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Ryan Randles Jones / createAndParseSACCT
93 commits behind the upstream repository.
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Saisri Vegesna authored8c217b75
README.md 1.39 KiB
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