From 8c217b75d76a34bef0a373fd68251fc0d230e5eb Mon Sep 17 00:00:00 2001 From: Saisri Vegesna <saisri@uab.edu> Date: Fri, 20 Mar 2020 13:17:24 -0500 Subject: [PATCH] Update README.md --- README.md | 33 ++++++++++++++++++++++++--------- 1 file changed, 24 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 721b24f..cfb9e52 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,32 @@ A yml and a set of instructions to build a functioning environment for the Research Computing -# clone this repo: -``` -$git clone https://gitlab.rc.uab.edu/rc-data-science/createandparsesacct.git /data/user/saisri/slurm-ds -``` -Now load the Anaconda module and create environment on Cheaha cluster: + +# clone this repo and update with the job composer + +Copy and paste the following job script into a job composer job on rc.uab.edu + ``` -$module load Anaconda3 -$conda env create -f environment-slurm-ds.yml +#!/bin/bash +#SBATCH --partition=pascalnodes +#SBATCH --gres=gpu:1 +#SBATCH --mem-per-cpu=4000 +module load cuda10.0/toolkit +module load Anaconda3 + +FOLDER=/data/user/$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/VariousNeurology/user/" -sacct -P -u $USER --starttime=2019-01-01 --format user,start,jobid,jobname,state,partition,maxrss,reqmem,reqcpus,node,nnodes,elapsed >> "$directoryToUse"userusage.db +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 -- GitLab