Computational Astrophysics and Cosmology最新文献

{"title":"On the parallelization of stellar evolution codes","authors":"David Martin,&nbsp;Jordi José,&nbsp;Richard Longland","doi":"10.1186/s40668-018-0025-5","DOIUrl":"https://doi.org/10.1186/s40668-018-0025-5","url":null,"abstract":"<p>Multidimensional nucleosynthesis studies with hundreds of nuclei linked through thousands of nuclear processes are still computationally prohibitive. To date, most nucleosynthesis studies rely either on hydrostatic/hydrodynamic simulations in spherical symmetry, or on post-processing simulations using temperature and density versus time profiles directly linked to huge nuclear reaction networks.</p><p>Parallel computing has been regarded as the main permitting factor of computationally intensive simulations. This paper explores the different pros and cons in the parallelization of stellar codes, providing recommendations on when and how parallelization may help in improving the performance of a code for astrophysical applications.</p><p>We report on different parallelization strategies succesfully applied to the spherically symmetric, Lagrangian, implicit hydrodynamic code <span>SHIVA</span>, extensively used in the modeling of classical novae and type I X-ray bursts.</p><p>When only matrix build-up and inversion processes in the nucleosynthesis subroutines are parallelized (a suitable approach for post-processing calculations), the huge amount of time spent on communications between cores, together with the small problem size (limited by the number of isotopes of the nuclear network), result in a much worse performance of the parallel application compared to the 1-core, sequential version of the code. Parallelization of the matrix build-up and inversion processes in the nucleosynthesis subroutines is not recommended unless the number of isotopes adopted largely exceeds 10,000.</p><p>In sharp contrast, speed-up factors of 26 and 35 have been obtained with a parallelized version of <span>SHIVA</span>, in a 200-shell simulation of a type I X-ray burst carried out with two nuclear reaction networks: a reduced one, consisting of 324 isotopes and 1392 reactions, and a more extended network with 606 nuclides and 3551 nuclear interactions. Maximum speed-ups of ～41 (324-isotope network) and ～85 (606-isotope network), are also predicted for 200 cores, stressing that the number of shells of the computational domain constitutes an effective upper limit for the maximum number of cores that could be used in a parallel application.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"5 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2018-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-018-0025-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4659116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A MODEST review","authors":"Anna Lisa Varri,&nbsp;Maxwell Xu Cai,&nbsp;Francisca Concha-Ramírez,&nbsp;František Dinnbier,&nbsp;Nora Lützgendorf,&nbsp;Václav Pavlík,&nbsp;Sara Rastello,&nbsp;Antonio Sollima,&nbsp;Long Wang,&nbsp;Alice Zocchi","doi":"10.1186/s40668-018-0024-6","DOIUrl":"https://doi.org/10.1186/s40668-018-0024-6","url":null,"abstract":"<p>We present an account of the state of the art in the fields explored by the research community invested in “Modeling and Observing DEnse STellar systems”. For this purpose, we take as a basis the activities of the MODEST-17 conference, which was held at Charles University, Prague, in September 2017. Reviewed topics include recent advances in fundamental stellar dynamics, numerical methods for the solution of the gravitational <i>N</i>-body problem, formation and evolution of young and old star clusters and galactic nuclei, their elusive stellar populations, planetary systems, and exotic compact objects, with timely attention to black holes of different classes of mass and their role as sources of gravitational waves.</p><p>Such a breadth of topics reflects the growing role played by collisional stellar dynamics in numerous areas of modern astrophysics. Indeed, in the next decade many revolutionary instruments will enable the derivation of positions and velocities of individual stars in the Milky Way and its satellites, and will detect signals from a range of astrophysical sources in different portions of the electromagnetic and gravitational spectrum, with an unprecedented sensitivity. On the one hand, this wealth of data will allow us to address a number of long-standing open questions in star cluster studies; on the other hand, many unexpected properties of these systems will come to light, stimulating further progress of our understanding of their formation and evolution.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"5 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2018-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-018-0024-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4596444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Entropy-limited hydrodynamics: a novel approach to relativistic hydrodynamics","authors":"Federico Guercilena,&nbsp;David Radice,&nbsp;Luciano Rezzolla","doi":"10.1186/s40668-017-0022-0","DOIUrl":"https://doi.org/10.1186/s40668-017-0022-0","url":null,"abstract":"<p>We present entropy-limited hydrodynamics (ELH): a new approach for the computation of numerical fluxes arising in the discretization of hyperbolic equations in conservation form. ELH is based on the hybridisation of an unfiltered high-order scheme with the first-order Lax-Friedrichs method. The activation of the low-order part of the scheme is driven by a measure of the locally generated entropy inspired by the artificial-viscosity method proposed by Guermond et al. (J.?Comput. Phys. 230(11):4248-4267, 2011, doi:10.1016/j.jcp.2010.11.043). Here, we present ELH in the context of high-order finite-differencing methods and of the equations of general-relativistic hydrodynamics. We study the performance of ELH in a series of classical astrophysical tests in general relativity involving isolated, rotating and nonrotating neutron stars, and including a case of gravitational collapse to black hole. We present a detailed comparison of ELH with the fifth-order monotonicity preserving method MP5 (Suresh and Huynh in J.?Comput. Phys. 136(1):83-99, 1997, doi:10.1006/jcph.1997.5745), one of the most common high-order schemes currently employed in numerical-relativity simulations. We find that ELH achieves comparable and, in many of the cases studied here, better accuracy than more traditional methods at a fraction of the computational cost (up to <span>({sim}50%)</span> speedup). Given its accuracy and its simplicity of implementation, ELH is a promising framework for the development of new special- and general-relativistic hydrodynamics codes well adapted for massively parallel supercomputers.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"4 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2017-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-017-0022-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4163780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PKDGRAV3: beyond trillion particle cosmological simulations for the next era of galaxy surveys","authors":"Douglas Potter,&nbsp;Joachim Stadel,&nbsp;Romain Teyssier","doi":"10.1186/s40668-017-0021-1","DOIUrl":"https://doi.org/10.1186/s40668-017-0021-1","url":null,"abstract":"<p>We report on the successful completion of a 2 trillion particle cosmological simulation to <span>(z=0)</span> run on the Piz Daint supercomputer (CSCS, Switzerland), using 4000+ GPU nodes for a little less than 80?h of wall-clock time or 350,000 node hours. Using multiple benchmarks and performance measurements on the US Oak Ridge National Laboratory Titan supercomputer, we demonstrate that our code PKDGRAV3, delivers, to our knowledge, the fastest time-to-solution for large-scale cosmological <i>N</i>-body simulations. This was made possible by using the Fast Multipole Method in conjunction with individual and adaptive particle time steps, both deployed efficiently (and for the first time) on supercomputers with GPU-accelerated nodes. The very low memory footprint of PKDGRAV3 allowed us to run the first ever benchmark with 8 trillion particles on Titan, and to achieve perfect scaling up to 18,000 nodes and a peak performance of 10 Pflops.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"4 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2017-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-017-0021-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"5023861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The black hole accretion code","authors":"Oliver Porth,&nbsp;Hector Olivares,&nbsp;Yosuke Mizuno,&nbsp;Ziri Younsi,&nbsp;Luciano Rezzolla,&nbsp;Monika Moscibrodzka,&nbsp;Heino Falcke,&nbsp;Michael Kramer","doi":"10.1186/s40668-017-0020-2","DOIUrl":"https://doi.org/10.1186/s40668-017-0020-2","url":null,"abstract":"<p>We present the black hole accretion code (<span>BHAC</span>), a new multidimensional general-relativistic magnetohydrodynamics module for the <span>MPI-AMRVAC</span>?framework. <span>BHAC</span> has been designed to solve the equations of ideal general-relativistic magnetohydrodynamics in arbitrary spacetimes and exploits adaptive mesh refinement techniques with an efficient block-based approach. Several spacetimes have already been implemented and tested. We demonstrate the validity of <span>BHAC</span> by means of various one-, two-, and three-dimensional test problems, as well as through a close comparison with the <span>HARM3D</span>?code in the case of a torus accreting onto a black hole. The convergence of a turbulent accretion scenario is investigated with several diagnostics and we find accretion rates and horizon-penetrating fluxes to be convergent to within a few percent when the problem is run in three dimensions. Our analysis also involves the study of the corresponding thermal synchrotron emission, which is performed by means of a new general-relativistic radiative transfer code, <span>BHOSS</span>. The resulting synthetic intensity maps of accretion onto black holes are found to be convergent with increasing resolution and are anticipated to play a crucial role in the interpretation of horizon-scale images resulting from upcoming radio observations of the source at the Galactic Center.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"4 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2017-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-017-0020-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4136169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The evolution of hierarchical triple star-systems","authors":"Silvia Toonen,&nbsp;Adrian Hamers,&nbsp;Simon Portegies Zwart","doi":"10.1186/s40668-016-0019-0","DOIUrl":"https://doi.org/10.1186/s40668-016-0019-0","url":null,"abstract":"<p>Field stars are frequently formed in pairs, and many of these binaries are part of triples or even higher-order systems. Even though, the principles of single stellar evolution and binary evolution, have been accepted for a long time, the long-term evolution of stellar triples is poorly understood. The presence of a third star in an orbit around a binary system can significantly alter the evolution of those stars and the binary system. The rich dynamical behaviour in three-body systems can give rise to Lidov-Kozai cycles, in which the eccentricity of the inner orbit and the inclination between the inner and outer orbit vary periodically. In turn, this can lead to an enhancement of tidal effects (tidal friction), gravitational-wave emission and stellar interactions such as mass transfer and collisions. The lack of a self-consistent treatment of triple evolution, including both three-body dynamics as well as stellar evolution, hinders the systematic study and general understanding of the long-term evolution of triple systems. In this paper, we aim to address some of these hiatus, by discussing the dominant physical processes of hierarchical triple evolution, and presenting heuristic recipes for these processes. To improve our understanding on hierarchical stellar triples, these descriptions are implemented in a public source code <span>TrES</span>, which combines three-body dynamics (based on the secular approach) with stellar evolution and their mutual influences. Note that modelling through a phase of stable mass transfer in an eccentric orbit is currently not implemented in <span>TrES</span>, but can be implemented with the appropriate methodology at a later stage.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"3 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2016-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-016-0019-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4886393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Riemann solvers and Alfven waves in black hole magnetospheres","authors":"Brian Punsly,&nbsp;Dinshaw Balsara,&nbsp;Jinho Kim,&nbsp;Sudip Garain","doi":"10.1186/s40668-016-0018-1","DOIUrl":"https://doi.org/10.1186/s40668-016-0018-1","url":null,"abstract":"<p>In the magnetosphere of a rotating black hole, an inner Alfven critical surface (IACS) must be crossed by inflowing plasma. Inside the IACS, Alfven waves are inward directed toward the black hole. The majority of the proper volume of the active region of spacetime (the ergosphere) is inside of the IACS. The charge and the totally transverse momentum flux (the momentum flux transverse to both the wave normal and the unperturbed magnetic field) are both determined exclusively by the Alfven polarization. Thus, it is important for numerical simulations of black hole magnetospheres to minimize the dissipation of Alfven waves. Elements of the dissipated wave emerge in adjacent cells regardless of the IACS, there is no mechanism to prevent Alfvenic information from crossing outward. Thus, numerical dissipation can affect how simulated magnetospheres attain the substantial Goldreich-Julian charge density associated with the rotating magnetic field. In order to help minimize dissipation of Alfven waves in relativistic numerical simulations we have formulated a one-dimensional Riemann solver, called HLLI, which incorporates the Alfven discontinuity and the contact discontinuity. We have also formulated a multidimensional Riemann solver, called MuSIC, that enables low dissipation propagation of Alfven waves in multiple dimensions. The importance of higher order schemes in lowering the numerical dissipation of Alfven waves is also catalogued.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"3 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2016-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-016-0018-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4556230","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In situ and in-transit analysis of cosmological simulations","authors":"Brian Friesen,&nbsp;Ann Almgren,&nbsp;Zarija Lukić,&nbsp;Gunther Weber,&nbsp;Dmitriy Morozov,&nbsp;Vincent Beckner,&nbsp;Marcus Day","doi":"10.1186/s40668-016-0017-2","DOIUrl":"https://doi.org/10.1186/s40668-016-0017-2","url":null,"abstract":"<p>Modern cosmological simulations have reached the trillion-element scale, rendering data storage and subsequent analysis formidable tasks. To address this circumstance, we present a new MPI-parallel approach for analysis of simulation data while the simulation runs, as an alternative to the traditional workflow consisting of periodically saving large data sets to disk for subsequent ‘offline’ analysis. We demonstrate this approach in the compressible gasdynamics/<i>N</i>-body code Nyx, a hybrid <span>(mbox{MPI}+mbox{OpenMP})</span> code based on the BoxLib framework, used for large-scale cosmological simulations. We have enabled on-the-fly workflows in two different ways: one is a straightforward approach consisting of all MPI processes periodically halting the main simulation and analyzing each component of data that they own (‘<i>in situ</i>’). The other consists of partitioning processes into disjoint MPI groups, with one performing the simulation and periodically sending data to the other ‘sidecar’ group, which post-processes it while the simulation continues (‘in-transit’). The two groups execute their tasks asynchronously, stopping only to synchronize when a new set of simulation data needs to be analyzed. For both the <i>in situ</i> and in-transit approaches, we experiment with two different analysis suites with distinct performance behavior: one which finds dark matter halos in the simulation using merge trees to calculate the mass contained within iso-density contours, and another which calculates probability distribution functions and power spectra of various fields in the simulation. Both are common analysis tasks for cosmology, and both result in summary statistics significantly smaller than the original data set. We study the behavior of each type of analysis in each workflow in order to determine the optimal configuration for the different data analysis algorithms.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"3 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2016-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-016-0017-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4918935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Achieving convergence in galaxy formation models by augmenting N-body merger trees","authors":"Andrew J Benson,&nbsp;Chris Cannella,&nbsp;Shaun Cole","doi":"10.1186/s40668-016-0016-3","DOIUrl":"https://doi.org/10.1186/s40668-016-0016-3","url":null,"abstract":"<p>Accurate modeling of galaxy formation in a hierarchical, cold dark matter universe requires the use of sufficiently high-resolution merger trees to obtain convergence in the predicted properties of galaxies. When semi-analytic galaxy formation models are applied to cosmological <i>N</i>-body simulation merger trees, it is often the case that those trees have insufficient resolution to give converged galaxy properties. We demonstrate a method to augment the resolution of <i>N</i>-body merger trees by grafting in branches of Monte Carlo merger trees with higher resolution, but which are consistent with the pre-existing branches in the <i>N</i>-body tree. We show that this approach leads to converged galaxy properties.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"3 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2016-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-016-0016-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4847779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulations of stripped core-collapse supernovae in close binaries","authors":"Alex Rimoldi,&nbsp;Simon Portegies Zwart,&nbsp;Elena Maria Rossi","doi":"10.1186/s40668-016-0015-4","DOIUrl":"https://doi.org/10.1186/s40668-016-0015-4","url":null,"abstract":"<p>We perform smoothed-particle hydrodynamical simulations of the explosion of a helium star in a close binary system, and study the effects of the explosion on the companion star as well as the effect of the presence of the companion on the supernova remnant. By simulating the mechanism of the supernova from just after core bounce until the remnant shell passes the stellar companion, we are able to separate the various phenomena leading to the final system parameters. In the final system, we measure the mass stripping and ablation from, and the additional velocity imparted to, the companion stars. Our results agree with recent work showing smaller values for these quantities compared to earlier estimates. We do find some differences, however, particularly in the velocity gained by the companion, which can be explained by the different ejecta structure that naturally results from the explosion in our simulations. These results indicate that predictions based on extrapolated Type?Ia simulations should be revised. We also examine the structure of the supernova ejecta shell. The presence of the companion star produces a conical cavity in the expanding supernova remnant, and loss of material from the companion causes the supernova remnant to be more metal-rich on one side and more hydrogen-rich (from the companion material) around the cavity. Following the impact of the shell, we examine the state of the companion after being heated by the shock.</p>","PeriodicalId":523,"journal":{"name":"Computational Astrophysics and Cosmology","volume":"3 1","pages":""},"PeriodicalIF":16.281,"publicationDate":"2016-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40668-016-0015-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4040844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}