View source for FurtherTopics/Advanced Batch Jobs

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==Other Directives==
===Mail When Done===
Including the directive ''#SBATCH --mail-user=your email'' means you will receive an email when your job has finished.
<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
#!/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
</pre>

===Time >1 Day===
Use ''#SBATCH -t 0-00:00:00'' (D-HH:MM:SS).

<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
#!/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
</pre>

==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 [[#highmem| high memory node]].
<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
#!/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
</pre>

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

<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
#!/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
</pre>

==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.

<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
#!/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
</pre>

===GPU===
Use ''--gres=gpu'' to use the GPU resource instead of the CPU on the node.
<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
#!/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
</pre>

== Array batch job ==

Array batch jobs offer a mechanism for submitting and managing collections of similar jobs quickly and easily with one batch file. This is very useful if you have multiple data sets that need processing separately but in the same way. Without this mechanism, you would have to write a separate batch file for each.

* All tasks are run by the scheduler and indexed by the variable ''$SLURM_ARRAY_TASK_ID''.
* All tasks must have the same initial options (e.g. size, time limit, etc.)
* All array tasks can be cancelled with a single ''scancel'' command
* It is implemented by using the following additional line '''#SBATCH --array=...''' in the job submission file, see the different examples below:


{| class="wikitable" style="margin:auto"
|-
|  '''#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, or
|-
|  '''#SBATCH --array=1,6,16,51-60''' || certain elements and a range, or
|-
| '''#SBATCH --array=1-15%4 ''' || a range, but limit the total number of tasks running to 4.
|-
|}


* As mentioned 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 shows how this is implemented and will execute '''calcFFTs db1.data''' to '''calcFFTs db10.data'''. 
* This will schedule ten instances of calcFFTs with the range of dbN.data sets. (N is between 1 to 10).


<pre class="mw-collapsible" style="background-color: #C8C8C8; color: black; font-family: monospace, sans-serif;">
#!/bin/bash
#SBATCH -J job         # 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
 
calcFFTs db$SLURM_ARRAY_TASK_ID.data
</pre>

===Viewing the job tasks===

<pre class="mw-collapsible" style="background-color: #000000; color: white; font-family: monospace, courier;">
$ squeue
 JOBID     PARTITION  NAME  USER  ST  TIME  NODES NODELIST(REASON)
1080_[6-10]  compute   job  mac  PD  0:00      1 (Resources)
1080_1        compute   job   mac   R  0:17      1 c001
1080_2        compute   job   mac   R  0:16      1 c002
1080_3        compute   job   mac   R  0:03      1 c003
1080_4        compute   job   mac   R  0:03      1 c004
</pre>

* Looking at our job id (1080) it now has multiple job task with 1080_1, 1080_2 etc.
* See [https://slurm.schedmd.com/job_array.html Job arrays on slurm.schedmd.com]



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