MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

RepFlow: Minimizing Flow Completion Times with Replicated Flows in Data Centers

Short TCP flows that are critical for many interactive applications in data centers are plagued by large flows and head-of-line blocking in switches. Hash-based load balancing schemes such as ECMP aggravate the matter and result in long-tailed flow completion times (FCT). Previous work on reducing FCT usually requires custom switch hardware and/or protocol changes. We propose RepFlow, a simple yet practically effective approach that replicates each short flow to reduce the completion times, without any change to switches or host kernels. With ECMP the original and replicated flows traverse distinct paths with different congestion levels, thereby reducing the probability of having long queueing delay. We develop a simple analytical model to demonstrate the potential improvement of RepFlow. Extensive NS-3 simulations and Mininet implementation show that RepFlow provides 50%--70% speedup in both mean and 99-th percentile FCT for all loads, and offers near-optimal FCT when used with DCTCP.Comment: To appear in IEEE INFOCOM 201

On the Modeling of Correct Service Flows with BPEL4WS

Frameworks for composing Web Services offer a promising approach for realizing enterprise-wide and cross-organizational business applications. With BPEL4WS a powerful composition language exists. BPEL implementations allow orchestrating complex, stateful interactions among Web Services in a process-oriented way. One important task in this context is to ensure that respective flow specifications can be correctly processed, i.e., there will be no bad surprises (e.g., deadlocks, invocation of service operations with missing input data) at runtime. In this paper we subdivide BPEL schemes into different classes and discuss to which extent instances of these classes can be analyzed for the absence of control flow errors and inconsistencies. Altogether our work shall contribute to a more systematic evolution of the BPEL standard instead of overloading it with too many features

Dataplane Specialization for High-performance OpenFlow Software Switching

OpenFlow is an amazingly expressive dataplane program- ming language, but this expressiveness comes at a severe performance price as switches must do excessive packet clas- sification in the fast path. The prevalent OpenFlow software switch architecture is therefore built on flow caching, but this imposes intricate limitations on the workloads that can be supported efficiently and may even open the door to mali- cious cache overflow attacks. In this paper we argue that in- stead of enforcing the same universal flow cache semantics to all OpenFlow applications and optimize for the common case, a switch should rather automatically specialize its dat- aplane piecemeal with respect to the configured workload. We introduce ES WITCH , a novel switch architecture that uses on-the-fly template-based code generation to compile any OpenFlow pipeline into efficient machine code, which can then be readily used as fast path. We present a proof- of-concept prototype and we demonstrate on illustrative use cases that ES WITCH yields a simpler architecture, superior packet processing speed, improved latency and CPU scala- bility, and predictable performance. Our prototype can eas- ily scale beyond 100 Gbps on a single Intel blade even with complex OpenFlow pipelines

A case study for NoC based homogeneous MPSoC architectures

The many-core design paradigm requires flexible and modular hardware and software components to provide the required scalability to next-generation on-chip multiprocessor architectures. A multidisciplinary approach is necessary to consider all the interactions between the different components of the design. In this paper, a complete design methodology that tackles at once the aspects of system level modeling, hardware architecture, and programming model has been successfully used for the implementation of a multiprocessor network-on-chip (NoC)-based system, the NoCRay graphic accelerator. The design, based on 16 processors, after prototyping with field-programmable gate array (FPGA), has been laid out in 90-nm technology. Post-layout results show very low power, area, as well as 500 MHz of clock frequency. Results show that an array of small and simple processors outperform a single high-end general purpose processo