How to cite EXESS ================= Here are the main papers that need to be cited depending on what capabilities from EXESS you are using. See :ref:`bibtex_format` for the citations in BibTex format. Main EXESS citation -------------------- - Galvez Vallejo, J. L.; Snowdon, C.; Stocks, R.; Kazemian, F.; Yan Yu, F. C.; Seidl, C.; Seeger, Z.; Alkan, M.; Poole, D.; Westheimer, B. M.; Basha, M.; De La Pierre, M.; Rendell, A.; Izgorodina, E. I.; Gordon, M. S.; Barca, G. M. J. Toward an Extreme-Scale Electronic Structure System. The Journal of Chemical Physics 2023, 159 (4), 044112. https://doi.org/10.1063/5.0156399. .. code-block:: bibtex @article{exess_jcp, title = {Toward an extreme-scale electronic structure system}, volume = {159}, issn = {0021-9606}, url = {https://doi.org/10.1063/5.0156399}, doi = {10.1063/5.0156399}, number = {4}, urldate = {2023-11-28}, journal = {The Journal of Chemical Physics}, author = {Galvez Vallejo, Jorge L. and Snowdon, Calum and Stocks, Ryan and Kazemian, Fazeleh and Yan Yu, Fiona Chuo and Seidl, Christopher and Seeger, Zoe and Alkan, Melisa and Poole, David and Westheimer, Bryce M. and Basha, Mehaboob and De La Pierre, Marco and Rendell, Alistair and Izgorodina, Ekaterina I. and Gordon, Mark S. and Barca, Giuseppe M. J.}, month = jul, year = {2023}, pages = {044112} } Fragmentation papers -------------------- - Barca, G. M. J.; Poole, D. L.; Vallejo, J. L. G.; Alkan, M.; Bertoni, C.; Rendell, A. P.; Gordon, M. S. Scaling the Hartree-Fock Matrix Build on Summit. In SC20: International Conference for High Performance Computing, Networking, Storage and Analysis; 2020; pp 1–14. https://doi.org/10.1109/SC41405.2020.00085. - Barca, G. M. J.; Vallejo, J. L. G.; Poole, D. L.; Alkan, M.; Stocks, R.; Rendell, A. P.; Gordon, M. S. Enabling Large-Scale Correlated Electronic Structure Calculations: Scaling the RI-MP2 Method on Summit. In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis; SC ’21; Association for Computing Machinery: New York, NY, USA, 2021; pp 1–15. https://doi.org/10.1145/3458817.3476222. - Barca, G. M. J.; Snowdon, C.; Vallejo, J. L. G.; Kazemian, F.; Rendell, A. P.; Gordon, M. S. Scaling Correlated Fragment Molecular Orbital Calculations on Summit; IEEE Computer Society, 2022; pp 72–85. .. code-block:: bibtex @inproceedings{fock_build_summit_sc20, title = {Scaling the {Hartree}-{Fock} {Matrix} {Build} on {Summit}}, doi = {10.1109/SC41405.2020.00085}, booktitle = {{SC20}: {International} {Conference} for {High} {Performance} {Computing}, {Networking}, {Storage} and {Analysis}}, author = {Barca, G. M. J. and Poole, D. L. and Vallejo, J. L. G. and Alkan, M. and Bertoni, C. and Rendell, A. P. and Gordon, M. S.}, month = nov, year = {2020}, keywords = {Instruction sets, Graphics processing units, Supercomputers, Heuristic algorithms, GPU, Hartree-Fock, Load management, Summit, Synchronization, Throughput}, pages = {1--14} } @inproceedings{rimp2_sc21, address = {New York, NY, USA}, series = {{SC} '21}, title = {Enabling large-scale correlated electronic structure calculations: scaling the {RI}-{MP2} method on summit}, isbn = {978-1-4503-8442-1}, shorttitle = {Enabling large-scale correlated electronic structure calculations}, url = {https://doi.org/10.1145/3458817.3476222}, doi = {10.1145/3458817.3476222}, urldate = {2021-11-01}, booktitle = {Proceedings of the {International} {Conference} for {High} {Performance} {Computing}, {Networking}, {Storage} and {Analysis}}, publisher = {Association for Computing Machinery}, author = {Barca, Giuseppe M. J. and Vallejo, Jorge L. Galvez and Poole, David L. and Alkan, Melisa and Stocks, Ryan and Rendell, Alistair P. and Gordon, Mark S.}, month = nov, year = {2021}, keywords = {MP2, quantum chemistry, GPU, SCF, summit}, pages = {1--15}, } @inproceedings{fmo-sc22, title = {Scaling {Correlated} {Fragment} {Molecular} {Orbital} {Calculations} on {Summit}}, isbn = {978-1-66545-444-5}, url = {https://www.computer.org/csdl/proceedings-article/sc/2022/544400a072/1I0bSLKTsKA}, language = {English}, urldate = {2022-11-21}, publisher = {IEEE Computer Society}, author = {Barca, Giuseppe M. J. and Snowdon, Calum and Vallejo, Jorge L. Galvez and Kazemian, Fazeleh and Rendell, Alistair P. and Gordon, Mark S.}, month = nov, year = {2022}, note = {ISSN: 2167-4337}, pages = {72--85} } General SCF routines -------------------- - Barca, G. M. J.; Galvez-Vallejo, J. L.; Poole, D. L.; Rendell, A. P.; Gordon, M. S. High-Performance, Graphics Processing Unit-Accelerated Fock Build Algorithm. J. Chem. Theory Comput. 2020, 16 (12), 7232–7238. https://doi.org/10.1021/acs.jctc.0c00768. - Barca, G. M. J.; Alkan, M.; Galvez-Vallejo, J. L.; Poole, D. L.; Rendell, A. P.; Gordon, M. S. Faster Self-Consistent Field (SCF) Calculations on GPU Clusters. J. Chem. Theory Comput. 2021, 17 (12), 7486–7503. https://doi.org/10.1021/acs.jctc.1c00720. - Galvez Vallejo, J. L.; Barca, G. M. J.; Gordon, M. S. High-Performance GPU-Accelerated Evaluation of Electron Repulsion Integrals. Molecular Physics 2022, 0 (0), e2112987. https://doi.org/10.1080/00268976.2022.2112987. .. code-block:: bibtex @article{fock_build_2021, title = {High-{Performance}, {Graphics} {Processing} {Unit}-{Accelerated} {Fock} {Build} {Algorithm}}, volume = {16}, issn = {1549-9618}, url = {https://doi.org/10.1021/acs.jctc.0c00768}, doi = {10.1021/acs.jctc.0c00768}, number = {12}, urldate = {2021-03-15}, journal = {Journal of Chemical Theory and Computation}, author = {Barca, Giuseppe M. J. and Galvez-Vallejo, Jorge L. and Poole, David L. and Rendell, Alistair P. and Gordon, Mark S.}, month = dec, year = {2020}, note = {Publisher: American Chemical Society}, pages = {7232--7238}, } @article{scf_2021, title = {Faster {Self}-{Consistent} {Field} ({SCF}) {Calculations} on {GPU} {Clusters}}, volume = {17}, issn = {1549-9618}, url = {https://doi.org/10.1021/acs.jctc.1c00720}, doi = {10.1021/acs.jctc.1c00720}, number = {12}, urldate = {2024-06-24}, journal = {Journal of Chemical Theory and Computation}, author = {Barca, Giuseppe M. J. and Alkan, Melisa and Galvez-Vallejo, Jorge L. and Poole, David L. and Rendell, Alistair P. and Gordon, Mark S.}, month = dec, year = {2021}, note = {Publisher: American Chemical Society}, pages = {7486--7503}, } @article{hgp-integrals-2022, title = {High-performance {GPU}-accelerated evaluation of electron repulsion integrals}, volume = {0}, issn = {0026-8976}, url = {https://doi.org/10.1080/00268976.2022.2112987}, doi = {10.1080/00268976.2022.2112987}, number = {0}, urldate = {2022-10-03}, journal = {Molecular Physics}, author = {Galvez Vallejo, Jorge Luis and Barca, Giuseppe M.J. and Gordon, Mark S.}, month = aug, year = {2022}, note = {Publisher: Taylor \& Francis}, keywords = {high performance computing, quantum chemistry, electronic structure theory, gpu, include these here if the journal requires them, two electron integrals}, pages = {e2112987}, } RI methodologies energy/gradients ---------------------------------- - Stocks, R.; Palethorpe, E.; Barca, G. M. J. High-Performance Multi-GPU Analytic RI-MP2 Energy Gradients. J. Chem. Theory Comput. 2024, 20 (6), 2505–2519. https://doi.org/10.1021/acs.jctc.3c01424. .. code-block:: bibtex @article{rimp2_grad_2024, title = {High-{Performance} {Multi}-{GPU} {Analytic} {RI}-{MP2} {Energy} {Gradients}}, volume = {20}, copyright = {https://doi.org/10.15223/policy-029}, issn = {1549-9618, 1549-9626}, url = {https://pubs.acs.org/doi/10.1021/acs.jctc.3c01424}, doi = {10.1021/acs.jctc.3c01424}, language = {en}, number = {6}, urldate = {2024-06-24}, journal = {Journal of Chemical Theory and Computation}, author = {Stocks, Ryan and Palethorpe, Elise and Barca, Giuseppe M. J.}, month = mar, year = {2024}, pages = {2505--2519}, } .. Q-Next ------- - Seidl, C.; Barca, G. M. J. Q-Next: A Fast, Parallel, and Diagonalization-Free Alternative to Direct Inversion of the Iterative Subspace. J. Chem. Theory Comput. 2022, 18 (7), 4164–4176. https://doi.org/10.1021/acs.jctc.2c00073. @article{q-next-2022, title = {Q-{Next}: {A} {Fast}, {Parallel}, and {Diagonalization}-{Free} {Alternative} to {Direct} {Inversion} of the {Iterative} {Subspace}}, volume = {18}, issn = {1549-9618}, shorttitle = {Q-{Next}}, url = {https://doi.org/10.1021/acs.jctc.2c00073}, doi = {10.1021/acs.jctc.2c00073}, abstract = {As computer systems dedicated to scientific calculations become massively parallel, the poor parallel performance of the Fock matrix diagonalization becomes a major impediment to achieving larger molecular sizes in self-consistent field (SCF) calculations. In this Article, a novel, highly parallel, and diagonalization-free algorithm for the accelerated convergence of the SCF procedure is presented. The algorithm, called Q-Next, draws on the second-order SCF, quadratically convergent SCF, and direct inversion of the iterative subspace (DIIS) approaches to enable fast convergence while replacing the Fock matrix diagonalization SCF bottleneck with higher parallel efficiency matrix multiplications. Performance results on both parallel multicore CPU and GPU hardware for a variety of test molecules and basis sets are presented, showing that Q-Next achieves a convergence rate comparable to the DIIS method while being, on average, one order of magnitude faster.}, number = {7}, urldate = {2022-10-03}, journal = {Journal of Chemical Theory and Computation}, author = {Seidl, Christopher and Barca, Giuseppe M. J.}, month = jul, year = {2022}, note = {Publisher: American Chemical Society}, pages = {4164--4176} }