HPC High Performance Computing: 5.2. Submitting basic jobs

The basic command to send a job is sbatch. 

test@login01:~$ sbatch sleep.sh
Submitted batch job 175

Once registered, the scheduler tells the job ID. Keep it handy, in case of problems you'll need this value to debug what happens.

Although you can specify the options when calling sbatch, when submitting a job execution request it is strongly advised that all options be provided within a job definition file (in these examples the file will be called “job.sh"). This file will contain the command you wish to execute and SLURM resource request options that you need.

#!/bin/bash
#SBATCH -J prova_uname10
#SBATCH -p short
#SBATCH -N 1
#SBATCH -n 2 
#SBATCH --chdir=/homedtic/test/slurm_jobs
#SBATCH --time=2:00
#SBATCH -o %N.%J.out # STDOUT
#SBATCH -e %N.%j.err # STDERR
 
ps -ef | grep slurm
uname -a >> /homedtic/test/uname.txt

The "-J" option sets the name of the job. This name is used to create the output log files for the job. We recommend using a capital letter for the job name is order to distinguish these log files from the other files in your working directory. This makes it easier to delete the log files later.

The "-p" option requests the queue in which the job should run. 

The "-N" option Request that a minimum of nodes be allocated to this job.

The "-n" option Request the number of tasks per node.

The “–time” option specify a a limit on the total run time of the job allocation.

The “–chdir” option  Set the working directory of the batch script to directory before it is executed.

The "-o" option instruct Slurm to connect the batch script's standard output directly to the file name specified in the "filename pattern".

The "-e" option instruct Slurm to connect the batch script's standard error directly to the file name specified in the "filename pattern".

We can monitor how our job is doing with the scontrol show job command: 

test@login01:~$ scontrol show job 173

   JobId=173 JobName=prova_uname10
   UserId=test(1039) GroupId=info_users(10376) MCS_label=N/A
   Priority=6501 Nice=0 Account=info QOS=normal
   JobState=PENDING Reason=Resources Dependency=(null)
   Requeue=1 Restarts=0 BatchFlag=1 Reboot=0 ExitCode=0:0
   RunTime=00:00:00 TimeLimit=08:00:00 TimeMin=N/A
   SubmitTime=2017-11-27T16:37:47 EligibleTime=2017-11-27T16:37:47
   StartTime=2017-11-27T16:50:21 EndTime=Unknown Deadline=N/A
   PreemptTime=None SuspendTime=None SecsPreSuspend=0
   Partition=medium AllocNode:Sid=node009:5743
   ReqNodeList=(null) ExcNodeList=(null)
   NodeList=(null) SchedNodeList=node[004,020]
   NumNodes=2-2 NumCPUs=4 NumTasks=4 CPUs/Task=1 ReqB:S:C:T=0:0:*:*
   TRES=cpu=4,mem=4096,node=2
   Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
   MinCPUsNode=1 MinMemoryCPU=1024M MinTmpDiskNode=0
   Features=(null) Gres=(null) Reservation=(null)
   OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
   Command=/homedtic/test/sleep.sh
   WorkDir=/homedtic/test
   StdErr=/homedtic/test/slurm.%N.173.err
   StdIn=/dev/null
   StdOut=/homedtic/test/slurm.%N.173.out
   Power=

The scontrol show job output shows the task ID of our job (jobId), priority (priority) who has launched it (userId), which is the state of the job (JobState) , when and where it has been registered (submitTime and partition), and how many slots it's been using (slots).

Each queue has specific policies that enforce how long jobs are allowed to execute: short* queues allow up to 2 hours, medium* queue allow up to  8 hours, and high* queues have no runtime limit. When you submit a job, you are either implicitly or explicitly indicating how long the job is expected to run. The first way to indicate the maximum runtime using the format

#!/bin/bash
#SBATCH -J prova_uname10
#SBATCH -p short
#SBATCH --time=2:00
 
ps -ef | grep slurm
srun -n8 uname -a >> $HOME/uname.txt

Here we have an example of time limit.  This script will stop when it reaches 2 minutes of execution. If the requested time limit exceeds the partition's time limit, the job will be left in a PENDING state (possibly indefinitely).

By default, if not specified otherwise, the scheduler will redirect the output of anuy job you launch to a couple of files, placed on your actual directory called <slurm-jobid.out> After a few executions and test, probably your $HOME will look like this:

As a general rule, you are advised to use the following flags to redirect the input and error files:

Of course, we can place this option on our job definition file:

#!/bin/bash
#SBATCH -J prova_dani_uname10
#SBATCH -p short
#SBATCH -N 1
#SBATCH -n 2 # number of cores
#SBATCH --chdir=/homedtic/test/slurm_jobs
#SBATCH --time=2:00
#SBATCH -o slurm.%N.%J.%u.out # STDOUT
#SBATCH -e slurm.%N.%J.%u.err # STDERR
 
ps -ef | grep slurm

And when launching the job, we'll see the output files created at /homedtic/test/slurm_jobs. If no error is reported, an empty file will be created.

test@node009:~/slurm_jobs$ ls
slurm.node005.206.test.err  slurm.node005.206.test.out
test@node009:~/slurm_jobs$ 
test@node009:~/slurm_jobs$ 
test@node009:~/slurm_jobs$ cat slurm.node005.206.test.out 
root      1138     1  0 Nov24 ?        00:00:00 /usr/sbin/slurmd
root      6714     1  0 20:04 ?        00:00:00 slurmstepd: [206]   
test   6719  6714  0 20:04 ?        00:00:00 /bin/bash /var/spool/slurmd/job00206/slurm_script
test   6724  6719  0 20:04 ?        00:00:00 grep slurm
test@node009:~/slurm_jobs$ 

We can modify the requeriments of a job while it's waiting to be processed. Once it's

Below I show a table of job reasons