Difference between revisions of "Useful Slurm Commands"

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==Sample slurm script for many independent jobs==
 
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  #!/bin/bash
 
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  #SBATCH --time=<desired time up to node upper time limit> #lower times get higher priority in the queuing system
 
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  #SBATCH --nodes=3
 
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  #SBATCH --ntasks=(# cores per node) * (# nodes) #this should equal the number of jobs you want to run at the same time
 
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  #SBATCH --job-name=<your_job_name>
 
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  #SBATCH --output=<std_out_filename>
 
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  #SBATCH -p <partition_name>
 
  
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  DOCK_PATH="<path to dock bin/executable>"
 
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  JOB_FILE="<your common input file>"
 
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  CDIR=$(pwd)
 
  
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  # Assuming your paths to experiments are listed line by line in a file named paths.txt
 
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  while IFS= read -r path; do
 
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    cp $JOB_FILE -t $path
 
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    cd $path
 
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    base=$(basename -s .in $JOB_FILE)
 
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    # You can modify this srun command based on your requirements, the -n1 requests 1 core for the srun job, the -N1 requests 1 node, the --exclusive prevents this job's cores from being used in other jobs, -W 0 tells the script to not give  the job a timelimit
 
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    srun --mem=6090 --exclusive -N1 -n1 -W 0 $DOCK_PATH/dock6.rdkit -i $base.in -o $base.out &
 
  
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    cd $CDIR
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==Basic Slurm commands==
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  done < paths.txt
 
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  wait #necessary to prevent the script from ending and terminating your jobs
 
  
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* squeue -u $(whoami) - displays your running jobs and their job ids
 +
* scancel <jobid> - remove the job from the queue
  
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==Basic PBS commands==
 
  
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* qsub <script> - will submit your script to the queue
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==Advanced Tricks==
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* qstat - will display a list of jobs running
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Delete all your jobs (use with caution)
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* qdel <jobid> - remove the job from the queue
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scancel -u $(whoami)
  
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Job id                    Name            User            Time Use S Queue
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Delete all your queued jobs only. Leaves all runnings jobs alone.
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  ------------------------- ---------------- --------------- -------- - -----
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  scancel -u $(whoami) -t "PENDING"
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514722.nagling            STDIN            liuxt12        1657:13: R batch
 
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514723.nagling            STDIN            liuxt12        3366:45: R batch
 
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514724.nagling            jet3dKn0.002PR20 wli            874:42:4 R batch
 
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514725.nagling            ...dKn0.002PR100 wli            855:59:2 R batch
 
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514803.nagling            jet3dKn0.002PR10 wli            596:48:0 R batch
 
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514809.nagling            SAM              mriessen        542:37:3 R batch
 
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514811.nagling            STDIN            justin          00:00:32 R batch
 
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514815.nagling            latency_test    penzhang              0 Q batch
 
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514822.nagling            flex_1.dock.csh  xinyu          34:26:46 R batch
 
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514839.nagling            flex_2.dock.csh  xinyu          31:22:33 R batch
 
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514856.nagling            flex_5.dock.csh  xinyu          26:33:35 R batch
 
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514859.nagling            ....1_2.dock.csh xinyu          06:13:43 R batch
 
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514862.nagling            p0.10            hjli            326:10:5 R batch
 
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514863.nagling            p0.4            hjli            325:49:5 R batch
 
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514864.nagling            p0.7            hjli            332:11:4 R batch
 
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514884.nagling            ...1_p0.0_11.csh xinyu          17:16:57 R batch
 
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514920.nagling            STDIN            lli            00:34:43 R batch
 
  
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On seawulf the 'nodes' command shows a list of free nodes
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View only idle nodes - displays available nodes (note: some nodes may have exclusive access to certain lab groups)
 +
sinfo -l -a | grep idle
  
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        avail  alloc  down
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Check out a node to run jobs interactively (so that you don't use the login nodes!!!)
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  nodes: 35      165    25
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  srun -N 1 -n 28 -t 8:00:00 -p long-28core --pty bash
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wulfie: 35      165    25
 
  
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Use the man or info command in Unix to get more details of usage for these commands.
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==Sample slurm script for many independent jobs==
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You can use PBS commands inside your script. These are usually optional, but can be useful.
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#!/bin/bash
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There is an example script see [[NAMD on Seawulf]]
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  #SBATCH --time=2-00:00:00  #lower times get higher priority in the queuing system
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  #SBATCH --nodes=3 #number
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  #PBS -l nodes=8:ppn=2
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  #SBATCH --ntasks=(# cores per node) * (# nodes) #this should equal the number of jobs you want to run at the same time
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#PBS -l walltime=08:00:00
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  #SBATCH --job-name=<your_job_name>
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  #PBS -N my_job_name
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  #SBATCH --output=<std_out_filename>
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  #PBS -M user@ic.sunysb.edu
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  #SBATCH -p <partition_name> 
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  #PBS -o namd.md01.out
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  #PBS -e namd.md01.err
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  DOCK_PATH="<path to dock bin/executable>"
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  #PBS -V
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JOB_FILE="<your common input file>"
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CDIR=$(pwd)
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Using these PBS directives will name the job, the output files etc.
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# Assuming your paths to experiments are listed line by line in a file named paths.txt, which should have # paths = # cores = # tasks
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  #PBS -j oe
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  while IFS= read -r path; do
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  #PBS -o pbs.out   
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  cp $JOB_FILE -t $path
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This will join the output and error streams into the output file.
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  cd $path
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$PBS_O_WORKDIR is an environment variable that contains the path the script was submitted in. Usually you want to define a specific workdir and use that instead of relying on this variable.
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  base=$(basename -s .in $JOB_FILE)
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+
  # You can modify this srun command based on your requirements, the -n1 requests 1 core for the srun job, the -N1 requests 1 node, the --exclusive prevents this job's cores from being used in other jobs, -W 0 tells the script to not give   the job a timelimit
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==Advanced Tricks==
+
  srun --mem=6090 --exclusive -N1 -n1 -W 0 $DOCK_PATH/dock6.rdkit -i $base.in -o $base.out &
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Delete all your jobs (either will work, check different versions of PBS)
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  cd $CDIR
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  qstat -u sudipto | awk -F. '/sudipto/{print $1}' | xargs qdel
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done < paths.txt
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qstat | grep sudipto | awk -F. '{print $1}' | xargs qdel
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wait #necessary to prevent the script from ending and terminating your jobs
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Delete all your queued jobs only. Leaves all runnings jobs alone.
 
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qstat -u sudipto | awk -F. '/00 Q /{printf $1" "}' | xargs qdel
 
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qstat -u sudipto | awk -F. '/ Q   --/{printf $1" " }' | xargs qdel
 
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List all working nodes in the queue
 
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pbsnodes | egrep '^node|state =' | grep -B 1 'state = free' | grep ^node
 
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set NODELIST=`pbsnodes | egrep '^node|state =' | grep -B 1 'state = free' | grep ^node`
 
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foreach node ($NODELIST)
 
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/usr/local/torque-2.1.6/bin/qsub -l nodes=${NODE} ${HOME}/get.nodes.stats.csh
 
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done
 
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Run on a particular type of node
 
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  qsub -l nodes=1:beta:ppn=1 ${script}
 

Latest revision as of 15:40, 22 February 2024


Basic Slurm commands

  • squeue -u $(whoami) - displays your running jobs and their job ids
  • scancel <jobid> - remove the job from the queue


Advanced Tricks

Delete all your jobs (use with caution) 

scancel -u $(whoami)

Delete all your queued jobs only. Leaves all runnings jobs alone. 

scancel -u $(whoami) -t "PENDING"

View only idle nodes - displays available nodes (note: some nodes may have exclusive access to certain lab groups) 

sinfo -l -a | grep idle

Check out a node to run jobs interactively (so that you don't use the login nodes!!!) 

srun -N 1 -n 28 -t 8:00:00 -p long-28core --pty bash

Sample slurm script for many independent jobs

#!/bin/bash
#SBATCH --time=2-00:00:00  #lower times get higher priority in the queuing system
#SBATCH --nodes=3 #number
#SBATCH --ntasks=(# cores per node) * (# nodes) #this should equal the number of jobs you want to run at the same time
#SBATCH --job-name=<your_job_name>
#SBATCH --output=<std_out_filename>
#SBATCH -p <partition_name>  
 
DOCK_PATH="<path to dock bin/executable>"
JOB_FILE="<your common input file>"
CDIR=$(pwd)
# Assuming your paths to experiments are listed line by line in a file named paths.txt, which should have # paths = # cores = # tasks
while IFS= read -r path; do
  cp $JOB_FILE -t $path
  cd $path
  base=$(basename -s .in $JOB_FILE)
  # You can modify this srun command based on your requirements, the -n1 requests 1 core for the srun job, the -N1 requests 1 node, the --exclusive prevents this job's cores from being used in other jobs, -W 0 tells the script to not give   the job a timelimit
  srun --mem=6090 --exclusive -N1 -n1 -W 0 $DOCK_PATH/dock6.rdkit -i $base.in -o $base.out &
  cd $CDIR
done < paths.txt
wait #necessary to prevent the script from ending and terminating your jobs
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