Schooner-Jacobian.md

Accessing Jacobian

Login to a schooner login node.

ssh jreynolds@schooner.oscer.ou.edu

Login into the Jacobian partion.

ssh c822

Setting up a conda environment

module load OpenMPI/4.0.3-GCC-9.3.0 
module load CUDA/11.3.1
module load cuDNN/8.2.1.32-CUDA-11.3.1
module load Miniconda3
source activate
conda create -n torch python=3.8
conda activate torch
conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch

Now you can run your code once your application's dependencies are installed in the conda environment.

Batch script on Jacobian

After finished setting up the conda environment on Jacobian, you can go ahead and logout of Jacobian if running a batch script. In other words, the batch script should be submitted from a login node.

A sample batch script sample.batch:

#!/bin/bash

#SBATCH --partition=jacobian
#SBATCH --ntasks=8
#SBATCH --output=_%J.log
#SBATCH --error=_%J.err
#SBATCH --nodelist c822
#SBATCH --time=00:15:00
#SBATCH --job-name=torch_catsvdogs
#SBATCH --chdir=/work/omicsbio/jreynolds/projects/pytorch-explore/pytorch_tutorials
#################################################

module purge
module load OpenMPI/4.0.3-GCC-9.3.0 
module load CUDA/11.3.1
module load cuDNN/8.2.1.32-CUDA-11.3.1
module load Miniconda3

source activate
conda activate torchy
python cnn_torch_catsvdogs.py -g 1
conda deactivate
conda deactivate
module remove Miniconda3

Submitting the batch script:

sbatch sample.batch