AEGIS: Scaling Long-Sequence Homomorphic Encrypted Transformer Inference via Hybrid Parallelism on Multi-GPU Systems

Encrypted AI using fully homomorphic encryption (FHE) enables inference directly over encrypted queries, providing strong privacy guarantees. However, its computational and memory overheads have limited practical deployment. Custom FHE accelerators improve performance, but rely on advanced manufacturing technologies that limit their accessibility. GPUs offer a more widely available alternative, yet achieving ASIC-class performance on GPUs is challenging. Large models such as LLMs compound these challenges by requiring optimized kernels, terabyte-scale memory management, and efficient execution across multiple devices. We present Cerium, a multi-GPU framework for large-scale FHE inference. Cerium combines a domain-specific language, an optimizing compiler, and a runtime system to automatically generate optimized GPU kernels, compress plaintext data, manage terabyte-scale memory footprints, and optimize multi-GPU communication. Implemented on NVIDIA GPUs, Cerium outperforms expert-written GPU libraries by up to 2.25x and achieves performance competitive with state-of-the-art FHE ASICs, matching the CraterLake ASIC. It is the first GPU system to execute CKKS bootstrapping in under 10 milliseconds, achieving 7.5 milliseconds, and is the first to demonstrate encrypted inference for BERT-Base and Llama3-8B prefill in 8 seconds and 43 seconds, respectively. The Cerium framework is open-source and available at https://github.com/CMU-CAOS/Cerium

Fully homomorphic encryption (FHE) enables computation on encrypted data, but practical encrypted Transformer inference is bottlenecked by the sequential composition of many nonlinear blocks. We study whether Structured Newton Layer Parallelism (SNLP) can make this inter-layer composition more FHE-friendly: each Transformer block still requires polynomial approximations for operations such as softmax and RMSNorm, but SNLP reduces the layerwise sequential nonlinear depth from L stages to a small number of solver iterations plus linear structured corrections. Using a simulation framework based on Chebyshev polynomial approximations, we measure error accumulation under sequential versus SNLP inference across 8 models and 4 architecture families. On a 0.5B IDN-trained model, SNLP reduces symbolic bootstraps from 53 to 20 (2.65x) with only +1.2% perplexity degradation, while lowering error amplification (1.36x vs. 1.42x). Across all tested models, SNLP has lower amplification than sequential inference. Ablations show that softmax approximation dominates the error budget and CKKS arithmetic noise is negligible in our setting, suggesting that SNLP is complementary to block-level FHE-friendly operator design rather than a replacement for it.

Fully homomorphic encryption (FHE) provides strong cryptographic guarantees for private inference, but deploying transformer models under FHE remains prohibitively expensive. A key bottleneck is that non-linear operations such as softmax, normalization, and activation must be replaced with polynomial approximations compatible with the CKKS scheme, and the multiplicative depth consumed by these approximations dominates inference cost. Recent frameworks have advanced approximation techniques, yet all rely on manually configured approximation hyperparameters (e.g., number of iterations, polynomial degree), applied uniformly across all layers. While convenient, this uniform-configuration approach is overly rigid: different layers can tolerate different levels of approximation error without degrading predictive accuracy, and uniform configurations cannot exploit this variability to reduce latency. Allowing each layer to adopt its own configuration, however, causes the search space to explode with model depth, reaching roughly $10^{84}$ configurations for BERT/ViT (12 layers) and $10^{225}$ for LLaMA3 (32 layers), rendering manual exploration practically impossible. We present ATLAS, an automated framework that configures per-layer approximation settings by formulating the problem as a multi-objective optimization over latency and predictive accuracy. The resulting problem is inherently difficult: 1) competing objectives over a large decision space (120 or 320 variables for BERT/ViT or LLaMA3); 2) expensive evaluation, as each configuration takes 70-1,000 seconds even in cleartext; and 3) sparse optimization signals, as 35-50% of candidate configurations yield numerically invalid solutions. ATLAS addresses these challenges through a two-stage optimization strategy that progressively relaxes layer-wise constraints, combined with surrogate models to accelerate evaluation.