Running Models on Sagehen HPC

Estimated time: 25 minutes

Overview

Questions

• How do I set up AI tools on Sagehen HPC?
• What modules and environments are needed?
• How do I access GPUs and submit AI jobs?

Objectives

• Load required modules for AI work (anaconda3, CUDA)
• Create conda environments for PyTorch and TensorFlow
• Access GPU resources via Slurm for interactive and batch jobs
• Configure model caching to avoid quota issues

Sagehen HPC Storage for AI Work

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Location	Quota	Use For
/rhome/<myusername>	100GB	Code, conda environments, notebooks
/bigdata/lab/<labname>	1TB shared (BeeGFS)	Large datasets, model checkpoints
/scratch	Temporary (deleted when the job ends)	Job I/O, intermediate results

Download large models to /bigdata or /scratch – not your home directory.

Loading Modules

---

BASH

module purge
module load anaconda3          # Python and package management
module load cuda/12.2.1        # NVIDIA CUDA toolkit (current default)
module list                    # Verify loaded modules

There is no separate cuDNN module on Sagehen – the GPU-enabled PyTorch and TensorFlow packages you install with conda bundle their own cuDNN libraries.

Creating a Conda Environment

---

BASH

module load anaconda3
conda create -n ai-pytorch python=3.11
conda activate ai-pytorch

# Install PyTorch with GPU support
conda install pytorch::pytorch torchvision torchaudio pytorch-cuda=12.1 \
    -c pytorch -c nvidia

# Install common packages
conda install numpy pandas scikit-learn matplotlib jupyter -c conda-forge

For TensorFlow, create a separate environment:

BASH

conda create -n ai-tensorflow python=3.11
conda activate ai-tensorflow
pip install tensorflow[and-cuda]

Configure Model Caching

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By default, Hugging Face downloads to ~/.cache/huggingface, which fills your home quota quickly. Redirect it:

BASH

mkdir -p /bigdata/lab/<labname>/huggingface_cache
export HF_HOME=/bigdata/lab/<labname>/huggingface_cache
# Add to your .bashrc or Slurm scripts to make permanent

Interactive GPU Sessions

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Before requesting a GPU, check the gpu partition’s current state with sinfo -p gpu:

Checking the gpu partition before requesting a session: sinfo -p gpu shows which GPU nodes are up.

BASH

srun --partition=gpu --gres=gpu:1 --mem=64G \
     --cpus-per-task=8 --time=04:00:00 --pty bash

module purge && module load anaconda3 cuda/12.2.1
conda activate ai-pytorch
python -c "import torch; print(torch.cuda.is_available())"

Batch Jobs for Model Training

---

BASH

#!/bin/bash
#SBATCH --job-name=llama-inference
#SBATCH --partition=gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=80G
#SBATCH --cpus-per-task=16
#SBATCH --time=08:00:00
#SBATCH --output=logs/%j.log

module purge && module load anaconda3 cuda/12.2.1
source activate ai-pytorch
export HF_HOME=/bigdata/lab/<labname>/huggingface_cache

python your_script.py

Submit with sbatch your_script.sh.

Callout

Start Small and Scale Up

When first testing an AI workflow, request a smaller GPU (L40S) with less time. Once your script works reliably, scale to larger GPUs or longer time limits. This saves compute hours and reduces queue wait time.

You can see which GPU types exist and how heavily they’re used with sinfo’s GRES columns:

Which GPU types the cluster advertises and how many are in use — useful for picking a less-contended GPU for testing.

Common Troubleshooting

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• “No module named torch”: Load anaconda3 and activate your conda environment
• “CUDA out of memory”: Use 4-bit quantization, reduce batch size, or request a larger GPU
• Home quota full from models: Set HF_HOME to /bigdata
• GPU not detected: Verify the cuda module is loaded and your job requested a GPU (--gres=gpu:1)

Challenge

Challenge: Write a GPU Setup Script

Write a Slurm script that loads modules, activates a conda environment, sets HF_HOME, and verifies GPU access by printing torch.cuda.is_available() and the GPU name.

Show me the solution

BASH

#!/bin/bash
#SBATCH --job-name=gpu-test
#SBATCH --partition=gpu
#SBATCH --gres=gpu:1
#SBATCH --mem=32G
#SBATCH --cpus-per-task=4
#SBATCH --time=00:10:00

module purge && module load anaconda3 cuda/12.2.1
conda activate ai-pytorch
export HF_HOME=/bigdata/lab/<labname>/huggingface_cache

python3 -c "
import torch
print(f'GPU available: {torch.cuda.is_available()}')
if torch.cuda.is_available():
    print(f'GPU: {torch.cuda.get_device_name(0)}')
    print(f'Memory: {torch.cuda.get_device_properties(0).total_mem / 1e9:.0f} GB')
"

Submit with sbatch gpu_test.sh and check output in slurm-*.out.

Key Points

• Load the anaconda3 and cuda modules before GPU work
• Use conda environments for reproducible, isolated Python setups
• Configure HF_HOME to /bigdata to avoid filling home quota with models
• Use srun for interactive GPU testing and sbatch for batch jobs
• Start with smaller GPUs and scale up once your workflow is validated