README.md

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=express
#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
```

# Configuring the environment

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 Anaconda3/2019.10
```

Under Extra jupyter arguments, specify

```
--notebook-dir=/data/user/$USER/slurm-ds
```

For partition, set partition to 
```
express
```
for time up to 2 hours. Also make sure to specify the number of hours field to match. For up to 12 hours, the  
```
short
```
partition can be used.

After the Jupyter notebook is started, click on the blue "Connect to Jupyter" button.

Once the Jupyter session is active, select the `slurm-2sql` notebook. Then change the kernel, via `Kernel->Change kernel->Python [conda env:.conda-slurm-ds]`

Verify the environment loaded correctly by running the first cell of the `slurm-2sql` notebook (with the library imports)

# Creating a text version of sacct output

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.txt
```