A Benchmark for Image Retrieval using Distributed Systems over the Internet: BIRDS-I

The performance of CBIR algorithms is usually measured on an isolated workstation. In a real-world environment the algorithms would only constitute a minor component among the many interacting components. The Internet dramati-cally changes many of the usual assumptions about measuring CBIR performance. Any CBIR benchmark should be designed from a networked systems standpoint. These benchmarks typically introduce communication overhead because the real systems they model are distributed applications. We present our implementation of a client/server benchmark called BIRDS-I to measure image retrieval performance over the Internet. It has been designed with the trend toward the use of small personalized wireless systems in mind. Web-based CBIR implies the use of heteroge-neous image sets, imposing certain constraints on how the images are organized and the type of performance metrics applicable. BIRDS-I only requires controlled human intervention for the compilation of the image collection and none for the generation of ground truth in the measurement of retrieval accuracy. Benchmark image collections need to be evolved incrementally toward the storage of millions of images and that scaleup can only be achieved through the use of computer-aided compilation. Finally, our scoring metric introduces a tightly optimized image-ranking window.Comment: 24 pages, To appear in the Proc. SPIE Internet Imaging Conference 200

More Bang for Your Buck: Improved use of GPU Nodes for GROMACS 2018

We identify hardware that is optimal to produce molecular dynamics trajectories on Linux compute clusters with the GROMACS 2018 simulation package. Therefore, we benchmark the GROMACS performance on a diverse set of compute nodes and relate it to the costs of the nodes, which may include their lifetime costs for energy and cooling. In agreement with our earlier investigation using GROMACS 4.6 on hardware of 2014, the performance to price ratio of consumer GPU nodes is considerably higher than that of CPU nodes. However, with GROMACS 2018, the optimal CPU to GPU processing power balance has shifted even more towards the GPU. Hence, nodes optimized for GROMACS 2018 and later versions enable a significantly higher performance to price ratio than nodes optimized for older GROMACS versions. Moreover, the shift towards GPU processing allows to cheaply upgrade old nodes with recent GPUs, yielding essentially the same performance as comparable brand-new hardware.Comment: 41 pages, 13 figures, 4 tables. This updated version includes the following improvements: - most notably, added benchmarks for two coarse grain MARTINI systems VES and BIG, resulting in a new Figure 13 - fixed typos - made text clearer in some places - added two more benchmarks for MEM and RIB systems (E3-1240v6 + RTX 2080 / 2080Ti

Cloud WorkBench - Infrastructure-as-Code Based Cloud Benchmarking

To optimally deploy their applications, users of Infrastructure-as-a-Service clouds are required to evaluate the costs and performance of different combinations of cloud configurations to find out which combination provides the best service level for their specific application. Unfortunately, benchmarking cloud services is cumbersome and error-prone. In this paper, we propose an architecture and concrete implementation of a cloud benchmarking Web service, which fosters the definition of reusable and representative benchmarks. In distinction to existing work, our system is based on the notion of Infrastructure-as-Code, which is a state of the art concept to define IT infrastructure in a reproducible, well-defined, and testable way. We demonstrate our system based on an illustrative case study, in which we measure and compare the disk IO speeds of different instance and storage types in Amazon EC2

Best bang for your buck: GPU nodes for GROMACS biomolecular simulations

The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD, multi-threading, and MPI-based SPMD/MPMD parallelism, while GPUs can be used as accelerators to compute interactions offloaded from the CPU. Here we evaluate which hardware produces trajectories with GROMACS 4.6 or 5.0 in the most economical way. We have assembled and benchmarked compute nodes with various CPU/GPU combinations to identify optimal compositions in terms of raw trajectory production rate, performance-to-price ratio, energy efficiency, and several other criteria. Though hardware prices are naturally subject to trends and fluctuations, general tendencies are clearly visible. Adding any type of GPU significantly boosts a node's simulation performance. For inexpensive consumer-class GPUs this improvement equally reflects in the performance-to-price ratio. Although memory issues in consumer-class GPUs could pass unnoticed since these cards do not support ECC memory, unreliable GPUs can be sorted out with memory checking tools. Apart from the obvious determinants for cost-efficiency like hardware expenses and raw performance, the energy consumption of a node is a major cost factor. Over the typical hardware lifetime until replacement of a few years, the costs for electrical power and cooling can become larger than the costs of the hardware itself. Taking that into account, nodes with a well-balanced ratio of CPU and consumer-class GPU resources produce the maximum amount of GROMACS trajectory over their lifetime

A fine-grain time-sharing Time Warp system

Although Parallel Discrete Event Simulation (PDES) platforms relying on the Time Warp (optimistic) synchronization protocol already allow for exploiting parallelism, several techniques have been proposed to further favor performance. Among them we can mention optimized approaches for state restore, as well as techniques for load balancing or (dynamically) controlling the speculation degree, the latter being specifically targeted at reducing the incidence of causality errors leading to waste of computation. However, in state of the art Time Warp systems, events’ processing is not preemptable, which may prevent the possibility to promptly react to the injection of higher priority (say lower timestamp) events. Delaying the processing of these events may, in turn, give rise to higher incidence of incorrect speculation. In this article we present the design and realization of a fine-grain time-sharing Time Warp system, to be run on multi-core Linux machines, which makes systematic use of event preemption in order to dynamically reassign the CPU to higher priority events/tasks. Our proposal is based on a truly dual mode execution, application vs platform, which includes a timer-interrupt based support for bringing control back to platform mode for possible CPU reassignment according to very fine grain periods. The latter facility is offered by an ad-hoc timer-interrupt management module for Linux, which we release, together with the overall time-sharing support, within the open source ROOT-Sim platform. An experimental assessment based on the classical PHOLD benchmark and two real world models is presented, which shows how our proposal effectively leads to the reduction of the incidence of causality errors, as compared to traditional Time Warp, especially when running with higher degrees of parallelism

A Metaheuristic Adaptive Cubature Based Algorithm to Find Bayesian Optimal Designs for Nonlinear Models

Finding Bayesian optimal designs for nonlinear models is a difficult task because the optimality criteriontypically requires us to evaluate complex integrals before we perform a constrained optimization. Wepropose a hybridized method where we combine an adaptive multidimensional integration algorithm anda metaheuristic algorithm called imperialist competitive algorithm to find Bayesian optimal designs. Weapply our numerical method to a few challenging design problems to demonstrate its efficiency. Theyinclude finding D-optimal designs for an item response model commonly used in education, Bayesianoptimal designs for survivalmodels, and Bayesian optimal designs for a four-parameter sigmoid Emax doseresponse model. Supplementary materials for this article are available online and they contain an R packagefor implementing the proposed algorithm and codes for reproducing all the results in this paper