feat: add inference.empty_cache_per_design flag to reduce CUDA allocator fragmentation (#451)

## Problem

When running RFdiffusion with variable-length contigs (e.g.
`contigmap.contigs=[A1-469/0 1-50]`) over hundreds or thousands of
designs, per-worker VRAM grows steadily from ~7 GB to 10–13 GB per
process. This limits how many workers can run in parallel on a single
GPU before exhausting VRAM.

Root cause: PyTorch's CUDA caching allocator accumulates fragmented
memory blocks across designs. With variable-length contigs each design
allocates differently-sized tensors; freed blocks are cached but cannot
be reused for different-sized allocations, causing steady VRAM growth.

## Fix

Add an optional `inference.empty_cache_per_design` flag (default
`False`, opt-in) that calls `torch.cuda.empty_cache()` at the end of
each design iteration. This releases all unused cached CUDA memory
blocks back to the CUDA memory manager, keeping each worker near its
initial VRAM footprint for the full run.

### Changes

**`config/inference/base.yaml`**
```yaml
  write_trajectory: True
  empty_cache_per_design: False   # NEW
```

**`scripts/run_inference.py`** — after the trajectory/PDB write block,
before `log.info`:
```python
        if conf.inference.empty_cache_per_design and torch.cuda.is_available():
            torch.cuda.empty_cache()

        log.info(f"Finished design in {(time.time()-start_time)/60:.2f} minutes")
```

## Measured impact

Tested on NVIDIA RTX 5090 32 GB running a long PPI campaign with
variable-length contigs:

| Setting | Per-worker VRAM (steady-state) |
|---------|-------------------------------|
| Without fix | 8–13 GB (grows over run) |
| With `empty_cache_per_design=True` | ~5.2 GB (stable) |

This allowed raising the number of parallel workers from 3 to 5 on a 32
GB GPU.

## Why opt-in

`torch.cuda.empty_cache()` adds a small per-design overhead (~1–2 ms)
and is only beneficial for long runs with variable-length contigs. For
short runs or fixed-length designs there is no fragmentation issue, so
the default remains `False` to preserve existing behavior.

## Testing

All 20 applicable tests in `tests/test_diffusion.py` pass with this
change. The one skipped test (`design_ppi_scaffolded`) fails due to a
missing `ppi_scaffolds/` directory in the test fixture — a pre-existing
issue unrelated to this PR.

## Notes

- Placement is after both the PDB write (`writepdb`) and the optional
trajectory block — every consumer of `denoised_xyz_stack` /
`px0_xyz_stack` has already finished before the cache is cleared.
- This does not affect memory held by live tensors — only frees
cached-but-unused blocks.
- Compatible with all existing RFdiffusion design modes (PPI, motif
scaffolding, unconditional).

Author: leonardomarino

config/inference/base.yaml

@@ -11,6 +11,7 @@ inference:
   model_only_neighbors: False
   output_prefix: samples/design
   write_trajectory: True
+  empty_cache_per_design: False
   scaffold_guided: False
   model_runner: SelfConditioning
   cautious: True

scripts/run_inference.py

@@ -188,6 +188,9 @@ def main(conf: HydraConfig) -> None:
                 chain_ids=sampler.chain_idx,
             )
 
+        if conf.inference.empty_cache_per_design and torch.cuda.is_available():
+            torch.cuda.empty_cache()
+
         log.info(f"Finished design in {(time.time()-start_time)/60:.2f} minutes")