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Modern Deep Learning (DL) models have grown to sizes requiring massive clusters of specialized, high-end nodes to train. Designing such clusters to maximize both performance and utilization to amortize their steep cost is a challenging task requiring careful balance of compute, memory, and network resources. Moreover, a plethora of each model's tuning knobs drastically affect the performance, with optimal values often depending on the underlying cluster's characteristics, which necessitates a complex cluster-workload co-design process. To facilitate the design space exploration of such massive DL training clusters, we introduce COMET a holistic cluster design methodology and workflow to jointly study the impact of parallelization strategies and key cluster resource provisioning on the performance of distributed DL training. We develop a step-by-step process to establish a reusable and flexible methodology, and demonstrate its application with a case study of training a Transformer-1T model on a cluster of variable compute, memory, and network resources. Our case study demonstrates COMET's utility in identifying promising architectural optimization directions and guiding system designers in configuring key model and cluster parameters.