The TChem open-source software is a toolkit for computing thermodynamic properties, source term, and source term’s Jacobian matrix for chemical kinetic models that involve gas and surface reactions.
CSPlib is an open source software library for analyzing general ordinary differential equation (ODE) systems and detailed chemical kinetic ODE/DAE systems. It relies on the computational singular perturbation (CSP) method for the analysis of these systems.
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Combustion Theory and Modelling
We have extended the computational singular perturbation (CSP) method to differential algebraic equation (DAE) systems and demonstrated its application in a heterogeneous-catalysis problem. The extended method obtains the CSP basis vectors for DAEs from a reduced Jacobian matrix that takes the algebraic constraints into account. We use a canonical problem in heterogeneous catalysis, the transient continuous stirred tank reactor (T-CSTR), for illustration. The T-CSTR problem is modelled fundamentally as an ordinary differential equation (ODE) system, but it can be transformed to a DAE system if one approximates typically fast surface processes using algebraic constraints for the surface species. We demonstrate the application of CSP analysis for both ODE and DAE constructions of a T-CSTR problem, illustrating the dynamical response of the system in each case. We also highlight the utility of the analysis in commenting on the quality of any particular DAE approximation built using the quasi-steady state approximation (QSSA), relative to the ODE reference case.
CSPlib is an open source software library for analyzing general ordinary differential equation (ODE) systems and detailed chemical kinetic ODE systems. It relies on the computational singular perturbation (CSP) method for the analysis of these systems. The software provides support for: General ODE models (gODE model class) for computing source terms and Jacobians for a generic ODE system; TChem model (ChemElemODETChem model class) for computing source term, Jacobian, other necessary chemical reaction data, as well as the rates of progress for a homogenous batch reactor using an elementary step detailed chemical kinetic reaction mechanism. This class relies on the TChem [2] library; A set of functions to compute essential elements of CSP analysis (Kernel class). This includes computations of the eigensolution of the Jacobian matrix, CSP basis vectors and co-vectors, time scales (reciprocals of the magnitudes of the Jacobian eigenvalues), mode amplitudes, CSP pointers, and the number of exhausted modes. This class relies on the Tines library; A set of functions to compute the eigensolution of the Jacobian matrix using Tines library GPU eigensolver; A set of functions to compute CSP indices (Index Class). This includes participation indices and both slow and fast importance indices.
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2019 IEEE High Performance Extreme Computing Conference, HPEC 2019
In this work we present a performance exploration on Eager K-truss, a linear-algebraic formulation of the K-truss graph algorithm. We address performance issues related to load imbalance of parallel tasks in symmetric, triangular graphs by presenting a fine-grained parallel approach to executing the support computation. This approach also increases available parallelism, making it amenable to GPU execution. We demonstrate our fine-grained parallel approach using implementations in Kokkos and evaluate them on an Intel Skylake CPU and an Nvidia Tesla V100 GPU. Overall, we observe between a 1.261. 48x improvement on the CPU and a 9.97-16.92x improvement on the GPU due to our fine-grained parallel formulation.
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Proceedings - 2018 IEEE 32nd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2018
We present a memory-scalable, parallel, sparse multifrontal solver for solving symmetric postive-definite systems arising in scientific and engineering applications. Factorizing sparse matrices requires memory for both the computed factors and the temporary workspaces for computing each frontal matrix - a data structure commonly used within multifrontal methods. To factorize multiple frontal matrices in parallel, the conventional approach is to allocate a uniform workspace for each hardware thread. In the manycore era, this results in increasing memory usage proportional to the number of hardware threads. We remedy this problem by using dynamic task parallelism with a scalable memory pool. Tasks are spawned while traversing an assembly tree and executed after their dependences are satisfied. We also use an idea to respawn the tasks when certain conditions are not met. Temporary workspace for frontal matrices in each task is allocated from a memory pool designed by us. If the requested memory space is not available in the memory pool, the task is respawned to yield the hardware thread to execute other tasks. The respawned task is executed after high priority tasks are executed. This approach allows to have robust parallel performance within a bounded memory space. Experimental results demonstrate the merits of our implementation on Intel multicore and manycore architectures.
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