Difference between revisions of "Kennedy manual"
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| + | ====slurm commands==== | ||
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Temporary quick start info can be found here. This is a work in progress until something official is made up. | Temporary quick start info can be found here. This is a work in progress until something official is made up. | ||
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request_48_thread_1.3TBRAM | request_48_thread_1.3TBRAM | ||
| − | #!/bin/bash -l '''# not the -l is essential now''' | + | #!/bin/bash -l '''# not the -l is essential now''' |
| − | #SBATCH -J fly_pilon #jobname | + | #SBATCH -J fly_pilon #jobname |
| − | #SBATCH -N 1 #node | + | #SBATCH -N 1 #node |
| − | #SBATCH --ntasks-per-node=48 | + | #SBATCH --ntasks-per-node=48 |
| − | #SBATCH --threads-per-core=2 | + | #SBATCH --threads-per-core=2 |
| − | #SBATCH -p bigmem | + | #SBATCH -p bigmem |
| − | #SBATCH --nodelist=kennedy150 # this is the specific node. This one has 1.5TB RAM | + | #SBATCH --nodelist=kennedy150 # this is the specific node. This one has 1.5TB RAM |
| − | #SBATCH --mem=1350GB | + | #SBATCH --mem=1350GB |
test_conda_activate | test_conda_activate | ||
| − | #!/bin/bash -l | + | #!/bin/bash -l |
| − | #SBATCH -J conda_test #jobname | + | #SBATCH -J conda_test #jobname |
| − | #SBATCH -N 1 #node | + | #SBATCH -N 1 #node |
| − | #SBATCH --tasks-per-node=1 | + | #SBATCH --tasks-per-node=1 |
| − | #SBATCH -p bigmem # big mem if for the BIOINF community | + | #SBATCH -p bigmem # big mem if for the BIOINF community |
| − | #SBATCH --mail-type=END # email at the end of the job | + | #SBATCH --mail-type=END # email at the end of the job |
| − | #SBATCH --mail-user=$USER@st-andrews.ac.uk # your email address | + | #SBATCH --mail-user=$USER@st-andrews.ac.uk # your email address |
cd /gpfs1/home/$USER/ | cd /gpfs1/home/$USER/ | ||
Revision as of 11:48, 6 May 2020
slurm commands
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 #!/bin/bash -l # not the -l is essential now #SBATCH -J fly_pilon #jobname #SBATCH -N 1 #node #SBATCH --ntasks-per-node=48 #SBATCH --threads-per-core=2 #SBATCH -p bigmem #SBATCH --nodelist=kennedy150 # this is the specific node. This one has 1.5TB RAM #SBATCH --mem=1350GB
test_conda_activate #!/bin/bash -l #SBATCH -J conda_test #jobname #SBATCH -N 1 #node #SBATCH --tasks-per-node=1 #SBATCH -p bigmem # big mem if for the BIOINF community #SBATCH --mail-type=END # email at the end of the job #SBATCH --mail-user=$USER@st-andrews.ac.uk # your email address
cd /gpfs1/home/$USER/
pyv="$(python -V 2>&1)"
echo "$pyv"
- 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
- SBATCH -J trimmo #jobname
- SBATCH -N 1 #node
- SBATCH --ntasks-per-node=12
- SBATCH --threads-per-core=2
- SBATCH -p bigmem
- SBATCH --mem=30GB
