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compute_slurm [2020/09/24 13:56]
pgh5a
compute_slurm [2022/04/04 14:25] (current)
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 The Computer Science Department uses a "job scheduler"​ called [[https://​en.wikipedia.org/​wiki/​Slurm_Workload_Manager|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 Computer Science Department uses a "job scheduler"​ called [[https://​en.wikipedia.org/​wiki/​Slurm_Workload_Manager|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.
 + 
 === Using SLURM === === Using SLURM ===
 **[[https://​slurm.schedmd.com/​pdfs/​summary.pdf| **[[https://​slurm.schedmd.com/​pdfs/​summary.pdf|
 Slurm Commands Cheat Sheet]]** Slurm Commands Cheat Sheet]]**
 +
 +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.
  
 === Information Gathering === === Information Gathering ===
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 <​code>​ <​code>​
-[pgh5a@portal04 ~]$ sinfo+[abc1de@portal04 ~]$ sinfo
 PARTITION AVAIL  TIMELIMIT ​ NODES  STATE NODELIST PARTITION AVAIL  TIMELIMIT ​ NODES  STATE NODELIST
 main*        up   ​infinite ​     3  drain falcon[3-5] main*        up   ​infinite ​     3  drain falcon[3-5]
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 <​code>​ <​code>​
-pgh5a@portal01 ~ $ squeue +abc1de@portal01 ~ $ squeue 
-             JOBID PARTITION ​    ​NAME ​    USER ST       ​TIME  NODES NODELIST(REASON) +             JOBID PARTITION ​    ​NAME ​    ​USER ​   ST     ​TIME  NODES NODELIST(REASON) 
-            467039 ​     main    my_job ​   ​pgh5a  ​R ​     0:06      1 artemis1+            467039 ​     main    my_job ​   ​abc1de ​ ​R ​     0:06      1 artemis1
 </​code>​ </​code>​
  
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 <​code>​ <​code>​
-pgh5a@portal01 ~ $ sinfo+abc1de@portal01 ~ $ sinfo
 PARTITION ​    ​AVAIL ​ TIMELIMIT ​ NODES  STATE NODELIST 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 ​    ​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]
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 === Jobs === === Jobs ===
  
-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.+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.
  
-Users can submit SLURM jobs from ''​%%portal.cs.virginia.edu%%''​.  ​From a shell, you can submit jobs using the commands [[https://​slurm.schedmd.com/​srun.html|srun]] or [[https://​slurm.schedmd.com/​sbatch.html|sbatch]]. ​ Let's look at a very simple example script and ''​%%sbatch%%''​ command.+Users can submit SLURM jobs from ''​%%portal.cs.virginia.edu%%''​.  ​You can submit jobs using the commands [[https://​slurm.schedmd.com/​srun.html|srun]] or [[https://​slurm.schedmd.com/​sbatch.html|sbatch]]. ​ Let's look at a very simple example script and ''​%%sbatch%%''​ command.
  
 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. 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.
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 <code bash> <code bash>
 #!/bin/bash #!/bin/bash
- +# --- this job will be run on any available node 
-#SBATCH ​--job-name="​Slurm Simple Test Job" #Name of the job which appears in squeue +and simply output the node's hostname to 
-+my_job.output 
-#SBATCH --mail-type=ALL +#SBATCH --job-name="Slurm Simple Test Job" 
-#SBATCH --mail-user=pgh5a@virginia.edu +#SBATCH --error="​my_job.err"​ 
-# +#SBATCH --output="​my_job.output"​ 
-#SBATCH --error="​my_job.err" ​                   # Where to write std err +echo "​$HOSTNAME"​
-#SBATCH --output="​my_job.output" ​               # Where to write stdout +
-#SBATCH --nodelist=slurm1 +
- +
-hostname+
 </​code>​ </​code>​
  
-Let's put this in a directory called ''​%%slurm-test%%''​ in our home directory.  ​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.+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.
  
 <​code>​ <​code>​
-pgh5a@portal01 ​~ $ cd slurm-test/  +[abc1de@portal04 ​~]sbatch ​slurm.test 
-pgh5a@portal01 ~/​slurm-test $ chmod +x test.sh  +Submitted batch job 640768 
-pgh5a@portal01 ~/slurm-test $ sbatch test.sh ​ +[abc1de@portal04 ​~]more my_job.output 
-Submitted batch job 466977 +cortado06
-pgh5a@portal01 ​~/slurm-test $ ls +
-my_job.err ​ my_job.output ​ test.sh +
-pgh5a@portal01 ~/​slurm-test ​cat my_job.output  +
-slurm1+
 </​code>​ </​code>​
  
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 <​code>​ <​code>​
-pgh5a@portal01 ~ $ srun -w slurm[1-5] -N5 hostname+abc1de@portal01 ~ $ srun -w slurm[1-5] -N5 hostname
 slurm4 slurm4
 slurm1 slurm1
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 slurm3 slurm3
 slurm5 slurm5
-</​code>​ 
- 
-=== Terminating Jobs === 
- 
-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 
- 
-<​code>​ 
-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 
 </​code>​ </​code>​
  
 === Direct login to servers (without a job script) === === 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. ​Directly logging in also reserves the node for your exclusive use. +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. ​This feature ​also reserves the server ​for your exclusive use. 
  
-To spawn a shell we must pass the ''​%%--pty%%''​ option to ''​%%srun%%''​ so output is directed to a pseudo-terminal:​+We must pass the ''​%%--pty%%''​ option to ''​%%srun%%''​ so output is directed to a pseudo-terminal:​
  
 <​code>​ <​code>​
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 The ''​%%-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 [[linux_environment_modules|Environment Modules]] The ''​%%-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 [[linux_environment_modules|Environment Modules]]
  
-If a node is in a partition other than the default "​main"​ partition (for example, the "​gpu"​ partition), then you must specify the partition in your command, for example:+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:
 <​code>​ <​code>​
 abc1de@portal ~$ srun -w lynx05 -p gpu --pty bash -i -l - abc1de@portal ~$ srun -w lynx05 -p gpu --pty bash -i -l -
 </​code>​ </​code>​
 +
 +=== Terminating Jobs ===
 +
 +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
 +
 +<​code>​
 +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
 +</​code>​
 +
 +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.:
 +<​code>​
 +abc1de@portal01 ~ $ scancel --signal=KILL 467039
 +</​code>​
 +
  
 === Queues/​Partitions === === Queues/​Partitions ===
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 Reservations for specific resources or nodes can be made by submitting a request to <​cshelpdesk@virginia.edu>​. ​ For more information about using reservations,​ see the main article on [[compute_slurm_reservations|SLURM Reservations]] Reservations for specific resources or nodes can be made by submitting a request to <​cshelpdesk@virginia.edu>​. ​ For more information about using reservations,​ see the main article on [[compute_slurm_reservations|SLURM Reservations]]
 +
 +=== Job Accounting ===
 +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.  ​
  
 === Note on Modules in Slurm === === Note on Modules in Slurm ===
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  • Last modified: 2020/09/24 13:56
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