The primary objective of this dissertation is to design and develop high-performance algorithms and software for the simulation of soil-foundation-structure interaction on large soil domains using finite elements and mixed time integration on parallel computers. Second, the dissertation presents a preliminary study, conducted with numerical simulations, of the response of simplified structural models to near-fault, pulse-type ground motion for varying soil conditions. The development of a scalable and efficient finite element software, is based on the external loading computation, the element state determination, the mixed time integration scheme and its implementation, and finally the communication scheme and the solution phase. The object-oriented paradigm is used for the software design because it allows for usage of existing software components for the remaining parts of the software that are modified for performance and scalability reasons. The external loading computation uses a novel method of effective seismic input, the Domain Reduction Method, which requires processing of large data sets that represent the wave field used to generate the input forces. Specialized classes are developed to implement this loading pattern. Explicit time integration with diagonal mass matrices is selected for regions dominated by wave propagation because it does not require factorization of the dynamic stiffness matrix, it has a minimal memory footprint, and it is highly scalable. To analyze structures implicit time integration is needed, and therefore the coupled problem is solved using a mixed time integration algorithm that is extended to handle nonlinear systems in the implicit partition by combining it with Newton-Raphson iterations. The software design for this algorithm allows for various types of communication between the implicit and explicit partitions via subclassing and use of virtual methods, for example within the same address space, within the same communicator or between subcommunicators of a communicator. The communication scheme used by the explicit time integration solver is designed to be tunable depending on the problem size, number of processors, hardware platform and message passing library. An efficient numbering scheme is presented for general purpose finite element degree of freedom numbering which is almost embarassingly parallel. Two methods for setting up the communication graph are presented, one based on the all-to-all multicast and one based on the one-to-all multicast. The second part of the dissertation consists of computational simulations of the soil-foundation-structure-interaction response of simple structural models on large soil domains. Initially the response of a large, near-fault soil domain to low-frequency pulse-type input is studied, and then compared to broadband input. The soil simulation for low-frequency input is repeated for a softer soil profile and increased spatial variability over the surface of the soil domain is observed. The low-frequency input is used to shake the same soil volume with single simplified structural models for two and four second vibration period systems. The results indicate that the simplified soil-foundation-structure interaction closed-form solutions tend to overestimate the effects of this interaction as far as period lengthening and damping. For the four second period systems reduction of the effective damping is observed which is due to rocking. Significant variability on the permanent offsets of yielding structures which have the same fundamental elastic period of vibration is observed. The interaction in most cases reduces the structural deformations. Finally, ..