HPC

Difference between revisions of "FurtherTopics/Advanced Batch Jobs"

From HPC
Jump to: navigation , search
m (→‎Array batch job)
m (→‎Array batch job)
Line 119: Line 119:
  
 
== Array batch job ==
 
== Array batch job ==
−
An array batch job allows multiple jobs to be executed with identical parameters based on a single job submission. By using the directive '''#SBATCH --array 1-10''' the same job will be run 10 times. The index specification identifies what array index values should be used. Multiple values may be specified using a comma-separated list and/or a range of values with a "-" separator. For example, "--array=0-15" or "--array=0,6,16-32".  
+
An array batch job allows multiple jobs to be executed with identical parameters based on a single job submission.  
  
−
A step function can also be specified with a suffix containing a colon and number. For example, "--array=0-15:4" is equivalent to "--array=0,4,8,12".  A maximum number of simultaneously running tasks from the job array may be specified using a "%" separator.  For example "--array=0-15%4" will limit the number of simultaneously running tasks from this job array to 4.
+
This is implemented by using the following additional line in the job submission file:
  
−
The variable ''$SLURM_ARRAY_TASK_ID'' can be used within the batch script, being replaced by the index of the job, for example as part of the input or data filename, etc.
+
{| class="wikitable" style="margin:auto"
 +
|+ Additional #SBATCH line
 +
|-
 +
! Header text !! Header text !! Header text
 +
|-
 +
| {| class="wikitable" style="margin:auto"
 +
|+ Caption text
 +
|-
 +
! Header text !! Header text !! Header text
 +
|-
 +
|  '''#SBATCH --array=1-10''' || (typical usage) the same job will be run 10 times, or
 +
|-
 +
| '''#SBATCH --array=1,6,16''' || certain elements ie 1,6 and 16
 +
|-
 +
|  '''#SBATCH --array=1,6,16,51-60''' || certain elements and a range
 +
|-
 +
| '''#SBATCH --array=1-15%4 ''' || a range, but limit simultaneous tasks to 4 concurrently.
 +
|}
  
−
When the batch script below is submitted, 10 jobs will run resulting in the ''command'' being run with the first argument corresponding to the array element of that task, for instance: ''command 1'', ''command 2'', through to ''command 10''. The output of each of these tasks will be logged to a different out and err file, with the format ''<node job ran on>.<job ID>.<array index>.out'' ''<node job ran on>.<job ID>.<array index>.err''.
+
* The variable ''$SLURM_ARRAY_TASK_ID'' can be used within the batch script, being replaced by the index of the job, for example as part of the input or data filename, etc.
−
 
+
The following batch file will execute program_name/1.bin, program_name/2.bin to program/10.bin
−
* Note that '''#SBATCH --mail-user''' has not been specified here as it does not process array jobs
 
  
 
<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
 
<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
Line 141: Line 157:
 
module add modulename
 
module add modulename
 
   
 
   
−
command $SLURM_ARRAY_TASK_ID
+
program_name/$SLURM_ARRAY_TASK_ID.bin
 +
 
 
</pre>
 
</pre>

Revision as of 11:21, 10 November 2022

Other Directives

Mail When Done

Including the directive #SBATCH --mail-user=your email means you will receive an email when your job has finished. 

#!/bin/bash
#SBATCH -J jobname                # Job name, you can change it to whatever you want
#SBATCH -n 4                      # Number of cores 
#SBATCH -o %N.%j.out              # Standard output will be written here
#SBATCH -e %N.%j.err              # Standard error will be written here
#SBATCH -p compute                # Slurm partition, where you want the job to be queued 
#SBATCH -t=20:00:00               # Run for 20 hours
#SBATCH --mail-user=your email    # Mail to email address when finished


module purge
module add modulename
 
command

Time >1 Day

Use #SBATCH -t=0-00:00:00 (D-HH:MM:SS). 

#!/bin/bash
#SBATCH -J jobname                # Job name, you can change it to whatever you want
#SBATCH -n 4                      # Number of cores 
#SBATCH -o %N.%j.out              # Standard output will be written here
#SBATCH -e %N.%j.err              # Standard error will be written here
#SBATCH -p compute                # Slurm partition, where you want the job to be queued 
#SBATCH -t=3-20:00:00             # Run for 3 days and 20 hours

 
module purge
module add modulename
 
command

Increase resources

Additional Memory

Use #SBATCH --mem=<amount>G to specify the amount of memory. For jobs needing more than 128GB you will need to use a high memory node. 

#!/bin/bash
#SBATCH -J jobname          # Job name, you can change it to whatever you want
#SBATCH -n 1                # Number of cores 
#SBATCH -o %N.%j.out        # Standard output will be written here
#SBATCH -e %N.%j.err        # Standard error will be written here
#SBATCH -p compute          # Slurm partition, where you want the job to be queued 
#SBATCH --mem=50G           # 500GB of memory
#SBATCH -t=20:00:00         # Run for 20 hours

 
module purge
module add modulename
 
command

Additional Nodes

Some parallel jobs require multiple nodes to be used, the number of nodes can be speficied by using: #SBATCH -N <number>. 

#!/bin/bash
#SBATCH -J jobname          # Job name, you can change it to whatever you want
#SBATCH -N 4                # Number of cores 
#SBATCH -o %N.%j.out        # Standard output will be written here
#SBATCH -e %N.%j.err        # Standard error will be written here
#SBATCH -p compute          # Slurm partition, where you want the job to be queued 
#SBATCH -t=20:00:00         # Run for 20 hours


module purge
module add modulename
 
command

Other Partition Queues

highmem

Standard compute nodes have 128GB of RAM available and there are dedicated high memory nodes that have a total of 1TB of RAM. If your job requires more than 128GB of RAM, submit it to the highmem partition.

Use #SBATCH --exclusive for the full 1TB or # SBATCH --mem=<amount>G for a specific amount of RAM. 

#!/bin/bash
#SBATCH -J jobname          # Job name, you can change it to whatever you want
#SBATCH -n 1                # Number of cores 
#SBATCH -o %N.%j.out        # Standard output will be written here
#SBATCH -e %N.%j.err        # Standard error will be written here
#SBATCH -p highmem          # Slurm partition, where you want the job to be queued 
#SBATCH --mem=500G          # 500GB of memory
#SBATCH -t=3-00:00:00       # Run for 3 days

 
module purge
module add modulename
 
command

gpu

Use --gres=gpu to use the GPU resource instead of the CPU on the node. 

#!/bin/bash
#SBATCH -J jobname          # Job name, you can change it to whatever you want
#SBATCH -n 1                # Number of cores 
#SBATCH -o %N.%j.out        # Standard output will be written here
#SBATCH -e %N.%j.err        # Standard error will be written here
#SBATCH --gres=gpu          # use the GPU resource not the CPU
#SBATCH -p gpu              # Slurm partition, where you want the job to be queued 
#SBATCH -t=00:40:00         # Run for 40 minutes

module purge
module add modulename
 
command

Array batch job

An array batch job allows multiple jobs to be executed with identical parameters based on a single job submission.

This is implemented by using the following additional line in the job submission file:

Additional #SBATCH line
Header text Header text Header text
class="wikitable" style="margin:auto"
Caption text
Header text Header text Header text
#SBATCH --array=1-10 (typical usage) the same job will be run 10 times, or
#SBATCH --array=1,6,16 certain elements ie 1,6 and 16
#SBATCH --array=1,6,16,51-60 certain elements and a range
#SBATCH --array=1-15%4 a range, but limit simultaneous tasks to 4 concurrently.
  • The variable $SLURM_ARRAY_TASK_ID can be used within the batch script, being replaced by the index of the job, for example as part of the input or data filename, etc.

The following batch file will execute program_name/1.bin, program_name/2.bin to program/10.bin 

#!/bin/bash
#SBATCH -J jobname          # Job name, you can change it to whatever you want
#SBATCH -n 1                # Number of cores 
#SBATCH -o %N.%A.%a.out     # Standard output will be written here
#SBATCH -e %N.%A.%a.err     # Standard error will be written here
#SBATCH -p compute          # Slurm partition, where you want the job to be queued 
#SBATCH --array 1-10
 
module purge
module add modulename
 
program_name/$SLURM_ARRAY_TASK_ID.bin
Retrieved from ‘http://hpc.mediawiki.hull.ac.uk/index.php?title=FurtherTopics/Advanced_Batch_Jobs&oldid=40720’