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using-slurm [2022/08/04 12:08] – aorthusing-slurm [2026/02/05 08:31] (current) – aorth
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 To see more information about the queue configuration, use ''sinfo -lNe''. To see more information about the queue configuration, use ''sinfo -lNe''.
  
-<code>[jbaka@hpc ~]$ sinfo -lNe +<code>$ sinfo -lNe 
-Fri Feb  1 15:27:44 2019+Thu Aug 04 15:08:48 2022
 NODELIST   NODES PARTITION       STATE CPUS    S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON               NODELIST   NODES PARTITION       STATE CPUS    S:C:T MEMORY TMP_DISK WEIGHT AVAIL_FE REASON              
-compute2       1     batch        idle   64   64:1:1      1        0     10   (null) none                 +compute03      1   highmem       idle  8       2:4:1 322249        0     10   (null) none 
-compute03      1     batch       mixed    8    8:1:1      1        0      5   (null) none                 +compute05      1     batch       mixed 48     2:24:1 386500        0     10   (null) none 
-compute03      1   highmem       mixed    8    8:1:1      1        0      5   (null) none                 +compute06      1     batch       mixed 64     2:32:1 257491        0      5   (null) none 
-compute04      1     batch       mixed    8    8:1:1      1        0      5   (null) none                 +compute07      1   highmem        idle 8       1:8:1 101956        0      5   (null) none 
-hpc            1    debug*        idle    4    4:1:1      1        0      1   (null) none                 +hpc            1    debug*        idle 4       1:4:1 128876        0      1   (null) none</code>
-mammoth        1   highmem        idle    8    8:1:1      1        0     30   (null) none                 +
-taurus         1     batch       mixed   64   64:1:1      1        0     20   (null) none        +
-</code>+
  
-The above tells you, for instance, that compute04 has 8 CPUs while compute2 has 64 CPUs. And that a job sent to the "highmem" partition (a SLURM verb equivalent to "queue", as per the vocabulary in use with other schedulers, e.g. Sun Grid Engine), then it will end up being run on either compute03 or mammoth. +The above tells you, for instance, that compute06 has 64 CPUs. And that a job sent to the "highmem" partition (a SLURM verb equivalent to "queue", as per the vocabulary in use with other schedulers, e.g. Sun Grid Engine), then it will end up being run on either compute03 or compute07. 
  
 ===== Submitting jobs ===== ===== Submitting jobs =====
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 <code>[aorth@hpc: ~]$ interactive  <code>[aorth@hpc: ~]$ interactive 
 salloc: Granted job allocation 1080 salloc: Granted job allocation 1080
-[aorth@taurus: ~]$</code>+[aorth@compute05: ~]$</code>
  
-**NB:** interactive jobs have a time limit of 8 hours: if you need more, then you should write a batch script.+**NB:** interactive jobs have a time limit of 8 hours: if you need more, then you should write an sbatch script.
  
 You can also open an interactive session on a specific node of the cluster by specifying it through the ''-w'' commandline argument: You can also open an interactive session on a specific node of the cluster by specifying it through the ''-w'' commandline argument:
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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.1659614887.txt.gz · Last modified: by aorth