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Implementing Parallel Differential Evolution on Spark
(Springer, 2016-04-02)
[Abstract] Metaheuristics are gaining increased attention as an efficient way of solving hard global optimization problems. Differential Evolution (DE) is one of the most popular algorithms in that class. However, its ...
Resilient MPI applications using an application-level checkpointing framework and ULFM
(Springer New York LLC, 2017-01)
[Abstract] Future exascale systems, formed by millions of cores, will present high failure rates, and long-running applications will need to make use of new fault tolerance techniques to ensure successful execution completion. ...
Analysis of Performance-impacting Factors on Checkpointing Frameworks: The CPPC Case Study
(Oxford University Press, 2011-11-01)
[Abstract] This paper focuses on the performance evaluation of Compiler for Portable Checkpointing (CPPC), a tool for the checkpointing of parallel message-passing applications. Its performance and the factors that impact ...
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
(BioMed Central Ltd., 2017)
[Abstract]
Background
The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear ...
Improving Scalability of Application-Level Checkpoint-Recovery by Reducing Checkpoint Sizes
(Springer Japan KK, 2013)
[Abstract] The execution times of large-scale parallel applications on nowadays multi/many-core systems are usually longer than the mean time between failures. Therefore, parallel applications must tolerate hardware failures ...
A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology
(Public Library of Science, 2017)
[Abstract]
Background:
We consider a general class of global optimization problems dealing with nonlinear dynamic models. Although this class is relevant to many areas of science and engineering, here we are interested ...
Assessing resilient versus stop-and-restart fault-tolerant solutions in MPI applications
(Springer New York LLC, 2017-01)
[Abstract] The Message Passing Interface (MPI) standard is the most popular parallel programming model for distributed systems. However, it lacks fault-tolerance support and, traditionally, failures are addressed with ...
Enhanced parallel Differential Evolution algorithm for problems in computational systems biology
(Elsevier BV, 2015)
[Abstract] Many key problems in computational systems biology and bioinformatics can be formulated and solved using a global optimization framework. The complexity of the underlying mathematical models require the use of ...
Reducing the overhead of an MPI application-level migration approach
(Elsevier BV * North-Holland, 2016)
[Abstract] Process migration provides many benefits for parallel environments including dynamic load balance, data access locality, or fault tolerance. This work proposes a solution that reduces the memory and I/O overhead ...
Towards cloud-based parallel metaheuristics: A case study in computational biology with Differential Evolution and Spark
(Sage Publications Ltd., 2016-11-28)
[Abstract]
Many key problems in science and engineering can be formulated and solved using global optimization techniques. In the particular case of computational biology, the development of dynamic (kinetic) models is ...