Distributed deduplication wherein runtime performance of dedup pipelines in all nodes is monitored. The bottleneck for each pipeline is identified and machine resources from different nodes are reallocated to seek to balance the costs of each stage of each task in each of the pipelines. While the overall cost for each task may remain the same, stalls may be eliminated such that the total cost to complete all the tasks is reduced. The global dedup ratio and the local compression ratio may be used to weight certain stage costs.