Sharing a Fabric with Collective Communication: Two Storage Penalties in Deep Learning Training

Abstract

Distributed DL training on HPC systems often shares one network fabric between NCCL/RCCL collective communication and parallel-filesystem I/O. Using a real GNN training workload on a Slingshot-11 system, we show that this sharing imposes two distinct costs. The primary cost is heavy-tailed DataLoader stalls: the typical DataLoader wait is just 15 ms at steady state, yet spikes to multiple seconds in 28% of Lustre iterations and 12% of VAST iterations. The secondary cost is traffic-class contention on collective communication: Lustre I/O stalls the all-reduce by up to 145$\times$ in an isolated benchmark. The two costs arise from different mechanisms. I/O stall latency affects any storage path that traverses the shared fabric, whereas all-reduce network contention occurs only when storage and collective communication share the same traffic class. Their common root cause is that storage I/O traverses the shared fabric. This work shows that node-local NVMe staging via DYAD (Our code is publicly available at https://github.com/flux-framework/dyad) eliminates both effects by keeping storage I/O off that path. Across a full training epoch, DYAD achieves a 7.4 times speedup over direct Lustre reads and a 1.06 times speedup over VAST. By the second epoch, once the local cache is fully warmed, DataLoader stalls are eliminated entirely, allowing DYAD to reach a 1.31 times speedup over VAST.