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The wide adoption of Docker containers for supporting agile and elastic enterprise applications has led to a broad proliferation of container images. The associated storage performance and capacity requirements place a high pressure on the infrastructure ofcontainer registriesthat store and distribute images andcontainer storage systemson the Docker client side that manage image layers and store ephemeral data generated at container runtime. The storage demand is worsened by the large amount of duplicate data in images. Moreover, container storage systems that use Copy-on-Write (CoW) file systems as storage drivers exacerbate the redundancy. Exploiting the high file redundancy in real-world images is a promising approach to drastically reduce the growing storage requirements of container registries and improve the space efficiency of container storage systems. However, existing deduplication techniques significantly degrade the performance of both registries and container storage systems because of data reconstruction overhead as well as the deduplication cost. We propose DupHunter, an end-to-end deduplication scheme that deduplicates layers for both Docker registries and container storage systems while maintaining a high image distribution speed and container I/O performance. DupHunter is divided into three tiers: registry tier, middle tier, and client tier. Specifically, we first build a high-performance deduplication engine at the registry tier that not only natively deduplicates layers for space savings but also reduces layer restore overhead. Then, we use deduplication offloading at the middle tier to eliminate the redundant files from the client tier and avoid bringing deduplication overhead to the clients. To further reduce the data duplicates caused by CoWs and improve the container I/O performance, we utilize a container-aware storage system at the client tier that reserves space for each container and arranges the placement of files and their modifications on the disk to preserve locality. Under real workloads, DupHunter reduces storage space by up to 6.9× and reduces theGETlayer latency up to 2.8× compared to the state-of-the-art. Moreover, DupHunter can improve the container I/O performance by up to 93% for reads and 64% for writes.