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This page presents a high walk-through of submitting jobs on the UC Merced Clusters.

To find more tailored and thorough, software-specific guides please visit our Running Jobs

Running Jobs on Clusters​

The command sbatch is used to submit jobs to the queue. Additional commands to work with and monitor the queue/scheduler are shown in the table below.

CommandDescription
squeuereports the state of jobs or job steps.
sinforeports the state of partitions and nodes managed by Slurm
scancelused to cancel a pending or running job or job step. It can also be used to send an arbitrary signal to all processes associated with a running job or job step.
#!/bin/bash
#SBATCH --nodes=1    # request only 1 node
#SBATCH --partition test      # this job will be submitted to test queue
#SBATCH --mem=96G #this job is asked for 96G of total memory, use 0 if you want to use entire node memory
#SBATCH --time=0-00:15:00 # 15 minute
#SBATCH --ntasks-per-node=56 # this job requests for 56 cores on a node
#SBATCH --output=my_%j.stdout    # standard output will be redirected to this file
# #SBATCH --constraint=bigmem   #uncomment this line if you need the access to the bigmem node for Pinnacles
# #SBATCH --constraint=gpu #uncomment this line if you need the access to GPU
# #SBATCH --gres=gpu:2   #uncomment this line if you need GPU access (2 GPUs)
#SBATCH --job-name=my_job    # this is your job’s name
##SBATCH --mail-user=UCMercedNetID@ucmerced.edu  
##SBATCH --mail-type=ALL  #uncomment the first two lines if you want to receive     the email notifications
#SBATCH --export=ALL

Note that for both MERCED and Pinnacles CPUs hyper-threading is turned off.

If you want to assess how busy the cluster is, please use the following Use sinfo to see the nodes state and check how many nodes are being allocated (alloc) or how many nodes are available (idle) If you want to estimate the job starting time sacct -X -j [JOBID] -o start,submit provides information for job estimated starting time or submitted time

Job Arrays​

Job arrays offer a mechanism for submitting and managing collections of similar jobs quickly and easily that utilizes only one job script. Submitting a job array can be useful in many of the following ways:

  1. Having a set of code or program that needs to run many different input variables or files.
  2. Running a single program repeatedly to analyze a single data file.
  3. Running the same program multiple times with varying parameters.

Job arrays allows users to run jobs at the same time or have the results of the previous job output to be used as input for the next job. While the output capacity from a job array is immense, the job configurations are the same for all jobs to be run in the job array.

The max number of jobs that can run at the same time is determined by the maximum number of jobs that can run on the selected partition and is different for each partition.< RETURN HERE TO ATTACH PARTITIONS>

Job Array Scripting​

#!/bin/bash
#SBATCH --nodes=1  #asked for 1 node
#SBATCH --ntasks=1 #asked for 1 cores
#SBATCH --partition medium  #this job will submit to medium partition
#SBATCH --array=1-5
#SBATCH --mem=1G  #this job is asked for 1G of total memory, use 0 if you want to use entire node memory
#SBATCH --time=0-00:15:00 # 15 minutes
#SBATCH --output=test_%A_%a.qlog  #the output information will put into test_$SLURM_ARRAY_JOB_ID_$SLURM_ARRAY_TASK_ID.qlog file
#SBATCH --job-name=test1  #the job name
#SBATCH --export=ALL
whoami
module load anaconda3
# This job will use one python input but takes different argument each time per job array
python3 python_test_array.py $SLURM_ARRAY_TASK_ID

Submitting and Managing Job Arrays​

When submitting a job array there will be a new argument, --array=x-y. The task id,x represents the starting index, and the task id y represents the last index - 1. The complete line to submit the array job will look similar to #SBATCH --array=x-y myjob.file. Where myjob.file will be replaced by the name of your job script.

The Task ID range specification arguments can also be configured to:

  1. Submit a job array with specified-comma separated index values. Ex. #SBATCH --array=6,36,1296. (6, 36 1296): total of 3 jobs.
  2. Submit a job array with index values incrementing by 1. Ex. #SBATCH --array=x-y Range from 1-10; total of 10 jobs.
  3. Submit a job array with index values that have a step or parse value that does not equal 1. Ex. #SBATCH --array=45-90:15. Range from index 45-90, with an step of 15 (45,60,75,90). Total of 4 jobs to be ran.

Job Dependencies in Job Arrays​

Jobs that depend on outputs of previous jobs of a job array or on the output of a whole job array after it is completed must declare itself as dependent using #SBATCH --depend=<Flag>:[jobid][IndexRange] <jobscript.file> after the independent job array has been submitted to the scheduler.

Below are flags that can be used to help declare the dependency of certain job(s) in the job array submission line after the first job array has been submitted to the scheduler.

CommandUSE
afterFlag is satisfied after all tasks in the job array start.
afteranyFlag is satisfied after all tasks in the job array complete.
aftercorrSatisfied after the corresponding task ID in the specified job has completed successfully
afterokFlag is satisfied after all tasks in the job array complete successfully
afternotokFlag satisfied after all tasks in the job array complete with at least one tasks not completing successfully.
Last updated on by Alex Villa