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| − | ====slurm commands====
| + | *[[quick start]] |
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| − | Temporary quick start info can be found here. This is a work in progress until something official is made up.
| + | *[[slurm commands]] |
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| − | https://github.com/peterthorpe5/How_to_use_Kennedy_HPC
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| − | The following are command line commands, or tags you can put in your shell script to achieve certain functionality.
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| − | request_48_thread_1.3TBRAM
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| − | #!/bin/bash -l '''# not the -l is essential now'''
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| − | #SBATCH -J fly_pilon #jobname
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| − | #SBATCH -N 1 #node
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| − | #SBATCH --ntasks-per-node=48
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| − | #SBATCH --threads-per-core=2
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| − | #SBATCH -p bigmem
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| − | #SBATCH --nodelist=kennedy150 # this is the specific node. This one has 1.5TB RAM
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| − | #SBATCH --mem=1350GB
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| − | test_conda_activate
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| − | #!/bin/bash -l
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| − | #SBATCH -J conda_test #jobname
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| − | #SBATCH -N 1 #node
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| − | #SBATCH --tasks-per-node=1
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| − | #SBATCH -p bigmem # big mem if for the BIOINF community
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| − | #SBATCH --mail-type=END # email at the end of the job
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| − | #SBATCH --mail-user=$USER@st-andrews.ac.uk # your email address
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| − | cd /gpfs1/home/$USER/
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| − | pyv="$(python -V 2>&1)"
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| − | echo "$pyv"
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| − | # conda to activate the software
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| − | echo $PATH
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| − | conda activate spades
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| − | pyv="$(python -V 2>&1)"
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| − | echo "$pyv"
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| − | conda deactivate
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| − | conda activate python27
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| − | pyv="$(python2 -V 2>&1)"
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| − | echo "$pyv"
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| − | 12threads_bigMeme_30G_RAM
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| − | !/bin/bash -l # essential
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| − | #SBATCH -J trimmo #jobname
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| − | #SBATCH -N 1 #node
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| − | #SBATCH --ntasks-per-node=12
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| − | #SBATCH --threads-per-core=2
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| − | #SBATCH -p bigmem
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| − | #SBATCH --mem=30GB
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