89 lines
2.7 KiB
Markdown
89 lines
2.7 KiB
Markdown
# HPC Guide
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Full documentation: [https://docs.hpc.ugent.be/](https://docs.hpc.ugent.be/)
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## Storage Overview
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- **Run Outputs**: Written to `$VSC_SCRATCH` during the job (fast I/O) and copied to `$VSC_DATA` at the end for persistence.
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- **Virtual Environments**: Managed on **`$VSC_DATA`** by mirroring configuration files. This avoids the 3GB home quota without requiring symlinks in the project root.
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## Initial Environment Setup
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Run **once** after cloning the repository. This script handles all modules, mirroring, and environment synchronization.
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```bash
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# Option A: Interactive (on a compute node)
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module swap cluster/donphan # Debug cluster (CPU only)
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# OR for GPU clusters:
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# module swap cluster/joltik
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# module swap cluster/accelgor
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# module swap cluster/litleo
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qsub -I -l nodes=1:gpus=1 # Only for GPU clusters
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cd "${PBS_O_WORKDIR}"
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bash scripts/hpc/install.sh
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# Option B: Batch (Run in background)
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# NOTE: GPU clusters (joltik/accelgor/litleo) require -l gpus=1 at runtime
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qsub -l gpus=1 scripts/hpc/install.sh
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```
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## Production vs. Debug Clusters
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Our scripts are cluster-agnostic and do **not** have hardcoded GPU requirements. Instead, you must request GPUs at runtime using the `-l gpus=1` flag when submitting to a production GPU cluster.
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### Debugging (Donphan)
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The `donphan` cluster does not support GPUs. Simply run the scripts without extra resource flags:
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```bash
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module swap cluster/donphan
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qsub scripts/hpc/train.pbs
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```
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### Production (Joltik, Accelgor, Litleo)
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These clusters provide GPU acceleration and **require** a GPU request at runtime:
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```bash
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module swap cluster/joltik # or accelgor/litleo
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qsub -l gpus=1 scripts/hpc/train.pbs
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```
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## Interactive Debugging
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To activate your environment for interactive work, simply run the same `install.sh` script.
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```bash
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qsub -I -l nodes=1:ppn=4 -l walltime=1:00:00
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cd "$PBS_O_WORKDIR"
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bash scripts/hpc/install.sh
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```
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### Verification Commands
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After installation, run these commands to ensure your environment is set up correctly:
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1. **Verify Quota Safety**:
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```bash
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ls -d venvs 2>/dev/null && echo "FAIL" || echo ">>> PASS: Project root is clean."
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```
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2. **Verify Library Versions (NumPy Fix)**:
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```bash
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python -c "import numpy; print(f'NumPy: {numpy.__version__}')"
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# Expected: 2.x.x (Venv version), not 1.2x (System version)
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```
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3. **Verify GPU Access**:
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```bash
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python -c "import torch, jax; print(f'GPU: {torch.cuda.is_available()}'); print(f'JAX: {jax.devices()}')"
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```
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## Managing Dependencies
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`env/hpc/requirements.txt` is auto-generated from `pyproject.toml`. To regenerate:
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```bash
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uv run scripts/hpc/export_requirements.py
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```
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Modules listed in `env/hpc/modules.txt` are automatically excluded from the pip requirements to save space and use HPC-optimized binaries.
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