Publications

Below is a list of publications based on or mentioning the 2DECOMP&FFT library

-Zarins, J., Weiland, M., Bartholomew, P., Lapworth, L., & Parsons, M. (2023, January). Detecting Scale-Induced Overflow Bugs in Production HPC Codes. In High Performance Computing. ISC High Performance 2022 International Workshops: Hamburg, Germany, May 29–June 2, 2022, Revised Selected Papers (pp. 33-43). Cham: Springer International Publishing.

-Liu, Z., Wang, Q., Lv, X., Liu, X., Meng, H., Zhu, G., … & Yang, G. (2023). swPHoToNs: Toward trillion‐body‐scale cosmological N‐body simulations on Sunway TaihuLight supercomputer. Engineering Reports, e12640.

-Crialesi-Esposito, M., Scapin, N., Demou, A. D., Rosti, M. E., Costa, P., Spiga, F., & Brandt, L. (2023). FluTAS: A GPU-accelerated finite difference code for multiphase flows. Computer Physics Communications, 284, 108602.

-Sarath, K. P., & Manu, K. V. (2023). The onset of turbulence in decelerating diverging channel flows. Journal of Fluid Mechanics, 962, A30.

-Abregu, W. I. M., Dari, E. A., & Teruel, F. E. (2023). DNS of heat transfer in a plane channel flow with spatial transition. International Journal of Heat and Mass Transfer, 209, 124110.

-Kim, K. H., Kang, J. H., Pan, X., & Choi, J. I. (2023). PaScaL_TCS: A versatile solver for large-scale turbulent convective heat transfer problems with temperature-dependent fluid properties. Computer Physics Communications, 108779.

-Romero, J., Costa, P., & Fatica, M. (2022, June). Distributed-memory simulations of turbulent flows on modern GPU systems using an adaptive pencil decomposition library. In Proceedings of the Platform for Advanced Scientific Computing Conference (pp. 1-11).

-Ayala, A., Tomov, S., Stoyanov, M., Haidar, A., & Dongarra, J. (2022, May). Performance Analysis of Parallel FFT on Large Multi-GPU Systems. In 2022 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) (pp. 372-381). IEEE.

-Serafini, F., Battista, F., Gualtieri, P., & Casciola, C. M. (2022). Drag Reduction in Polymer-Laden Turbulent Pipe Flow. Fluids, 7(11), 355.

-Mathias, M. S., & de Medeiros, M. A. F. (2022). Optimal computational parameters for maximum accuracy and minimum cost of Arnoldi-based time-stepping methods for flow global stability analysis. Theoretical and Computational Fluid Dynamics, 1-24.

-Kwon, O. K., Kang, J. H., Lee, S., Kim, W., & Song, J. (2022, October). Efficient Task-Mapping of Parallel Applications Using a Space-Filling Curve. In Proceedings of the International Conference on Parallel Architectures and Compilation Techniques (pp. 384-397).

-Villodi, N., & KV, M. (2022). Characteristics of boundary-layer transition driven by diverse streamwise vortices. Physics of Fluids, 34(7), 074113.

-Karzhaubayev, K., Wang, L. P., & Zhakebayev, D. (2022). An efficient parallel spectral code for 3D periodic flow simulations. SoftwareX, 20, 101244.

-Khorasani, S. M. H., Lācis, U., Pasche, S., Rosti, M. E., & Bagheri, S. (2022). Near-wall turbulence alteration with the transpiration-resistance model. Journal of Fluid Mechanics, 942, A45.

-Zhao, W. L., Wang, W., & Wang, Q. (2022). Optimization of cosmological N-body simulation with FMM-PM on SIMT accelerators. The Journal of Supercomputing, 78(5), 7186-7205.

-Wilbert, M., Giesecke, A., & Grauer, R. (2022). Numerical investigation of the flow inside a precession-driven cylindrical cavity with additional baffles using an immersed boundary method. Physics of Fluids, 34(9), 096607.

-Poblador-Ibanez, J., & Sirignano, W. A. (2022). Temporal atomization of a transcritical liquid n-decane jet into oxygen. International Journal of Multiphase Flow, 153, 104130.

-Bazesefidpar, K., Brandt, L., & Tammisola, O. (2022). A dual resolution phase‐field solver for wetting of viscoelastic droplets. International Journal for Numerical Methods in Fluids, 94(9), 1517-1541.

-Dalla Barba, F., Zaccariotto, M., Galvanetto, U., & Picano, F. (2022). 3D fluid–structure interaction with fracturing: A new method with applications. Computer Methods in Applied Mechanics and Engineering, 398, 115210.

-Poblador-Ibanez, J., & Sirignano, W. A. (2022). A volume-of-fluid method for variable-density, two-phase flows at supercritical pressure. Physics of Fluids, 34(5), 053321.

-Lin, F., Wan, Z. H., Zhu, Y., Liu, N., Lu, X. Y., & Khomami, B. (2022). High-fidelity robust and efficient finite difference algorithm for simulation of polymer-induced turbulence in cylindrical coordinates. Journal of Non-Newtonian Fluid Mechanics, 307, 104875.

-Gong, Z., Deng, G., An, C., Wu, Z., & Fu, X. (2022). A high order finite difference solver for simulations of turbidity currents with high parallel efficiency. Computers & Mathematics with Applications, 128, 21-33.

-Suter, I., Grylls, T., Sützl, B. S., Owens, S. O., Wilson, C. E., & van Reeuwijk, M. (2022). uDALES 1.0: a large-eddy simulation model for urban environments. Geoscientific Model Development, 15(13), 5309-5335.

-Leu, B., Aseeri, S., & Muite, B. (2021, January). A Comparison of Parallel Profiling Tools for Programs utilizing the FFT. In The International Conference on High Performance Computing in Asia-Pacific Region Companion (pp. 36-45).

-Himeno, F. H., Mathias, M., & Medeiros, M. (2021). DNS of a Tollmien-Schlichting Wave Interacting with a Roughness Modeled via Body-fitted and Approximation Methods. In AIAA AVIATION 2021 FORUM (p. 2500).

-Mathias, M., & Medeiros, M. (2021). Spatial instability of boundary layers over small cavities and comparison to global modes. In AIAA AVIATION 2021 FORUM (p. 2931).

-Pekurovsky, D. (2021, August). A Portable Framework for Multudimensional Spectral-like Transforms At Scale. In Proceedings of the 2021 Improving Scientific Software Conference.

-Miquel, B. (2021). Coral: a parallel spectral solver for fluid dynamics and partial differential equations. Journal of Open Source Software, 6(65), 2978.

-Abdelsamie, A., Chi, C., Nanjaiah, M., Skenderović, I., Suleiman, S., & Thévenin, D. (2021). Direct numerical simulation of turbulent spray combustion in the SpraySyn burner: impact of injector geometry. Flow, Turbulence and Combustion, 106, 453-469.

-Xie, J., He, J., Bao, Y., & Chen, X. (2021). A low-communication-overhead parallel DNS method for the 3D incompressible wall turbulence. International Journal of Computational Fluid Dynamics, 35(6), 413-432.

-Gong, Z., & Fu, X. (2021). A pencil distributed direct numerical simulation solver with versatile treatments for viscous term. Computers & Mathematics with Applications, 100, 141-151.

-Mathias, M. S., & Medeiros, M. A. (2021). The effect of incoming boundary layer thickness and Mach number on linear and nonlinear Rossiter modes in open cavity flows. Theoretical and Computational Fluid Dynamics, 35(4), 495-513.

-Dalla Barba, F., Scapin, N., Demou, A. D., Rosti, M. E., Picano, F., & Brandt, L. (2021). An interface capturing method for liquid-gas flows at low-Mach number. Computers & Fluids, 216, 104789.

-Abdelsamie, A., Lartigue, G., Frouzakis, C. E., & Thevenin, D. (2021). The Taylor–Green vortex as a benchmark for high-fidelity combustion simulations using low-Mach solvers. Computers & Fluids, 223, 104935.

-Hamzehloo, A., Bartholomew, P., & Laizet, S. (2021). Direct numerical simulations of incompressible Rayleigh–Taylor instabilities at low and medium Atwood numbers. Physics of Fluids, 33(5), 054114.

-Chi, C., Janiga, G., & Thévenin, D. (2021). On-the-fly artificial neural network for chemical kinetics in direct numerical simulations of premixed combustion. Combustion and Flame, 226, 467-477.

-Mathias, M., & Medeiros, M. (2020). Interaction between Rossiter and Görtler modes in the compressible flow in an open cavity. In AIAA AVIATION 2020 FORUM (p. 3074).

-Foster, I. (2020). Batched 3D-distributed FFT kernels towards practical DNS codes. Parallel Computing: Technology Trends, 36, 169.

-Hasbestan, J. J., Xiao, C. N., & Senocak, I. (2020). PittPack: An open-source Poisson’s equation solver for extreme-scale computing with accelerators. Computer Physics Communications, 254, 107272.

-Guo, W., Shams, A., Sato, Y., & Niceno, B. (2020). Influence of buoyancy in a mixed convection liquid metal flow for a horizontal channel configuration. International Journal of Heat and Fluid Flow, 85, 108630.

-Wang, H., & Chandramowlishwaran, A. (2020, November). Pencil: A pipelined algorithm for distributed stencils. In SC20: International Conference for High Performance Computing, Networking, Storage and Analysis (pp. 1-16). IEEE.

-Margairaz, F., Pardyjak, E. R., & Calaf, M. (2020). Surface thermal heterogeneities and the atmospheric boundary layer: the thermal heterogeneity parameter. Boundary-Layer Meteorology, 177, 49-68.

-Chi, C., Abdelsamie, A., & Thévenin, D. (2020). A directional ghost-cell immersed boundary method for incompressible flows. Journal of Computational Physics, 404, 109122.

-Bartholomew, P., Deskos, G., Frantz, R. A., Schuch, F. N., Lamballais, E., & Laizet, S. (2020). Xcompact3D: An open-source framework for solving turbulence problems on a Cartesian mesh. SoftwareX, 12, 100550.

-Yao, J., & Hussain, F. (2020). A physical model of turbulence cascade via vortex reconnection sequence and avalanche. Journal of Fluid Mechanics, 883, A51.

-Cloutier, B., Muite, B. K., & Parsani, M. (2019). Fully implicit time stepping can be efficient on parallel computers. Supercomputing Frontiers and Innovations, 6(2), 75-85.

-Aseeri, S., Muite, B. K., & Takahashi, D. (2019, March). Reproducibility in benchmarking parallel fast Fourier transform based applications. In Companion of the 2019 ACM/SPEC International Conference on Performance Engineering (pp. 5-8).

-Jocksch, A., Kraushaar, M., & Daverio, D. (2019). Optimized all‐to‐all communication on multicore architectures applied to FFTs with pencil decomposition. Concurrency and Computation: Practice and Experience, 31(16), e4964.

-Mathias, M., & Medeiros, M. F. (2019). Global instability analysis of a boundary layer flow over a small cavity. In AIAA Aviation 2019 Forum (p. 3535).

-Bauweraerts, P., & Meyers, J. (2019). On the feasibility of using large-eddy simulations for real-time turbulent-flow forecasting in the atmospheric boundary layer. Boundary-Layer Meteorology, 171, 213-235.

-de Motta, J. B., Costa, P., Derksen, J. J., Peng, C., Wang, L. P., Breugem, W. P., … & Renon, N. (2019). Assessment of numerical methods for fully resolved simulations of particle-laden turbulent flows. Computers & Fluids, 179, 1-14.

-Dalcin, L., Mortensen, M., & Keyes, D. E. (2019). Fast parallel multidimensional FFT using advanced MPI. Journal of Parallel and Distributed Computing, 128, 137-150.

-Doukkali, H., Abide, S., Lhassane Lahlaouti, M., & Khamlichi, A. (2018). Large Eddy Simulation of turbulent natural convection in an inclined tall cavity. Numerical Heat Transfer, Part A: Applications, 74(4), 1175-1189.

-Khokhriakov, S., Manumachu, R. R., & Lastovetsky, A. (2018, December). Performance optimization of multithreaded 2d FFT on multicore processors: Challenges and solution approaches. In 2018 IEEE 25th International Conference on High Performance Computing Workshops (HiPCW) (pp. 8-17). IEEE.

-Bauweraerts, P., & Meyers, J. (2018, June). Towards an adjoint based 4D-Var state estimation for turbulent flow. In Journal of Physics: Conference Series (Vol. 1037, No. 7, p. 072055). IOP Publishing.

-Khokhriakov, S., Manumachu, R. R., & Lastovetsky, A. (2018). Performance optimization of multithreaded 2d fast fourier transform on multicore processors using load imbalancing parallel computing method. IEEE Access, 6, 64202-64224.

-Abide, S., Viazzo, S., Raspo, I., & Randriamampianina, A. (2018). Higher-order compact scheme for high-performance computing of stratified rotating flows. Computers & Fluids, 174, 300-310.

-Mathias, M. S., & Medeiros, M. (2018). Direct numerical simulation of a compressible flow and matrix-free analysis of its instabilities over an open cavity. Journal of Aerospace Technology and Management, 10.

-Margairaz, F., Giometto, M. G., Parlange, M. B., & Calaf, M. (2018). Comparison of dealiasing schemes in large-eddy simulation of neutrally stratified atmospheric flows. Geoscientific Model Development, 11(10), 4069-4084.

-Roytershteyn, V., & Delzanno, G. L. (2018). Spectral approach to plasma kinetic simulations based on Hermite decomposition in the velocity space. Frontiers in Astronomy and Space Sciences, 5, 27.

-Flajslik, M., Borch, E., & Parker, M. A. (2018). Megafly: A topology for exascale systems. In High Performance Computing: 33rd International Conference, ISC High Performance 2018, Frankfurt, Germany, June 24-28, 2018, Proceedings 33 (pp. 289-310). Springer International Publishing.

-Costa, P. (2018). A FFT-based finite-difference solver for massively-parallel direct numerical simulations of turbulent flows. Computers & Mathematics with Applications, 76(8), 1853-1862.

-Zhu, X., Phillips, E., Spandan, V., Donners, J., Ruetsch, G., Romero, J., … & Stevens, R. J. (2018). AFiD-GPU: a versatile Navier–Stokes solver for wall-bounded turbulent flows on GPU clusters. Computer physics communications, 229, 199-210.

-Costantini, R., Mollicone, J. P., & Battista, F. (2018). Drag reduction induced by superhydrophobic surfaces in turbulent pipe flow. Physics of Fluids, 30(2), 025102.

-Valente, A., & Marchetti, E. (2017, July). From cards to digital games: closing the loop. In 2017 6th IIAI International Congress on Advanced Applied Informatics (IIAI-AAI) (pp. 507-510). IEEE.

-Boschung, J., Hennig, F., Denker, D., Pitsch, H., & Hill, R. J. (2017). Analysis of structure function equations up to the seventh order. Journal of Turbulence, 18(11), 1001-1032.

-Göbbert, J. H., Iliev, H., Ansorge, C., & Pitsch, H. (2017). Overlapping of communication and computation in nb3dfft for 3d fast fourier transformations. In High-Performance Scientific Computing: First JARA-HPC Symposium, JHPCS 2016, Aachen, Germany, October 4–5, 2016, Revised Selected Papers 1 (pp. 151-159). Springer International Publishing.

-Abide, S., Binous, M. S., & Zeghmati, B. (2017). An efficient parallel high-order compact scheme for the 3D incompressible Navier–Stokes equations. International Journal of Computational Fluid Dynamics, 31(4-5), 214-229.

-Alizad Banaei, A., Loiseau, J. C., Lashgari, I., & Brandt, L. (2017). Numerical simulations of elastic capsules with nucleus in shear flow. European Journal of Computational Mechanics, 26(1-2), 131-153.

-Scholtissek, A., Dietzsch, F., Gauding, M., & Hasse, C. (2017). In-situ tracking of mixture fraction gradient trajectories and unsteady flamelet analysis in turbulent non-premixed combustion. Combustion and Flame, 175, 243-258.

-Munters, W., & Meyers, J. (2017). An optimal control framework for dynamic induction control of wind farms and their interaction with the atmospheric boundary layer. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 375(2091), 20160100.

-Jiang, Y., & Chen, J. Z. (2016). Theories for Polymer Melts Consisting of Rod–Coil Polymers. Self‐Assembling Systems: Theory and Simulation, 230-253.

-Duy, T. V. T., & Ozaki, T. (2016). Hybrid and 4-D FFT implementations of an open-source parallel FFT package OpenFFT. The Journal of Supercomputing, 72, 391-416.

-Boschung, J., Hennig, F., Gauding, M., Pitsch, H., & Peters, N. (2016). Generalised higher-order Kolmogorov scales. Journal of Fluid Mechanics, 794, 233-251.

-Song, S., & Hollingsworth, J. K. (2016). Computation–communication overlap and parameter auto-tuning for scalable parallel 3-D FFT. Journal of computational science, 14, 38-50.

-He, P. (2016). A high order finite difference solver for massively parallel simulations of stably stratified turbulent channel flows. Computers & Fluids, 127, 161-173.

-Jung, J., Kobayashi, C., Imamura, T., & Sugita, Y. (2016). Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations. Computer Physics Communications, 200, 57-65.

-Motheau, E., & Abraham, J. (2016). A high-order numerical algorithm for DNS of low-Mach-number reactive flows with detailed chemistry and quasi-spectral accuracy. Journal of Computational Physics, 313, 430-454.

-Nemati, H., Patel, A., Boersma, B. J., & Pecnik, R. (2016). The effect of thermal boundary conditions on forced convection heat transfer to fluids at supercritical pressure. Journal of Fluid Mechanics, 800, 531-556.

-Mortensen, M., & Langtangen, H. P. (2016). High performance Python for direct numerical simulations of turbulent flows. Computer Physics Communications, 203, 53-65.

-Gholami, A., Malhotra, D., Sundar, H., & Biros, G. (2016). FFT, FMM, or multigrid? A comparative study of state-of-the-art Poisson solvers for uniform and nonuniform grids in the unit cube. SIAM Journal on Scientific Computing, 38(3), C280-C306.

-Abdelsamie, A., Fru, G., Oster, T., Dietzsch, F., Janiga, G., & Thévenin, D. (2016). Towards direct numerical simulations of low-Mach number turbulent reacting and two-phase flows using immersed boundaries. Computers & Fluids, 131, 123-141.

-Boschung, J. (2015). Exact relations between the moments of dissipation and longitudinal velocity derivatives in turbulent flows. Physical Review E, 92(4), 043013.

-Ng, J., Wang, X., Singh, A. K., & Mak, T. (2015, March). Defrag: Defragmentation for efficient runtime resource allocation in noc-based many-core systems. In 2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (pp. 345-352). IEEE.

-Lirkov, I., Paprzycki, M., Ganzha, M., Sedukhin, S., & Gepner, P. (2014, September). Performance analysis of a scalable algorithm for 3D linear transforms. In 2014 Federated Conference on Computer Science and Information Systems (pp. 613-622). IEEE.

-García‐Risueño, P., Alberdi‐Rodriguez, J., Oliveira, M. J., Andrade, X., Pippig, M., Muguerza, J., … & Rubio, A. (2014). A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations. Journal of computational chemistry, 35(6), 427-444.

-Gautier, R., Laizet, S., & Lamballais, E. (2014). A DNS study of jet control with microjets using an immersed boundary method. International Journal of Computational Fluid Dynamics, 28(6-10), 393-410.

-Wei, F., & Yılmaz, A. E. (2013). A more scalable and efficient parallelization of the adaptive integral method—Part I: Algorithm. IEEE Transactions on Antennas and Propagation, 62(2), 714-726.

-Pippig, M., & Potts, D. (2013). Parallel three-dimensional nonequispaced fast Fourier transforms and their application to particle simulation. SIAM Journal on Scientific Computing, 35(4), C411-C437.

-Pippig, M. (2013). PFFT: An extension of FFTW to massively parallel architectures. SIAM Journal on Scientific Computing, 35(3), C213-C236.

-Orozco, D., Garcia, E., Pavel, R., Ayala, O., Wang, L. P., & Gao, G. (2012). Demystifying Performance Predictions of Distributed FFT3D Implementations. In Network and Parallel Computing: 9th IFIP International Conference, NPC 2012, Gwangju, Korea, September 6-8, 2012. Proceedings 9 (pp. 196-207). Springer Berlin Heidelberg.

-Kriksin, Y. A., & Khalatur, P. G. (2012). Parallel algorithm for 3D SCF simulation of copolymers with flexible and rigid blocks. Macromolecular theory and simulations, 21(6), 382-399.

-Laizet, S., & Li, N. (2011). Incompact3d: A powerful tool to tackle turbulence problems with up to O (10^5) computational cores. International Journal for Numerical Methods in Fluids, 67(11), 1735-1757.