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