PeterThorpe at 12:25, 6 May 2020

2020-05-06T12:25:14Z

PeterThorpe: /* slurm commands */

2020-05-06T11:58:07Z

‎slurm commands

PeterThorpe: Created page with " == slurm commands == note the BIOINF community are supposed to use the -p bigmem queue. The following are command line commands, or tags you can put in your shell scrip..."

2020-05-06T11:56:44Z

Created page with " == slurm commands == note the BIOINF community are supposed to use the -p bigmem queue. The following are command line commands, or tags you can put in your shell scrip..."

New page

== slurm commands ==

note the BIOINF community are supposed to use the -p bigmem queue.

The following are command line commands, or tags you can put in your shell script (or at the command line) 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

← Older revision		Revision as of 12:25, 6 May 2020
Line 65:		Line 65:
	#SBATCH -p bigmem		#SBATCH -p bigmem
	#SBATCH --mem=30GB		#SBATCH --mem=30GB
		+
		+
		+	Request an interactive job with one GPU:
		+	# srun --gres=gpu:1 -N 1 -p singlenode --pty /bin/bash

← Older revision		Revision as of 11:58, 6 May 2020
Line 4:		Line 4:

	note the BIOINF community are supposed to use the -p bigmem queue.		note the BIOINF community are supposed to use the -p bigmem queue.
		+
		+	Sun Grid Engines (what we use on Marvin) to slurm command conversion:
		+	https://srcc.stanford.edu/sge-slurm-conversion

Slurm commands - Revision history

PeterThorpe at 12:25, 6 May 2020

PeterThorpe: /* slurm commands */

PeterThorpe: Created page with " == slurm commands == note the BIOINF community are supposed to use the -p bigmem queue. The following are command line commands, or tags you can put in your shell scrip..."