Accelerating 3D Cellular Automata Computation with GP GPU in the Context of Integrative Biology

In this paper we explore the possibility of using GP GPU technology (General Purpose Graphical Processing Unit) in the context of integrative biology. For more than a decade, 3D cellular automata represent a promising approach to handling multi-scale modeling of organs. However, the computing time of such huge automata has limited the experiments. Current GP GPUs now allow the execution of hundreds of threads with a regular PC hosting a device card. This capability can be exploited in the case of cellular automata where each cell has to compute the same algorithm. We have implemented two algorithms to compare different memory usage. The performances show very significant speedup even when compared to the latest CPU processors. The interconnection of GP GPU boards and servers will be considered to build a local grid of hybrid machines

Warp-Level Parallelism: Enabling Multiple Replications In Parallel on GPU

Best paper awardInternational audienceStochastic simulations need multiple replications in order to build confidence intervals for their results. Even if we do not need a large amount of replications, it is a good practice to speed-up the whole simulation time using the Multiple Replications In Parallel (MRIP) approach. This approach usually supposes to have access to a parallel computer such as a symmetric mul-tiprocessing machine (with many cores), a computing cluster or a computing grid. In this paper, we propose Warp-Level Parallelism (WLP), a GP-GPU-enabled solution to compute MRIP on GP-GPUs (General-Purpose Graphics Processing Units). These devices display a great amount of parallel computational power at low cost, but are tuned to process efficiently the same operation on several data, through different threads. Indeed, this paradigm is called Single Instruction, Multiple Threads (SIMT). Our approach proposes to rely on small threads groups, called warps, to perform independent computations such as replications. We have benchmarked WLP with three different models: it allows MRIP to be computed up to six times faster than with the SIMT computing paradigm

Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses

Harnessing Aspect Oriented Programming on GPU: Application to Warp-Level Parallelism (WLP)

International audienceStochastic simulations involve multiple replications in order to build confidenceintervals for their results, and Designs Of Experiments (DOEs) to explore their parameters set. Inthis paper, we propose Warp-Level Parallelism (WLP), a GPU-enabled solution to compute MultipleReplications In Parallel (MRIP) on GPUs (Graphics Processing Units). GPUs are intrinsicallytuned to process efficiently the same operation on several data, which is not suited to parallelizeMRIP or DOEs. Our approach proposes to rely on small thread groups, called warps, to performindependent computations such as replications. This approach has proved to be efficient on threeclassical simulation models, but originally lacked the transparency users might expect. In thiswork, we enhance WLP using Aspect Oriented Programming (AOP). Our work describes the wayto combine CUDA and AOP, and brings forward the techniques available to exploit AOP in aCUDA-enabled development