Embodiments of the present invention provide high-throughput computing in a hybrid processing system. A set of high-throughput computing service level agreements (SLAs) is analyzed. The set of high-throughput computing SLAs are associated with a hybrid processing system. The hybrid processing system includes at least one server system that includes a first computing architecture and a set of accelerator systems each including a second computing architecture that is different from the first computing architecture. A first set of resources at the server system and a second set of resources at the set of accelerator systems are monitored. A set of data-parallel workload tasks is dynamically scheduled across at least one resource in the first set of resources and at least one resource in the second set of resources. The dynamic scheduling of the set of data-parallel workload tasks substantially satisfies the set of high-throughput computing SLAs.