Demonstration of Parallel Multi-QPU Execution for Fragment-Based Quantum Chemistry Using On-Premises Hardware
Nils Herrmann, Mariam Akhtar, Luke W. Bertels, Leigh Cameron, Raymond Chan, Lei Cheng, Daniel Claudino, Mark de Burgh, Simon Gemmell, Rugang Geng, Geoff Gillett, Travis Humble, Stephan Irle, John P. McMahon, Christian Ortiz, Florian Preis, Andreas Sawadsky, Bianca Sawyer, Reuben Singer, Sai Meghana Tunikipati, Cameron Walters, Lachlan Whichello, Adam Zegelin, Marcus W. Doherty
quant-phphysics.chem-phphysics.comp-phSubmitted Oct 6, 2026• Announced Oct 7, 2026• 0 citations
Fragment molecular orbital (FMO) quantum chemistry offers a natural route to parallel quantum computing: large molecular calculations can be decomposed into smaller quantum subproblems that can, in principle, run concurrently. Their practical benefit on real quantum hardware, however, has remained unclear. We demonstrate parallel FMO calculations on three room-temperature diamond-based 'Quoll' quantum computers installed on-site at the Oak Ridge Leadership Computing Facility. Helium clusters (He$_{n}$, $n=2,4,8,10,14$) served as a testbed for total energy calculations using the Quantum Wave Function Sampler (QWFS), a selected configuration interaction (SCI) approach. We compare two execution modes: synchronous shot-parallel execution, in which quantum processors jointly sample QWFS circuits and combine their SPAM-corrected counts into a single probability distribution; and asynchronous fragment-parallel execution, in which processors independently evaluate FMO fragments using device-specific optimized circuits. Both modes increase quantum sampling throughput without systematic loss of accuracy. The three-QPU shot-parallel workflow reaches a parallel efficiency of $93.60\%$, while the fragment-parallel workflow achieves a measured efficiency of $75.01\%$, increasing to $95.17\%$ when excluding the non-useful idle time associated with non-interruptible submitted jobs. In both cases, the assembled FMO-QWFS energies remain chemically accurate compared to the classical ideal. These results provide a proof-of-concept demonstration that parallel quantum execution can improve the practical throughput of quantum chemistry workflows on prototype hardware, motivating the development of future HPC environments with many fault-tolerant quantum processors operating as a distributed resource for molecular and materials simulation.
Fragment molecular orbital (FMO) quantum chemistry offers a natural route to parallel quantum computing: large molecular calculations can be decomposed into smaller quantum subproblems that can, in principle, run concurrently. Their practical benefit on real quantum hardware, however, has remained unclear. We demonstrate parallel FMO calculations on three room-temperature diamond-based 'Quoll' quantum computers installed on-site at the Oak Ridge Leadership Computing Facility. Helium clusters (Hen, n=2,4,8,10,14) served as a testbed for total energy calculations using the Quantum Wave Function Sampler (QWFS), a selected configuration interaction (SCI) approach. We compare two execution modes: synchronous shot-parallel execution, in which quantum processors jointly sample QWFS circuits and combine their SPAM-corrected counts into a single probability distribution; and asynchronous fragment-parallel execution, in which processors independently evaluate FMO fragments using device-specific optimized circuits. Both modes increase quantum sampling throughput without systematic loss of accuracy. The three-QPU shot-parallel workflow reaches a parallel efficiency of 93.60%, while the fragment-parallel workflow achieves a measured efficiency of 75.01%, increasing to 95.17% when excluding the non-useful idle time associated with non-interruptible submitted jobs. In both cases, the assembled FMO-QWFS energies remain chemically accurate compared to the classical ideal. These results provide a proof-of-concept demonstration that parallel quantum execution can improve the practical throughput of quantum chemistry workflows on prototype hardware, motivating the development of future HPC environments with many fault-tolerant quantum processors operating as a distributed resource for molecular and materials simulation.
Present-day sample-based quantum algorithms within quantum-centric supercomputing workflows require substantial classical post-processing, large circuit depths to produce chemically relevant samples, and long QPU times to execute the many circuits needed for molecules of chemically relevant size. We introduce FMO-QVM-HCI-HSQD, a resource-efficient sample-based framework that breaks a large problem into fragments, runs the fragments in parallel on virtual regions of the QPU, and reduces circuit depth through a half-qubit ansatz whose samples seed an HCI expansion. We demonstrate the algorithm on ibm_marrakesh and ibm_boston for the water trimer and the carmofur_Mpro complex with up to 52 qubits, benchmarking against FMO-CCSD(T), FMO-CASCI and FMO-HCI. For the water trimer (14 spin orbitals for monomers, 28 for dimers), our method reduces the two-qubit depth by 39% compared to FMO-QVM-SQD and the QPU time by 82% compared to sequential FMO-SQD, and accesses 3% of the determinant subspace versus 40% for FMO-SQD, while achieving more accurate energies. For the carmofur_Mpro complex (16 and 32 spin orbitals), it reduces the two-qubit depth by 47% and the QPU time by 20% compared to FMO-QVM-SQD, and accesses 0.007% of the determinant subspace versus 40%, while remaining within chemical accuracy. Extending the carmofur_Mpro active space in the 6-31G basis to 52 and 104 spin orbitals, sampled on 26 and 52 qubits, the total energy deviates from FMO-HCI by only 1.22 mHa. These results show that combining fragmentation, virtual QPU partitioning and half-qubit sampling makes sample-based quantum simulation of chemically relevant systems feasible on current hardware.
We develop a workflow decomposing a molecule into fragments via quantum embedding and simulating them with a heterogeneous quantum-classical (HQC) method. We sample fragment electronic configurations on two 156-qubit quantum processors (ibm_cleveland, ibm_kobe), using up to 94 qubits, running 21,006 circuits for over 239 hours, collecting 3.0⋅109 measurement outcomes -- the most resource-intensive HQC computation for quantum chemistry to date. We compute fragment wavefunctions via optimized subspace diagonalization on supercomputers Fugaku, Miyabi-G, and ROQUO, achieving 72.5% parallel efficiency with scalable distributed linear algebra kernels. We simulate two protein-ligand complexes spanning dispersion- and electrostatics-dominated regimes (11,608, 12,635 atoms), demonstrate >40× increase in system size and up to 210× improvement in accuracy over previous state-of-the-art, with HQC matching coupled-cluster (CCSD) accuracy in fragment energies. We present the first HQC protein-ligand binding prediction using a mixed-basis set and an automated end-to-end workflow enabling practical HQC calculations of large protein systems.
Today's quantum processors have tens to hundreds of physical qubits, but reliable execution of arbitrary circuits remains limited to fewer than 30 entangled qubits across hardware modalities. Building upon prior work, we introduce an error- and topology-aware method for mapping multiple independent circuits onto disjoint regions of a single large-scale QPU for parallel circuit execution. For applications with many similarly sized circuits, such as observable estimation for Hamiltonian simulation, this approach can reduce billed QPU execution time, with ideal speedup proportional to the number of usable partitions. We demonstrate the approach on IBM's 156-qubit ibm_boston processor using standard QED-C benchmark and Hamiltonian-based observable-estimation workloads. Compared with standard sequential execution, parallel execution reduces billed execution time by 3.5-5.5x while retaining 83-92% of the sequential fidelity. We further evaluate the scaling of parallel circuit execution using GPU-accelerated classical simulation, distributing measurement circuits across GPUs via MPI. Using CUDA-Q on the NERSC Perlmutter system, we achieve up to 13.8x speedup on 16 GPUs (86% parallel efficiency) for an H2 electronic-structure simulation, with scaling evaluated across multiple Hamiltonians and circuit counts. These results provide an indication of the performance ceiling that parallel execution on future quantum hardware may eventually approach. Both execution modes are implemented as a runtime option within the QED-C Application-Oriented Benchmark suite. Together, the results show that circuit-level parallelism can reduce execution cost on current quantum hardware and simulation time on GPU clusters, with the potential for greater benefits as device quality and qubit counts increase.
Predicting the chemico-physical properties of large molecular systems is a formidable challenge in chemistry and materials science. Traditional quantum mechanical methods, while accurate, have impractical scaling for large molecules with thousands of atoms, which are crucial in the development of novel therapeutics, catalysts, and nanomaterials. To address this, molecular fragmentation algorithms have been proposed to improve scalability and enable extensive parallelism. In this article, we introduce a significant enhancement to the Fragment Molecular Orbital (FMO) method, termed the Coulomb-Perturbed Fragmentation (CPF) method. CPF incorporates algorithmic improvements and implementation enhancements to optimize performance on heterogeneous computing systems equipped with a large number of GPUs. Key developments include a significant simplification of iteratitve self-consistent field (SCF) algorithm, advanced data management through a one-sided communication model, topology-aware optimizations, and a hybrid communication strategy for intra-group exchanges. Moreover, CPF integrates a distributed dynamic multi-layer load balancing scheme to optimise fragment distribution and workload management across nodes and GPUs. Performance evaluations on a 420-atom benzene molecule system comprising 35 fragments reveal that CPF outperforms existing GPU/CPU-based FMO algorithms in both efficiency and accuracy. When deployed on the Gadi supercomputer, CPF achieves over 97% parallel efficiency on 20 nodes, with scalability maintaining above 98% and 90% efficiency in weak-scaling tests for smaller and larger systems, respectively. Notably, CPF matches or exceeds the computational accuracy of conventional FMO methods, marking a substantial progress in the field of computational chemistry for fragmentation-based large-scale molecular modelling.
In the context of quantum computing, efficient resource management is crucial for optimizing throughput on cloud-based platforms and maximizing hardware utilization. In the present work, we propose an approach to tackle quantum chemistry problems via quantum multi-programming of the Local Unitary Cluster Jastrow (LUCJ) ansätze. The ground-state energy of the molecular system is obtained via Sample-based quantum diagonalization (SQD), further refined by its extended version (ext-SQD). Building upon the Qiskit Experiments package, which already supports parallel execution functionality for general tasks, we developed a novel parallel experiment class tailored for quantum chemistry problems. Cross-talk is a known issue in the multi-programming frameworks and can corrupt the ground-energy estimation of the simulated systems. To assess its impact within our approach, we simulated two conformations of the ethanol molecule: one at the equilibrium state (EtOHEq), and one with the O-H bond stretched to 1.2 A˚ (EtOH1.2). We defined three different layouts that we executed in a randomized fashion, alternating serial and parallel execution within 10 independent replicates. The single modality of each circuit was kept as a baseline to evaluate the effect of cross-talk induced by quantum multi-programming. The energies obtained at the first-, last- and ext-SQD iteration were compared to the classical Heat-bath Configuration Interaction (HCI) reference. Our findings highlight the viability of a quantum multi-programming workflow for quantum chemistry as the robust post-processing protocol effectively mitigates possible cross-talk induced noise. At the final step of the configuration recovery process, the energy difference relative to the HCI reference is negligible, within 0.001 kcal/mol.
Neutral atom Quantum Processing Units (QPUs) are emerging as a popular quantum computing technology due to their large qubit counts and flexible connectivity. However, performance challenges arise as large circuits experience significant fidelity drops, while small circuits underutilize hardware and face initialization latency issues. To tackle these problems, we propose multi-programming on neutral atom QPUs, allowing the co-execution of multiple circuits by logically partitioning the qubit array. This approach increases resource utilization and mitigates initialization latency while maintaining result fidelity. Currently, state-of-the-art compilers for neutral atom architectures do not support multi-programming.
To fill this gap, we introduce MultiQ, the first system designed for this purpose. MultiQ addresses three main challenges: (i) it compiles circuits into a virtual zone layout to optimize spatio-temporal hardware utilization; (ii) it parallelizes the execution of co-located circuits, allowing single hardware instructions to operate on different circuits; and (iii) it includes an algorithm to verify the functional independence of the bundled circuits. MultiQ functions as a cross-layer system comprising a compiler, controller, and checker. Our compiler generates \emph{virtual zone layouts} to enhance performance, while the controller efficiently maps these layouts onto the hardware and resolves any conflicts. The checker ensures the correct bundling of circuits.
Experimental results show a throughput increase from 3.8× to 12.3× when multi-programming 4 to 14 circuits, with fidelity largely maintained, ranging from a 1.3% improvement for four circuits to only a 3.5% loss for fourteen circuits. Overall, MultiQ facilitates concurrent execution of multiple quantum circuits, boosting throughput and hardware utilization.