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Commit 8c217b75 authored by Saisri Vegesna's avatar Saisri Vegesna
Browse files

Update README.md

parent e0a20660
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
......
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