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Commit f44de1a4 authored by William Stonewall Monroe's avatar William Stonewall Monroe
Browse files

Merge branch 'Branch' into 'master'

Branch

See merge request rc-data-science/createandparsesacct!5
parents 11da58b5 4642d869
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
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