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using-slurm [2022/08/04 12:10] – aorthusing-slurm [2026/02/05 08:31] (current) – aorth
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 ==== Batch jobs ==== ==== Batch jobs ====
 We are writing a SLURM script below. The parameters in its header request 4 CPUs for in the ''batch'' partition, and name our job "blastn". This name is only used internally by SLURM for reporting purposes. So let's go ahead and ceate a file //blast.sbatch//: We are writing a SLURM script below. The parameters in its header request 4 CPUs for in the ''batch'' partition, and name our job "blastn". This name is only used internally by SLURM for reporting purposes. So let's go ahead and ceate a file //blast.sbatch//:
-<code>#!/usr/bin/bash -l # <--- DO NOT FORGET '-l', it enables the module command+<code>#!/usr/bin/bash -l
 #SBATCH -p batch #SBATCH -p batch
 #SBATCH -J blastn #SBATCH -J blastn
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 # run the blast with 4 CPU threads (cores) # run the blast with 4 CPU threads (cores)
 blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4</code> blastn -query ~/data/sequences/drosoph_14_sequences.seq -db nt -num_threads 4</code>
 +
 +In the above, please **DO NOT FORGET the '-l' option** on the first ("sha-bang") line, as it is compulsory for correct interpretation of the ''module load'' commands.
  
 We then submit the script with the ''sbatch'' command: We then submit the script with the ''sbatch'' command:
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 Instead, you can use a local "scratch" folder on the compute nodes to alleviate this burden, for example: Instead, you can use a local "scratch" folder on the compute nodes to alleviate this burden, for example:
  
-<code>#!/usr/bin/bash -l # <--- DO NOT FORGET '-l', it enables the module command+<code>#!/usr/bin/bash -l
 #SBATCH -p batch #SBATCH -p batch
 #SBATCH -J blastn #SBATCH -J blastn
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 All output is directed to ''$WORKDIR/'', which is the temporary folder on the compute node. See these slides from [[https://alanorth.github.io/hpc-users-group3/#/2|HPC Users Group #3]] for more info. All output is directed to ''$WORKDIR/'', which is the temporary folder on the compute node. See these slides from [[https://alanorth.github.io/hpc-users-group3/#/2|HPC Users Group #3]] for more info.
 +
 +==== Run job using a GPU ====
 +Currently there is only one compute node with GPU capabilities. As of February 2026, compute06 has an NVIDIA Tesla v100 with 32GB of RAM. In order to use this you will need to add an extra "gres" line to your SLURM sbatch job specification.
 +
 +For example, ''beast-gpu.sbatch'':
 +
 +<code>#!/usr/bin/bash
 +#SBATCH -p batch
 +#SBATCH -w compute06
 +#SBATCH --gres=gpu:v100:1
 +#SBATCH -n 8
 +#SBATCH -J beast-GPU
 +
 +# load module(s)
 +module load beagle/3.1.2
 +module load beast/1.10.4
 +
 +beast -beagle_info</code>
 +
  
 ==== Check queue status ==== ==== Check queue status ====
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  746885     batch    model-selection    jjuma  R 4-20:45:15      8 compute06  746885     batch    model-selection    jjuma  R 4-20:45:15      8 compute06
  746998     batch        interactive  afeleke  R      30:09      1 compute06  746998     batch        interactive  afeleke  R      30:09      1 compute06
- 746999     batch             blastp    aorth  R       7:20      6 compute05 + 746999     batch             blastp    aorth  R       7:20      6 compute05</code>
-</code>+
using-slurm.1659615029.txt.gz · Last modified: by aorth