A Framework to Analyze the Performance of Load Balancing Schemes for Ensembles of Stochastic Simulations

Ensembles of simulations are employed to estimate the statistics of possible future states of a system, and are widely used in important applications such as climate change and biological modeling. Ensembles of runs can naturally be executed in parallel. However, when the CPU times of individual simulations vary considerably, a simple strategy of assigning an equal number of tasks per processor can lead to serious work imbalances and low parallel efficiency. This paper presents a new probabilistic framework to analyze the performance of dynamic load balancing algorithms for ensembles of simulations where many tasks are mapped onto each processor, and where the individual compute times vary considerably among tasks. Four load balancing strategies are discussed: most-dividing, all-redistribution, random-polling, and neighbor-redistribution. Simulation results with a stochastic budding yeast cell cycle model is consistent with the theoretical analysis. It is especially significant that there is a provable global decrease in load imbalance for the local rebalancing algorithms due to scalability concerns for the global rebalancing algorithms. The overall simulation time is reduced by up to 25%, and the total processor idle time by 85%

Abstract State Machines 1988-1998: Commented ASM Bibliography

An annotated bibliography of papers which deal with or use Abstract State Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm

Parallel Load Balancing Strategies for Ensembles of Stochastic Biochemical Simulations

The evolution of biochemical systems where some chemical species are present with only a small number of molecules, is strongly influenced by discrete and stochastic effects that cannot be accurately captured by continuous and deterministic models. The budding yeast cell cycle provides an excellent example of the need to account for stochastic effects in biochemical reactions. To obtain statistics of the cell cycle progression, a stochastic simulation algorithm must be run thousands of times with different initial conditions and parameter values. In order to manage the computational expense involved, the large ensemble of runs needs to be executed in parallel. The CPU time for each individual task is unknown before execution, so a simple strategy of assigning an equal number of tasks per processor can lead to considerable work imbalances and loss of parallel efficiency. Moreover, deterministic analysis approaches are ill suited for assessing the effectiveness of load balancing algorithms in this context. Biological models often require stochastic simulation. Since generating an ensemble of simulation results is computationally intensive, it is important to make efficient use of computer resources. This paper presents a new probabilistic framework to analyze the performance of dynamic load balancing algorithms when applied to large ensembles of stochastic biochemical simulations. Two particular load balancing strategies (point-to-point and all-redistribution) are discussed in detail. Simulation results with a stochastic budding yeast cell cycle model confirm the theoretical analysis. While this work is motivated by cell cycle modeling, the proposed analysis framework is general and can be directly applied to any ensemble simulation of biological systems where many tasks are mapped onto each processor, and where the individual compute times vary considerably among tasks

Polynomial Response Surface Approximations for the Multidisciplinary Design Optimization of a High Speed Civil Transport

Surrogate functions have become an important tool in multidisciplinary design optimization to deal with noisy functions, high computational cost, and the practical difficulty of integrating legacy disciplinary computer codes. A combination of mathematical, statistical, and engineering techniques, well known in other contexts, have made polynomial surrogate functions viable for MDO. Despite the obvious limitations imposed by sparse high fidelity data in high dimensions and the locality of low order polynomial approximations, the success of the panoply of techniques based on polynomial response surface approximations for MDO shows that the implementation details are more important than the underlying approximation method (polynomial, spline, DACE, kernel regression, etc.). This paper surveys some of the ancillary techniques—statistics, global search, parallel computing, variable complexity modeling—that augment the construction and use of polynomial surrogates

A parallel Viterbi decoder for block cyclic and convolution codes

We present a parallel version of Viterbi's decoding procedure, for which we are able to demonstrate that the resultant task graph has restricted complexity in that the number of communications to or from any processor cannot exceed 4 for BCH codes. The resulting algorithm works in lock step making it suitable for implementation on a systolic processor array, which we have implemented on a field programmable gate array and demonstrate the perfect scaling of the algorithm for two exemplar BCH codes. The parallelisation strategy is applicable to all cyclic codes and convolution codes. We also present a novel method for generating the state transition diagrams for these codes