Building a 1000-Qubit Neutral Atom Quantum Processor for High-Performance Computing Centers

We report on the design and implementation of a 1000-qubit neutral atom quantum processor engineered for operation in a high-performance computing (HPC) environment. The system, developed by planqc and deployed at the Leibniz Supercomputing Centre (LRZ), is based on a multicore architecture using neutral Ytterbium atoms. MAQCS (Multicore Atomic Quantum Computing System) is integrated directly into the LRZ HPC software stack, enabling tight coupling between classical HPC resources and the quantum processing unit. We will present the system architecture and focus on the engineering challenges of operating large scale neutral atom hardware in an HPC environment, including stability, long-term autonomous operation and infrastructure integration. We will also show early benchmarks that characterize system capacity and operational performance, illustrating the transition from laboratory systems to deployable quantum hardware.