cylonplus

High-Performance Distributed Data frames for Machine Learning/Deep Learning Model

Installation instructions UVA CS cluster

Login to cluster

ssh your_computing_id@gpusrv08 -J your_computing_id@portal.cs.virginia.edu

Setup Cylon

ssh your_computing_id@gpusrv08 -J your_computing_id@portal.cs.virginia.edu
git clone https://github.com/arupcsedu/cylonplus.git
cd cylonplus
module load anaconda3

conda create -n cyp-venv python=3.9
conda activate cyp-venv

conda install pytorch torchvision torchaudio pytorch-cuda=12.1 -c pytorch -c nvidia
DIR=/u/$USER/anaconda3/envs/cyp-venv 


export CUDA_HOME=$DIR/bin
export PATH=$DIR/bin:$PATH LD_LIBRARY_PATH=$DIR/lib:$LD_LIBRARY_PATH PYTHONPATH=$DIR/lib/python3.9/site-packages 

pip install petastorm

cd src/model
python multi-gpu-cnn.py

Installation instructions UVA Rivanna cluster

We assume that you are able to ssh into rivanna instead of using the ondemand system. This is easily done by following instructions given on https://infomall.org. Make sure to modify your .ssh/config file and add the host rivanna. If you use Windows we recommand not to use putty but use gitbash as it mimics a bash environment that is typical also for Linux systems and thus we only have to maintaine one documentation.

Login to cluster

ssh rivanna

Login into a GPU worker node

source target/rivanna/activate.sh a100

Make sure your ~/.condarc file looks like

cat ~/.condarc

env_prompt: '({name}) '
pkgs_dirs:
  - /scratch/thf2bn/.conda/pkgs

change the value of thf2bn to the value of $USER

Setup a PROJECT dir

We assume you will deplyt the code in /scratch/$USER. Note this directory is not backed up. Make sure to backup your changes regularly elsewhere with rsync or use github.

NOTE: the following is yet untested

export SCRATCH=/scratch/$USER/workdir
export PROJECT=/scratch/$USER/workdir/cylonplus
mkdir -p $SCRATCH
cd $SCRATCH

Setup Cylonplus

We created two simple scripts. The first removes the coonda environment if existing, the second installs it.

source target/rivanna/clean.sh
source target/rivanna/install.sh

The scripts are available in github at

• https://github.com/laszewsk/cylonplus/blob/main/target/rivanna/clean.sh
• https://github.com/laszewsk/cylonplus/blob/main/target/rivanna/install.sh

Once it is installed you can in a shell just activate it so you do not need to reiinstall it all the time with

source target/rivanna/activate.sh

• https://github.com/laszewsk/cylonplus/blob/main/activate.sh

Running the program on the interactivenode

source target/rivanna/run.sh

Using a slurm script to do the install, activation, and run

sbatch target/rivanna/run-simple.slurm

squeue --me

or use 

```bash
watch sbatch script.slurm

for a continious uppdate every second.