{"title":"GPU-friendly data structures for real time simulation.","authors":"Vincent Magnoux, Benoît Ozell","doi":"10.1186/s40323-021-00192-7","DOIUrl":"https://doi.org/10.1186/s40323-021-00192-7","url":null,"abstract":"<p><p>Simulators for virtual surgery training need to perform complex calculations very quickly to provide realistic haptic and visual interactions with a user. The complexity is further increased by the addition of cuts to virtual organs, such as would be needed for performing tumor resection. A common method for achieving large performance improvements is to make use of the graphics hardware (GPU) available on most general-use computers. Programming GPUs requires data structures that are more rigid than on conventional processors (CPU), making that data more difficult to update. We propose a new method for structuring graph data, which is commonly used for physically based simulation of soft tissue during surgery, and deformable objects in general. Our method aligns all nodes of the graph in memory, independently from the number of edges they contain, allowing for local modifications that do not affect the rest of the structure. Our method also groups memory transfers so as to avoid updating the entire graph every time a small cut is introduced in a simulated organ. We implemented our data structure as part of a simulator based on a meshless method. Our tests show that the new GPU implementation, making use of the new graph structure, achieves a 10 times improvement in computation times compared to the previous CPU implementation. The grouping of data transfers into batches allows for a 80-90% reduction in the amount of data transferred for each graph update, but accounts only for a small improvement in performance. The data structure itself is simple to implement and allows simulating increasingly complex models that can be cut at interactive rates.</p>","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":"8 1","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40323-021-00192-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39877312","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}
Felix K. Schwab, A. Reiter, C. Herrmann, D. Schneider, B. Nestler
{"title":"Phase-inherent linear visco-elasticity model for infinitesimal deformations in the multiphase-field context","authors":"Felix K. Schwab, A. Reiter, C. Herrmann, D. Schneider, B. Nestler","doi":"10.1186/s40323-020-00178-x","DOIUrl":"https://doi.org/10.1186/s40323-020-00178-x","url":null,"abstract":"","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":"7 1","pages":"1-32"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40323-020-00178-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41981591","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}
B. Wassermann, N. Korshunova, S. Kollmannsberger, E. Rank, G. Elber
{"title":"Finite cell method for functionally graded materials based on V-models and homogenized microstructures","authors":"B. Wassermann, N. Korshunova, S. Kollmannsberger, E. Rank, G. Elber","doi":"10.1186/s40323-020-00182-1","DOIUrl":"https://doi.org/10.1186/s40323-020-00182-1","url":null,"abstract":"","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40323-020-00182-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47530096","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}
C. Kruse, V. Darrigrand, N. Tardieu, M. Arioli, U. Rüde
{"title":"Application of an iterative Golub-Kahan algorithm to structural mechanics problems with multi-point constraints","authors":"C. Kruse, V. Darrigrand, N. Tardieu, M. Arioli, U. Rüde","doi":"10.1186/s40323-020-00181-2","DOIUrl":"https://doi.org/10.1186/s40323-020-00181-2","url":null,"abstract":"","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43310039","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}
Hailu Shimels Gebremedhen, D. Woldemichael, F. M. Hashim
{"title":"A firefly algorithm based hybrid method for structural topology optimization","authors":"Hailu Shimels Gebremedhen, D. Woldemichael, F. M. Hashim","doi":"10.1186/s40323-020-00183-0","DOIUrl":"https://doi.org/10.1186/s40323-020-00183-0","url":null,"abstract":"","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40323-020-00183-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47358737","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}
Hanane Khatouri, T. Benamara, P. Breitkopf, Jean Demange, Paul Feliot
{"title":"Constrained multi-fidelity surrogate framework using Bayesian optimization with non-intrusive reduced-order basis","authors":"Hanane Khatouri, T. Benamara, P. Breitkopf, Jean Demange, Paul Feliot","doi":"10.1186/s40323-020-00176-z","DOIUrl":"https://doi.org/10.1186/s40323-020-00176-z","url":null,"abstract":"","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40323-020-00176-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65853563","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":"Compressible flow simulation with moving geometries using the Brinkman penalization in high-order Discontinuous Galerkin","authors":"N. E. Pour, Anand Nikhil, H. Klimach, S. Roller","doi":"10.21203/rs.3.rs-93466/v1","DOIUrl":"https://doi.org/10.21203/rs.3.rs-93466/v1","url":null,"abstract":"In this work we investigate the Brinkman volume penalization technique in the context of a high-order Discontinous Galerkin method to model moving wall boundaries for compressible fluid flow simulations. High-order approximations are especially of interest as they require few degrees of freedom to represent smooth solutions accurately. This reduced memory consumption is attractive on modern computing systems where the memory bandwidth is a limiting factor. Due to their low dissipation and dispersion they are also of particular interest for aeroacoustic problems. However, a major problem for the high-order discretization is the appropriate representation of wall geometries. In this work we look at the Brinkman penalization technique, which addresses this problem and allows the representation of geometries without modifying the computational mesh. The geometry is modelled as an artificial porous medium and embedded in the equations. As the mesh is independent of the geometry with this method, it is not only well suited for high-order discretizations but also for problems where the obstacles are moving. We look into the deployment of this strategy by briefly discussing the Brinkman penalization technique and its application in our solver and investigate its behavior in fundamental one-dimensional setups, such as shock reflection at a moving wall and the formation of a shock in front of a piston. This is followed by the application to setups with two and three dimensions, illustrating the method in the presence of curved surfaces.","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":"8 1","pages":"1-23"},"PeriodicalIF":0.0,"publicationDate":"2020-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67971151","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":"Computational homogenization of transient chemo-mechanical processes based on a variational minimization principle","authors":"E. Polukhov, Marc‐André Keip","doi":"10.1186/s40323-020-00161-6","DOIUrl":"https://doi.org/10.1186/s40323-020-00161-6","url":null,"abstract":"","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40323-020-00161-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65853006","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":"Correction to: Enhanced numerical integration scheme based on image-compression techniques: application to fictitious domain methods","authors":"Márton Petö, F. Duvigneau, Sascha Eisenträger","doi":"10.1186/s40323-020-00165-2","DOIUrl":"https://doi.org/10.1186/s40323-020-00165-2","url":null,"abstract":"","PeriodicalId":37424,"journal":{"name":"Advanced Modeling and Simulation in Engineering Sciences","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40323-020-00165-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65853367","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}