Kennedy manual

Temporary quick start info can be found here. This is a work in progress until something official is made up.

https://github.com/peterthorpe5/How_to_use_Kennedy_HPC

The following are command line commands, or tags you can put in your shell script to achieve certain functionality.

request_48_thread_1.3TBRAM

1. !/bin/bash -l # not the -l is essential now
2. SBATCH -J fly_pilon #jobname
3. SBATCH -N 1 #node
4. SBATCH --ntasks-per-node=48
5. SBATCH --threads-per-core=2
6. SBATCH -p bigmem
7. SBATCH --nodelist=kennedy150 # this is the specific node. This one has 1.5TB RAM
8. SBATCH --mem=1350GB

test_conda_activate

1. !/bin/bash -l
2. SBATCH -J conda_test #jobname
3. SBATCH -N 1 #node
4. SBATCH --tasks-per-node=1
5. SBATCH -p bigmem # big mem if for the BIOINF community
6. SBATCH --mail-type=END # email at the end of the job
7. SBATCH --mail-user=$USER@st-andrews.ac.uk # your email address

cd /gpfs1/home/$USER/

pyv="$(python -V 2>&1)"

echo "$pyv"

1. conda to activate the software

echo $PATH

conda activate spades

pyv="$(python -V 2>&1)"

echo "$pyv"

conda deactivate

conda activate python27

pyv="$(python2 -V 2>&1)"

echo "$pyv"

12threads_bigMeme_30G_RAM

!/bin/bash -l # essential

1. SBATCH -J trimmo #jobname
2. SBATCH -N 1 #node
3. SBATCH --ntasks-per-node=12
4. SBATCH --threads-per-core=2
5. SBATCH -p bigmem
6. SBATCH --mem=30GB