Defining Uniform and Hybrid Memory Consistency Models on a Unified Framework

Abstrac

A Model for Energy-Awareness in Federated Cloud Computing Systems with Service-Level Agreements

International audienceAs data centers increase in size and computational capac- ity, numerous infrastructure issues become critical. Energy efficient is one of these issues because of the constantly increasing power consump- tion of CPUs, memory, and storage devices. A study shows that the whole energy consumed by data centers will be extremely high and it is like to overtake airlines in terms of carbon emissions. In that scenario, Cloud computing is gaining popularity since it can help companies to reduce costs and carbon footprint, usually distributing execution of ser- vices across distributed data centers. The research aims of this work are to propose and evaluate a Model for Federated Clouds that takes into account power consumption and Quality of Service (QoS) requirements. In our model, the energy reduction shall not result in negative impacts to the agreements between Cloud users and Cloud providers. Therefore, the model should ensure both energy-efficiency and QoS parameters, which sets up possibly conflicting objectives

A Fine-grained Approach for Power Consumption Analysis and Prediction

Power consumption has became a critical concern in modern computing systems for various reasons including financial savings and environmental protection. With battery powered devices, we need to care about the available amount of energy since it is limited. For the case of supercomputers, as they imply a large aggregation of heavy CPU activities, we are exposed to a risk of overheating. As the design of current and future hardware is becoming more and more complex, energy prediction or estimation is as elusive as that of time performance. However, having a good prediction of power consumption is still an important request to the computer science community. Indeed, power consumption might become a common performance and cost metric in the near future. A good methodology for energy prediction could have a great impact on power-aware programming, compilation, or runtime monitoring. In this paper, we try to understand from measurements where and how power is consumed at the level of a computing node. We focus on a set of basic programming instructions, more precisely those related to CPU and memory. We propose an analytical prediction model based on the hypothesis that each basic instruction has an average energy cost that can be estimated on a given architecture through a series of micro-benchmarks. The considered energy cost per operation includes all of the overhead due to context of the loop where it is executed. Using these precalculated values, we derive an linear extrapolation model to predict the energy of a given algorithm expressed by means of atomic instructions. We then use three selected applications to check the accuracy of our prediction method by comparing our estimations with the corresponding measurements obtained using a multimeter. We show a 9.48\% energy prediction on sorting

Local DNA sequence alignment in a cluster of workstations : algorithms and tools

Distributed Shared Memory systems allow the use of the shared memory programming paradigm in distributed architectures where no physically shared memory exist. Scope consistent software DSMs provide a relaxed memory model that reduces the coherence overhead by ensuring consistency only at synchronization operations, on a per-lock basis. Much of the work in DSM systems is validated by benchmarks and there are only a few examples of real parallel applications running on DSM systems. Sequence comparison is a basic operation in DNA sequencing projects, and most of sequence comparison methods used are based on heuristics, that are faster but do not produce optimal alignments. Recently, many organisms had their DNA entirely sequenced, and this reality presents the need for comparing long DNA sequences, which is a challenging task due to its high demands for computational power and memory. In this article, we present and evaluate a parallelization strategy for implementing a sequence alignment algorithm for long sequences. This strategy was implemented in JIAJIA, a scope consistent software DSM system. Our results on an eight-machine cluster presented good speedups, showing that our parallelization strategy and programming support were appropriate

A protein sequence analysis hardware accelerator based on divergences

The Viterbi algorithm is one of the most used dynamic programming algorithms for protein comparison and identification, based on hidden markov Models (HMMs). Most of the works in the literature focus on the implementation of hardware accelerators that act as a prefilter stage in the comparison process. This stage discards poorly aligned sequences with a low similarity score and forwards sequences with good similarity scores to software, where they are reprocessed to generate the sequence alignment. In order to reduce the software reprocessing time, this work proposes a hardware accelerator for the Viterbi algorithm which includes the concept of divergence, in which the region of interest of the dynamic programming matrices is delimited. We obtained gains of up to 182x when compared to unaccelerated software. The performance measurement methodology adopted in this work takes into account not only the acceleration achieved by the hardware but also the reprocessing software stage required to generate the alignment

Excalibur: An Autonomic Cloud Architecture for Executing Parallel Applications

International audienceIaaS providers often allow the users to specify many re-quirements for their applications. However, users without advanced technical knowledge usually do not provide a good specification of the cloud environment, leading to low per-formance and/or high monetary cost. In this context, the users face the challenges of how to scale cloud-unaware ap-plications without re-engineering them. Therefore, in this paper, we propose and evaluate a cloud architecture, namely Excalibur, to execute applications in the cloud. In our ar-chitecture, the users provide the applications and the archi-tecture sets up the whole environment and adjusts it at run-time accordingly. We executed a genomics workflow in our architecture, which was deployed in Amazon EC2. The ex-periments show that the proposed architecture dynamically scales this cloud-unaware application up to 10 instances, re-ducing the execution time by 73% and the cost by 84% when compared to the execution in the configuration specified by the user

Exact parallel alignment of megabase genomic sequences with tunable work distribution

Sequence Alignment is a basic operation in Bioinformatics that is performed thousands of times, on daily basis. The exact methods for pairwise alignment have quadratic time complexity. For this reason, heuristic methods such as BLAST are widely used. To obtain exact results faster, parallel strategies have been proposed but most of them fail to align huge biological sequences. This happens because not only the quadratic time must be considered but also the space should be reduced. In this paper, we evaluate the performance of Z-align, a parallel exact strategy that runs in user-restricted memory space. Also, we propose and evaluate a tunable work distribution mechanism. The results obtained in two clusters show that two sequences of size 24MBP (Mega Base Pairs) and 23MBP, respectively, were successfully aligned with Z-align. Also, in order to align two 3MBP sequences, a speedup of 34.35 was achieved for 64 processors. The evaluation of our work distribution mechanism shows that the execution times can be sensibly reduced when appropriate parameters are chosen. Finally, when comparing Z-align with BLAST, it is clear that, in many cases, Z-align is able to produce alignments with higher score

A distributed computation of Interpro Pfam, PROSITE and ProDom for protein annotation

Interpro is a widely used tool for protein annotation in genome sequencing projects, demanding a large amount of computation and representing a huge time-consuming step. We present a strategy to execute programs using databases Pfam, PROSITE and ProDom of Interpro in a distributed environment using a Java-based messaging system. We developed a two-layer scheduling architecture of the distributed infrastructure. Then, we made experiments and analyzed the results. Our distributed system gave much better results than Interpro Pfam, PROSITE and ProDom running in a centralized platform. This approach seems to be appropriate and promising for highly demanding computational tools used for biological applications