2gb --time=01:00:00 salloc: Granted job allocation 159 username@nexuscml00:srun /usr/bin/hostname tron33.umiacs.umd.edu username@nexuscml00:exit exit salloc: Relinquishing job allocation 159
Please note that any commands not invoked with srun will be run locally on the submit node. Please be careful when using salloc.
sbatch
The sbatch command allows you to write a batch script to be submitted and run non-interactively on the compute nodes. To run a simple Hello World command on the compute nodes you could write a file, helloWorld.sh with the following contents:
#!/bin/bash srun bash -c 'echo Hello World from `hostname`'
Then you need to submit the script with sbatch and request resources:
username@nexuscml00:sbatch --qos=default --mem=1gb --time=1:00:00 helloWorld.sh Submitted batch job 121
SLURM will return a job number that you can use to check the status of your job with squeue:
username@nexuscml00:squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
121 tron helloWor username R 0:01 1 tron32
Advanced Batch Scripts
You can also write a batch script with all of your resources/options defined in the script itself. This is useful for jobs that need to be run 10s/100s/1000s of times. You can then handle any necessary environment setup and run commands on the resources you requested by invoking commands with srun. The srun commands can also be more complex and be told to only use portions of your entire job allocation, each of these distinct srun commands makes up one "job step". The batch script will be run on the first node allocated as part of your job allocation and each job step will be run on whatever resources you tell them to. In the following example, we have a batch job that will request 2 nodes in the cluster. We then load a specific version of Python into our environment and submit two job steps, each one using one node. Since srun is blocks until the command finishes, we use the '&' operator to background the process so that both job steps can run at once; however, this means that we then need to use the wait command to block processing until all background processes have finished.
#!/bin/bash # Lines that begin with #SBATCH specify commands to be used by SLURM for scheduling #SBATCH --job-name=helloWorld # sets the job name #SBATCH --output=helloWorld.out.%j # indicates a file to redirect STDOUT to; %j is the jobid. Must be set to a file instead of a directory or else submission will fail. #SBATCH --error=helloWorld.out.%j # indicates a file to redirect STDERR to; %j is the jobid. Must be set to a file instead of a directory or else submission will fail. #SBATCH --time=00:05:00 # how long you think your job will take to complete; format=hh:mm:ss #SBATCH --qos=default # set QOS, this will determine what resources can be requested #SBATCH --nodes=2 # number of nodes to allocate for your job #SBATCH --ntasks=4 # request 4 cpu cores be reserved for your node total #SBATCH --ntasks-per-node=2 # request 2 cpu cores be reserved per node #SBATCH --mem=1gb # memory required by job; if unit is not specified MB will be assumed module load Python/2.7.9 # run any commands necessary to setup your environment srun -N 1 --mem=512mb bash -c "hostname; python --version" & # use srun to invoke commands within your job; using an '&' srun -N 1 --mem=512mb bash -c "hostname; python --version" & # will background the process allowing them to run concurrently wait # wait for any background processes to complete # once the end of the batch script is reached your job allocation will be revoked
Another useful thing to know is that you can pass additional arguments into your sbatch scripts on the command line and reference them as ${1} for the first argument and so on.
More Examples
scancel
The scancel command can be used to cancel job allocations or job steps that are no longer needed. It can be passed individual job IDs or an option to delete all of your jobs or jobs that meet certain criteria.
scancel 255cancel job 255scancel 255.3cancel job step 3 of job 255scancel --user username --partition=troncancel all jobs for username in the tron partition
Identifying Resources and Features
The sinfo can show you additional features of nodes in the cluster but you need to ask it to show some non-default options using a command like sinfo -o "%40N %8c %8m %20f %35G".
username@nexuscml00:sinfo -o "%40N %8c %8m %20f %35G" NODELIST CPUS MEMORY AVAIL_FEATURES GRES tron[22-33,35-45] 16 128521+ rhel8,Zen,EPYC-7302 gpu:rtxa4000:4 tron[06-09,12-15,21] 16 128520+ rhel8,Zen,EPYC-7302P gpu:rtxa4000:4 tron[10-11,16-20,34] 16 128524 rhel8,Zen,EPYC-7313P gpu:rtxa4000:4 legacy00 48 128248 rhel8,Zen,EPYC-7402 (null) legacy[01-09] 12 128436 rhel8,Xeon,E5-2620 (null) clip07 8 257570 rhel8,Xeon,E5-2623 gpu:gtx1080ti:3 clip08 32 257565 rhel8,Xeon,E5-2683 gpu:gtx1080ti:8 clip09 32 385350 rhel8,Xeon,6130 gpu:rtx2080ti:5,gpu:gtx1080ti:3 clip00 32 257583 rhel8,Xeon,E5-2683 gpu:gtxtitanx:3 clip01 32 257583 rhel8,Xeon,E5-2683 gpu:gtxtitanx:1,gpu:gtxtitanxp:2 clip02 20 128562 rhel8,Xeon,E5-2630 gpu:gtx1080ti:3 clip03 20 128562 rhel8,Xeon,E5-2630 gpu:rtx2080ti:1,gpu:gtx1080ti:2 clip04 32 257540 rhel8,Zen,EPYC-7302 gpu:rtx3090:4 clip[05-06] 24 128523 rhel8,Zen,EPYC-7352 gpu:rtxa6000:2 gammagpu[01-03] 32 257541 rhel8,Zen,EPYC-7313 gpu:rtxa5000:8 legacy14 20 322068 rhel8,Xeon,E5-2650 gpu:gtxtitanx:4 legacy[15-16] 16 257587 rhel8,Xeon,E5-2630 gpu:teslak80:2 legacy17 44 515501 rhel8,Xeon,E5-2699 gpu:gtx1080ti:4 twist[00-01] 16 64031 rhel8,Xeon,E5-1660 (null) twist[02-05] 48 257452 rhel8,Xeon,E5-2650 (null) tron[00-05] 32 257540 rhel8,Zen,EPYC-7302 gpu:rtxa6000:8 tron[46-61] 48 257539 rhel8,Zen,EPYC-7352 gpu:rtxa5000:8
Note that all of the nodes shown by this may not necessarily be in a partition you are able to submit to.
There is also a prewritten alias show_nodes on all of our SLURM computing clusters that shows each node's name, number of CPUs, memory, processor type (as AVAIL_FEATURES), GRES, State, and partitions that can submit to it.
You can identify further specific information about a node using scontrol with various flags.
Requesting GPUs
If you need to do processing on a GPU, you will need to request that your job have access to GPUs just as you need to request processors or CPU cores. You will also need to make sure that you submit your job to the correct partition since nodes with GPUs are often put into their own partition to prevent the nodes from being tied up by jobs that don't utilize GPUs. In SLURM, GPUs are considered "generic resources" also known as GRES. To request some number of GPUs be reserved/available for your job, you can use the flag --gres=gpu:2. If there are multiple types of GPUs available in the cluster and you need a specific type, you can provide the type option to the gres flag e.g. --gres=gpu:rtxa5000:1. If you do not request a specific type of GPU, you may be scheduled on the oldest/lowest specced GPU available.
username@nexuscml00:srun --pty --gres=gpu:2 nvidia-smi Thu Aug 25 15:22:15 2022 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 470.129.06 Driver Version: 470.129.06 CUDA Version: 11.4 | |-------------------------------+----------------------+----------------------+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 NVIDIA RTX A4000 Off | 00000000:01:00.0 Off | Off | | 30% 23C P8 20W / 140W | 0MiB / 16376MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ | 1 NVIDIA RTX A4000 Off | 00000000:41:00.0 Off | Off | | 30% 24C P8 15W / 140W | 0MiB / 16376MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ +-----------------------------------------------------------------------------+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |=============================================================================| | No running processes found | +-----------------------------------------------------------------------------+
Please note that your job will only be able to see/access the GPUs you requested. If you only need 1 GPU, please only request 1 GPU. The others on the node (if any) will be left available for other users.
username@nexuscml00:srun --pty --gres=gpu:rtxa5000:1 nvidia-smi Thu Aug 25 15:22:15 2022 +-----------------------------------------------------------------------------+ | NVIDIA-SMI 470.129.06 Driver Version: 470.129.06 CUDA Version: 11.4 | |-------------------------------+----------------------+----------------------+ | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | | | | MIG M. | |===============================+======================+======================| | 0 NVIDIA RTX A5000 Off | 00000000:01:00.0 Off | Off | | 30% 23C P8 20W / 230W | 0MiB / 24256MiB | 0% Default | | | | N/A | +-------------------------------+----------------------+----------------------+ +-----------------------------------------------------------------------------+ | Processes: GPU Memory | | GPU PID Type Process name Usage | |=============================================================================| | No running processes found | +-----------------------------------------------------------------------------+
As with all other flags, the --gres flag may also be passed to sbatch and salloc rather than directly to srun.
MPI example
To run MPI jobs, you will need to include the --mpi=pmix flag in your submission arguments.
#!/usr/bin/bash #SBATCH --job-name=mpi_test # Job name #SBATCH --nodes=4 # Number of nodes #SBATCH --ntasks=8 # Number of MPI ranks #SBATCH --ntasks-per-node=2 # Number of MPI ranks per node #SBATCH --ntasks-per-socket=1 # Number of tasks per processor socket on the node #SBATCH --time=00:30:00 # Time limit hrs:min:sec srun --mpi=pmix /nfshomes/username/testing/mpi/a.out