A yml and a set of instructions to build a functioning environment for the Research Computing # clone this repo and update with the job composer Copy and paste the following job script into a job composer job on rc.uab.edu ``` #!/bin/bash #SBATCH --partition=pascalnodes #SBATCH --gres=gpu:1 #SBATCH --mem-per-cpu=4000 module load cuda10.0/toolkit module load Anaconda3 FOLDER=/data/user/$USER/slurm-ds URL=https://gitlab.rc.uab.edu/rc-data-science/createandparsesacct.git if [ ! -d "$FOLDER" ] ; then git clone "$URL" "$FOLDER" conda env create -f /data/user/$USER/slurm-ds/environment-slurm-ds.yml else cd $FOLDER git pull "$URL" conda env update -f /data/user/$USER/slurm-ds/environment-slurm-ds.yml fi ``` If we have to create a database from sacct ``` directoryToUse="/data/user/$USER/group" sacct -P -u $USER --starttime=2019-01-01 --format user,start,jobid,jobname,state,partition,maxrss,reqmem,reqcpus,node,nnodes,elapsed >> "$directoryToUse"group.db ``` # Check to see if the environment works After the environment is created, you can start up an interactive Jupyter notebook session through rc.uab.edu to check if the environment works. Under environment setup, specify ``` # Load required modules module load cuda10.0/toolkit module load Anaconda3 ``` Under Extra jupyter arguments, specify ``` --notebook-dir=/data/user/$USER/slurm-ds ``` For partition, specify ``` pascalnodes ```