Job Specifications

Each user has a list of valid account/partition/QoS combinations they may specify, and each partition has a list of valid accounts which may submit jobs to that partition. For example, to submit a job under the campus partition, use the below batch header:

#SBATCH --account ACF-UTK0011 (or #SBATCH -A ACF-UTK0011)
#SBATCH --partition=campus-<partition-name> (or #SBATCH -p campus)
#SBATCH --qos=campus (or #SBATCH -q condo)

To submit a job under a private condo, use the below batch header:

#SBATCH --account ACF-UTK<project-number>
#SBATCH --partition=condo-<condo-name>
#SBATCH --qos=condo

Important Note: It is the combination of a partition, QoS, and project account which the SLURM scheduler program uses to allocate computing resources from the cluster for each job. If a user does not appropriately specify all three, the SLURM utility may not be able to process the user’s job as submitted due to a lack of information from the user.

isaac-sinfo is used to view partition and each partition’s node information for a system running Slurm. The command isaac-sinfo is a customized wrapper that allows easier access to information about certain classes of partitions. For example, if you type isaac-sinfo help, it will show: 

Usage: isaac-sinfo <campus,gpu,bigmem,long,condo> 

Then, if you type isaac-sinfo campus will show information only about the campus partitions. 

Likewise, if a user attempts to specify an account or QoS that’s not valid for a partition, or attempts to request an invalid account/qos combination for their netid, their job will be rejected. Detailed information about all the partitions and the respective nodes on ISAAC-Legacy can be viewed using the following command:

 $ sinfo -Nel

For more information on the flags used by commands, please refer to the Slurm documentation. There are a handful of partitions that will be returned by the above command which are not documented below. These are reserved for administrative purposes, and end users should ignore them.

You can always see the valid accounts for a partition with

$ scontrol show PartitionName=<partition-name> | grep AllowAccounts

You can always see your netid’s valid account/qos combinations with

$ sacctmgr show assoc | grep <netid>

However, this is not usually necessary. As a general rule, the valid QoS and accounts combinations for partitions will be as follows:

The general association between allowed accounts and QoS will be as follows:

TABLE 2.3: ALLOWED QOS BY ACCOUNT

You can always determine your current active accounts or request access to new accounts in the user portal.

Please note that in addition to the above two directives (project account and partition), users also need to specify the type of nodes, number of nodes, number of cores, and estimated maximum amount of wall time as parameters or other optional SBATCH directives when submitting a job script. 

Once a job is submitted, the SLURM scheduler checks for the available resources and allocate them to the jobs to launch the tasks.

Important Note: users can choose to run a job exclusively on entire node by using the exclusive flag while also using srun to distribute tasks among different CPUs. Check table 3.3 to see how to use this flag.

The order in which jobs are run depends on the following factors:

• Number of nodes requested – jobs that request more nodes get a higher priority.
• Queue wait time – a job’s priority increases along with its queue wait time (not counting blocked jobs as they are not considered “queued.”)
• Number of jobs – a maximum of ten jobs per user, at a time, will be eligible to run.

In certain special cases, the priority of a job may be manually increased upon request. To request priority change you may contact the OIT HelpDesk. They will need the job ID and reason to submit the request.

SLURM Commands/Variables

In the table below, are listed few important SLURM commands (with a description of the command) which are most often used while working with SLURM scheduler, and can be used on the ISAAC-Legacy login nodes.

TABLE 3.1: COMMON SLURM COMMANDS AND ASSOCIATED DESCRIPTIONS

SLURM Variables

Below are tabulated few important Slurm variables which ISAAC-Legacy users may find useful.

TABLE 3.2: SLURM VARIABLES USED TO GET THE INFORMATION OF AN ISAAC-Legacy RUNNING JOB

SBATCH Flags

The jobs a user submits to the ISAAC-Legacy cluster are submitted using a sbatch command which passes the request for the resources a user has requested in the job script to the SLURM scheduler. The resources in the job script are requested using the “SBATCH” directive. Note that SLURM scheduler can accept SBATCH directives in two formats. Users can choose to use either of the two formats at their own discretion. The description of each of the SBATCH flags is given below:

TABLE 3.3: SLURM FLAGS USED IN CREATING JOB SCRIPTS WITH DESCRIPTIONS

Submitting Jobs with SLURM

On ISAAC-Legacy, batch jobs can be submitted in two ways: (i) interactive batch mode, and (ii) non-interactive batch mode.

Interactive Batch Mode

Interactive batch jobs give users the interactive access to compute nodes. In interactive batch mode, users can request that the SLURM scheduler allocate the resources of compute nodes, directly on the terminal (e.g., using a terminal’s command line interface (CLI)). A common use for interactive batch jobs is to debug a calculation or a program before submitting non-interactive batch jobs for production runs. This section demonstrates how to run interactive jobs through the batch system and provides common usage tips.

Interactive batch mode can be invoked on an ISAAC-Legacy login node by using the salloc command followed by specific SBATCH flags to request specific resources to which the user would like access. The different SBATCH flags are given in table 3.3.

$ salloc -A projectaccount --nodes=1 --ntasks=1 --partition=campus --time=01:00:00
or 
$ salloc -A projectaccount -N 1 -n 1 -p campus -t 01:00:00

The salloc command interprets the user’s request to the SLURM scheduler, and as a result, allows the user to request the resources. In the example command above, we requested that the SLURM scheduler allocate one node and one CPU core for a total time of 1 hour using the “campus” partition. Note that if the salloc command is executed without specifying the resources (i.e., number of nodes, number of CPUs, tasks, and wall clock time etc.), then the SLURM scheduler will allocate the default resources.

Important Note: The default resources on ISAAC-Legacy are: one processor (1 CPU on 1 node) located under the campus partition, with a maximum wall clock time of 1 hour.

When the SLURM scheduler allocates the resources, the user who submitted the job gets a message on the terminal (as shown below) containing the information about the jobid and the hostname of the compute node where the resources are allocated. Notice that in the below example the jobid is “1234” and the hostname of the compute node is “nodename.”

 $ salloc --nodes=1 --ntasks=1 --time=01:00:00 --partition=campus
  salloc: Granted job allocation 1234
  salloc: Waiting for resource configuration
  salloc: Nodes nodename are ready for job
 $

Once the interactive job starts, the user needs to ssh to the allocated node or one of the allocated nodes (for the jobs requesting more than one node) and should change their working directories to a Lustre file system project space or scratch space to run the user’s computationally intense applications. It is best to run large user jobs in Lustre scratch space rather than Lustre project space because there is no size limit to the amount of data that a user may place on Lustre scratch space; however, there is a limit to how much data that a user may place on Lustre project space. Please visit File System for more information. If users have questions about how to best run their interactive jobs, users are welcome to send their questions to HPSC staff by submitting HPSC Service Request.

To run the parallel executable, we recommend using srun followed by the executable as shown below:

 $ srun executable
or
 $ srun -n <nprocs> executable

Important Note: Users do not necessarily need to include the number of processors they will require, before running the parallel executable while calling srun. The SLURM wrapper srun will execute your calculations in parallel on the number of processors requested in the user’s job script. Serial applications (that is, non-parallel applications) can be run both with and without srun.

Non-Interactive Batch Mode

In non-interactive batch mode, the set of resources as well as the commands for the application to be run are written in a text file, which is referred to as a “batch file” or “batch script”. A user’s “batch script” for their particular job is submitted to the SLURM scheduler by using the sbatch command. Batch scripts are very useful for users who want to run productions jobs. This is because batch scripts allow users to work on a cluster non-interactively. In batch jobs, users submit a group of commands to SLURM and then simply check the job’s status and the output of the commands from time to time. However, sometimes it is very useful to run a job interactively (primarily for debugging). Click here to check how to run the batch jobs interactively. A typical example of a non-interactive batch script/job script is given below:

 #!/bin/bash
 #This file is a submission script to request the ISAAC resources from SLURM 
 #SBATCH -J job			       #The name of the job
 #SBATCH -A ACF-UTK0011              # The project account to be charged
 #SBATCH --nodes=1                     # Number of nodes
 #SBATCH --ntasks-per-node=48          # cpus per node 
 #SBATCH --partition=campus            # If not specified then default is "campus"
 #SBATCH --time=0-01:00:00             # Wall time (days-hh:mm:ss)
 #SBATCH --error=job.e%J	       # The file where run time errors will be dumped
 #SBATCH --output=job.o%J	       # The file where the output of the terminal will be dumped
 #SBATCH --qos=campus

 # Now list your executable command/commands.
 # Example for code compiled with a software module:
 module load example/test

 hostname
 sleep 100
 srun executable

The above job script can be divided into three sections:

1. Shell interpreter (one line)
   • The first line of the script specifies the script’s interpreter. The syntax of this line is #!/bin/shellname (sh, bash, csh, ksh, zsh)
   • This line is important and essential. If not mentioned, then scheduler will print an error.
2. SLURM submission options
   • The second section contains a bunch of lines starting with ‘#SBATCH’.
   • These lines are not the comments, but by format start with ‘#’.
   • #SBATCH is a SLURM directive which communicates information regarding the resources requested by the user in the batch script file.
   • #SBATCH options after the first non-comment line are ignored by SLURM scheduler
   • The description about each of the flags is mentioned in table 3.3
   • The command sbatch on the terminal is used to submit the non-interactive batch script.
3. Shell commands
   • The shell command follows the last #SBATCH line.
   • These commands are a set of commands or tasks which a user wants to run. This also includes any software modules which may be needed to access a particular application.
   • To run the parallel application, it is recommended to use srun followed by the name of the full path and name of the executable if the executable path is not loaded into Slum environment while submitting the script.

For the quick start, we have also provided a collection of complete sample job scripts that are available on the ISAAC-Legacy cluster at /lustre/isaac/examples/jobs

Job Arrays

SLURM offers a useful option of submitting jobs that use array flags, for users whose batch jobs require identical resources. Using the array flag in a job script, users can submit multiple jobs with with a single sbatch command. Although the job script is submitted only once using sbatch command, the individual jobs in the array (of jobs) are scheduled independently with unique job array identifiers ($SLURM_ARRAY_JOB_ID). Each of the individual jobs can be differentiated using SLURM’s environmental variable $SLURM_ARRAY_TASK_ID. To understand this variable, let us consider an example of a SLURM script given below:

#!/bin/bash
#SBATCH -J myjob
#SBATCH -A ACF-UTK0011
#SBATCH -N 1
#SBATCH --ntasks-per-node=30  ###-ntasks is used when we want to define total number of processors
#SBATCH --time=01:00:00
#SBATCH --partition=campus     #####
##SBATCH -e myjob.e%j   ## Errors will be written in this file
#SBATCH -o myjob%A_%a.out    ## Separate output file will be created for each array. %A will be replaced by jobid and %a will be replaced by array index
#SBATCH --qos=campus
#SBATCH --array=1-30
       # Submit array of jobs numbered 1 to 30
###########   Perform some simple commands   ########################
set -x
###########   Below code is used to create 30 script files needed to submit the array of jobs   ###############
for i in {1..30}; do cp sleep_test.sh 'sleep_test'$i'.sh';done

###########   Run your executable   ###############
sh sleep_test$SLURM_ARRAY_TASK_ID.sh

In the above example, 30 sleep_test$index.sh executable files were created, and these jobs have names are differentiated by an index. One understands that the 30 executable files can be run by either submitting 30 individual jobs or by using SLURM arrays. A SLURM array would take these files in the form of an array named sleep_test[1-30].sh and execute these files. The variable SLURM_ARRAY_TASK_ID is set to array index value [between 1 and 30], with 30 being the total number of jobs in the array in this example, and the index value is defined in the SLURM script (above) using the #SBATCH directive

#SBATCH --array=1-30

The simultaneous number of jobs using a job array can also be limited by using a %n flag along with –array flag. For example: To run only 5 jobs at a time in a SLURM array, users can include the SLURM directive

#SBATCH --array=1-30%5

In order to create a separate output file for each of the submit jobs using SLURM arrays, use %A and %a, which represents the jobid and job array index as shown in the above example.

Exclusive Access to Nodes

As explained in the Scheduling Policy, jobs that are submitted by the same user can share computational nodes. However, if desired, users can request in their job scripts that whole node(s) be reserved to run their jobs without sharing them with other jobs. To do that use the below command:

Interactive batch mode:

 $ salloc -A projectaccount --nodes=1 --ntasks=1 --partition=campus --time=01:00:00 --exclusive --qos=campus

Non-Interactive batch mode:

Add the below line in your job script

 #SBATCH --exclusive

Monitoring Job Status

Users can regularly check status of their jobs by using the squeue command.

$ squeue -u <netID>
              JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
              1202    campus     Job3 username PD       0:00      2 (Resources)
              1201    campus     Job1 username  R       0:05      2 node[001-002]
              1200    campus     Job2 username  R       0:10      2 node[004-005]

The description of each of the columns of the output from squeue command is given below:

TABLE 3.4: SQUEUE COMMAND OUTPUTS

Description of the output

When a user submits a job, it passes through various states. The values of these states for a job is given by squeue command under the column ST. The possible values of the job under ST column are given below:

TABLE 3.5: POSSIBLE STATES OF A SLURM JOB

Altering Batch Jobs

The users are allowed to change the attributes of their jobs until the job starts running. In this section, we will describe how to alter your batch jobs with examples.

Remove a Job from Queue

User can remove the jobs in any state which are submitted by them using the command scancel.

To remove a job with a JOB ID 1234, use the command:

scancel 1234

Modifying the Job Details

Users can make use of the SLURM command scontrol which is used to alter a variety of SLURM parameters. Most of the commands using scontrol can only be executed by an ISAAC-Legacy System Adminstrator; however, users are granted some permissions to use scontrol for use on the jobs they have submitted, provided the jobs are not in the running mode.

Release/Hold a job

scontrol release/hold jobid

Modify the name of the job

scontrol update JobID=jobid JobName=any_new_name

Modify the total number of tasks

scontrol update JobID=jobid NumTasks=Total_tasks

Modify the number of CPUs per node

scontrol update JobID=jobid MinCPUsNode=CPUs

Modify the wall time of the job

scontrol update JobID=jobid TimeLimit=day-hh:mm:ss