Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids

A parallel multidomain strategy to compute turbulent flows in fan-stirred closed vessels

This paper presents a parallel multidomain strategy to compute the turbulent flow in a closed vessel stirred by six fans. The method is based on running multiple instances of the same solver, working on different subdomains and communicating through small overlapping zones where interpolations allow to handle moving meshes. First the accuracy of this Multi Instances Solver Coupled on Overlapping Grids (MISCOG) approach is evaluated for the convection of a single vortex. Load balancing issues on parallel machines are discussed and a performance model is proposed to allocate cores to each code instance. Then, the method is applied to the LES of a closed vessel stirred by six fans. Mean and fluctuating fields obtained by the LES are compared to experimental data. Finally, the structure of the turbulence generated at the center of the vessel is studied and the mechanisms allowing turbulence to travel from the fans to the center of the vessel are analyzed

A Novel Workload Allocation Strategy for Batch Jobs

The distribution of computational tasks across a diverse set of geographically distributed heterogeneous resources is a critical issue in the realisation of true computational grids. Conventionally, workload allocation algorithms are divided into static and dynamic approaches. Whilst dynamic approaches frequently outperform static schemes, they usually require the collection and processing of detailed system information at frequent intervals - a task that can be both time consuming and unreliable in the real-world. This paper introduces a novel workload allocation algorithm for optimally distributing the workload produced by the arrival of batches of jobs. Results show that, for the arrival of batches of jobs, this workload allocation algorithm outperforms other commonly used algorithms in the static case. A hybrid scheduling approach (using this workload allocation algorithm), where information about the speed of computational resources is inferred from previously completed jobs, is then introduced and the efficiency of this approach demonstrated using a real world computational grid. These results are compared to the same workload allocation algorithm used in the static case and it can be seen that this hybrid approach comprehensively outperforms the static approach

Heterogeneous Computing on Mixed Unstructured Grids with PyFR

PyFR is an open-source high-order accurate computational fluid dynamics solver for mixed unstructured grids that can target a range of hardware platforms from a single codebase. In this paper we demonstrate the ability of PyFR to perform high-order accurate unsteady simulations of flow on mixed unstructured grids using heterogeneous multi-node hardware. Specifically, after benchmarking single-node performance for various platforms, PyFR v0.2.2 is used to undertake simulations of unsteady flow over a circular cylinder at Reynolds number 3 900 using a mixed unstructured grid of prismatic and tetrahedral elements on a desktop workstation containing an Intel Xeon E5-2697 v2 CPU, an NVIDIA Tesla K40c GPU, and an AMD FirePro W9100 GPU. Both the performance and accuracy of PyFR are assessed. PyFR v0.2.2 is freely available under a 3-Clause New Style BSD license (see www.pyfr.org).Comment: 21 pages, 9 figures, 6 table

A multidomain spectral method for solving elliptic equations

We present a new solver for coupled nonlinear elliptic partial differential equations (PDEs). The solver is based on pseudo-spectral collocation with domain decomposition and can handle one- to three-dimensional problems. It has three distinct features. First, the combined problem of solving the PDE, satisfying the boundary conditions, and matching between different subdomains is cast into one set of equations readily accessible to standard linear and nonlinear solvers. Second, touching as well as overlapping subdomains are supported; both rectangular blocks with Chebyshev basis functions as well as spherical shells with an expansion in spherical harmonics are implemented. Third, the code is very flexible: The domain decomposition as well as the distribution of collocation points in each domain can be chosen at run time, and the solver is easily adaptable to new PDEs. The code has been used to solve the equations of the initial value problem of general relativity and should be useful in many other problems. We compare the new method to finite difference codes and find it superior in both runtime and accuracy, at least for the smooth problems considered here.Comment: 31 pages, 8 figure

Effectiveness of segment routing technology in reducing the bandwidth and cloud resources provisioning times in network function virtualization architectures

Network Function Virtualization is a new technology allowing for a elastic cloud and bandwidth resource allocation. The technology requires an orchestrator whose role is the service and resource orchestration. It receives service requests, each one characterized by a Service Function Chain, which is a set of service functions to be executed according to a given order. It implements an algorithm for deciding where both to allocate the cloud and bandwidth resources and to route the SFCs. In a traditional orchestration algorithm, the orchestrator has a detailed knowledge of the cloud and network infrastructures and that can lead to high computational complexity of the SFC Routing and Cloud and Bandwidth resource Allocation (SRCBA) algorithm. In this paper, we propose and evaluate the effectiveness of a scalable orchestration architecture inherited by the one proposed within the European Telecommunications Standards Institute (ETSI) and based on the functional separation of an NFV orchestrator in Resource Orchestrator (RO) and Network Service Orchestrator (NSO). Each cloud domain is equipped with an RO whose task is to provide a simple and abstract representation of the cloud infrastructure. These representations are notified of the NSO that can apply a simplified and less complex SRCBA algorithm. In addition, we show how the segment routing technology can help to simplify the SFC routing by means of an effective addressing of the service functions. The scalable orchestration solution has been investigated and compared to the one of a traditional orchestrator in some network scenarios and varying the number of cloud domains. We have verified that the execution time of the SRCBA algorithm can be drastically reduced without degrading the performance in terms of cloud and bandwidth resource costs