diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..cfb9e52c1b46185ce2df4177fb7fb4c01efa0d98 --- /dev/null +++ b/README.md @@ -0,0 +1,55 @@ +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 +``` \ No newline at end of file