Algorithm 944

Parallel graph generation algorithms for shared and distributed memory machines

Parallelizing software is a popular way of achieving high energy efficiency since parallel applications can be mapped on many cores and the clock frequency can be lowered. Perfect parallelism is, however, not often reached and different program phases usually contain different levels of parallelism due to data dependencies. Applications have currently no means of expressing the level of parallelism, and the power management is mostly done based on only the workload. In this work, we provide means of expressing QoS and levels of parallelism in applications for more tight integration with the power management to obtain optimal energy efficiency in multi-core systems. We utilize the dataflow framework PREESM to create and analyze program structures and expose the parallelism in the program phases to the power management. We use the derived parameters in a NLP (Non Linear Programming) solver to determine the minimum power for allocating resources to the applications.

A new method to retrieve aerosol optical thickness from satellite images on a parallel system

Chapter 6 - Multiprocessor Machines

Graph algorithms are notorious for not getting good speedup on parallel architectures. These algorithms tend to suffer from irregular dependencies and a high synchronization cost that prevent an efficient execution on distributed memory machines. Hence such algorithms are mostly parallelized on shared memory machines. However, current commodity shared memory machines do not typically offer enough parallelism to process these problems. In this paper, we are presenting an early investigation of the scalability of such algorithms on Intel's upcoming Many Integrated Core (Intel MIC) architecture which, when it will be released in 2012, is expected to provide more than 50 physical cores with SMT capability. The Intel MIC architecture can be programmed through many programming models, here we investigate the three most popular of these models namely OpenMP, Cilk Plus and Intel's TBB. We present scalability results of a parallel graph coloring algorithm, three variations of a breadth-first search algorithm and a micro benchmark for irregular computations using these three programming models. Our results on a prototype board show that the multi-threaded architecture of Intel MIC can be effectively used for hiding latencies in irregular applications to achieve almost perfect speedup.

Among elliptic boundary value problems, the class of problems with separable variables can be solved fast and directly. Elliptic problems with separable variables usually assume that the computational domains are simple e.g., rectangle or circle, and constant coefficients [1]. This kind of problems can serve to generate preconditioners in iterative procedures for more complex methods. They can also be used in low-accuracy models similar to the ones used in Numerical Weather Simulations. A straightforward implementation of solvers for such problems makes them considered as too simple to pay much attention to them. For instance, NETLIB* contains the codes of various solvers for problems with separable variables. We are not aware if such solvers are provided as separate solvers in other software packages except NETLIB Fishpack* and Intel$\textcircled{\tiny{\,R}}$ Math Kernel Library (Intel$\textcircled{\tiny{\,R}}$ MKL) together with Intel$\textcircled{\tiny{\,R}}$ Cluster Poisson Solver Library (Intel$\textcircled{\tiny{\,R}}$ CPSL). The problems with the separable variables can be suboptimal in the sense that they require slightly more arithmetic operations (up to logarithmic factor) than the number of unknowns to compute the solution to the problem. This statement is true if, for example, the sizes of the discretized problems are powers of 2. Computational Mathematics suggests that we take into consideration not only arithmetic operations, but also the cost of memory operations as well. Modern computers can perform computations at a very high speed, while lacking the ability to deliver data to the computational units. Keeping in mind that a memory operation can easily be dozen to hundred times slower than an arithmetic one, a computationally optimal algorithm could compute the solution slower than memory optimal algorithm. The recent developments in processor industry resulted in multicore processors become standard processors not only for powerful clusters, but also for home computers and laptops. Therefore, the algorithm can also be non-optimal from the parallelization point of view. Optimality here can be understood in terms of the number of synchronization points and/or in terms of the amount of data that needs to be transferred between different cores/processors. In summary, the modern computational algorithm should focus on 3 key aspects, namely, parallelization, memory operations, and arithmetic costs. The purpose of this paper is to demonstrate on a simple 2D problem with separable variables that taking into account modern model the solution can be computed efficiently and fast. This would also help developers to compute solution to the problem with separable variables really negligible with respect to other computations. To complete our goal, we will evaluate software provided by Intel Corporation. In particular, we focus on the comparison (where possible) of NETLIB Fishpack* and Intel$\textcircled{\tiny{\,R}}$ CPSL provided at [2] as well as Intel$\textcircled{\tiny{\,R}}$ MKL provided at [3]. This paper is organized as follows. First we are solving a 2D Helmholtz problem using single precision on a shared memory machine with two 4-Core Intel$\textcircled{\tiny{\,R}}$ Xeon$\textcircled{\tiny{\,R}}$ Processors E5462. Next we do the same but use double precision arithmetic. Lastly we use double precision on a distributed memory machine using MPI.

Publishing the research works on academic publications is an important part of the scientific process. Since the development of computer science research is very fast, researchers tend to publish the research works in a fast way, such as conferences whose review processes are faster than the journals. In the past decades, one conference usually focuses on a specific research field and the topic or method overlap between conferences is low. We have noticed that, in recent years, some topics or methods which were once studied in a small number of specific research fields have become popular in many other fields. Naturally, we come up with two research questions: (1) Do the conferences indeed become similar? and (2) How do conferences become similar? In this paper, we first use a trans-temporal heterogeneous graph network to model academic conferences in recent 20 years. Due to the large number of conferences, we categorize these conferences into 6 research fields for brevity. Then, we first quantitatively and qualitatively assess “Do the research fields become similar?” and then focus on exploring “How do research fields become similar?”. From the result, we find the reason for the research fields in computer science become similar is that AI becomes pervasive and researchers tend to apply the machine learning methods to different application fields. Since the methods become universal between different research fields, researchers should pay more attention to advanced information in other fields to motivate more interdisciplinary works. To assist the researchers to explore related interdisciplinary advanced information, it is crucial to measure the cross-field impact of papers using the citation information and recommend the paper which has a high cross-field impact on the related researchers. As for the newly published papers which do not have any citations, we also propose a cross-field impact prediction model to recommend the cutting-edge research works to related researchers accurately. Experiments conducted on real-world datasets verify the effectiveness of the proposed method.

Distributed memory parallel machines are increasingly being used by the scientific community to provide computational power for solving problems. Building a distributed memory parallel machine offers a tremendous advantage in terms of cost and scalability over building a shared memory parallel machine. Unfortunately, distributed memory machines are much more difficult to program, mainly due to the lack of a single global address space. Communication between processors in a distributed memory machine is accomplished by message passing. The time cost for acquiring data from another processor's memory is significantly greater than the time cost of acquiring data from local memory. To assist the programmer in using a distributed memory machine, compilers have been developed which alleviate the need for the programmer to manage the lack of a global address space. These compilers will generate semantically correct code containing communication routines to produce a logically shared memory machine on a physically distributed memory machine. However, the runtime performance of the code emitted from some of these compilers can be further improved. This thesis is primarily concerned with advanced compilation techniques which will provide better runtime performance of programs written in imperative languages for regular scientific programs. The optimization of communication generation for distributed memory machines is used to produce this result. We look at two "state of the art" compilation systems and find that improvement in the communication code generated by these compilers is still possible. We have simplified existing descriptions of the various formalisms found in these compilers, while still providing enough formalism to study the problems in depth. We have extended some existing optimization techniques by enhancing the elimination of masks, by extending the notion of relaxing the owner computes rule, by extending the notion of replicating computation, and by extending the notion of replicating data. This thesis has discussed a novel technique to split loops so that they do not contain any guarded statements. Finally, we have suggested avenues for future research, as it is clear from this thesis that more work is required before compilation systems for distributed memory parallel machines will be widely used for general purpose computing.

Multi-trace acoustic impedance inversion with multiplicative regularization

Biomedical Engineering, usually known as Bioengineering, is among the fastest developing and one of most important interdisciplinary fields today. It connects natural and technical sciences, for all of which biological and medical phenomena, computation, and data management play important roles in science and industry. Distributed computing and parallel algorithms have proved to be effective in solving the problem with high computational complexity in a wide range of domains, including areas of computational bioengineering. This special edition collects high-quality research papers in the field of application of distributed computing systems in bioengineering applications. This issue is the achievement of the developments of modern computer and biomedical technology. Most bioengineering or bioinformatics methods need to access and analyses large amounts of data. For that it is necessary to achieve an effective way that from Big data creates knowledge and useful applications. The nature of such scientific data/information/knowledge demands the use of a powerful computing and intelligent database management systems. Areas of current and future research include advanced topics in this special issue. The paper from Juhasz et al. present a novel, GPU-based streaming architecture that has the potential for drastically reducing execution times and at the same time providing simultaneous 2D and 3D visualization facilities. The system uses a highly-optimised and re-configurable pipeline of CPU and GPU cores that attempts to exploit the tremendous computing power whenever possible. The system can process live data arriving from an EEG device or data stored in EEG data files. The computer drives a large display wall system of four 46 monitors that provides a 4K-resolution drawing surface for visualizing raw EEG data, potential maps and various 3D views of the patient's head. Authors from the group of M. Gusev presents the scalable balancer in Cloud computing extended to Dew Computing level. Given a successful implementation of scalable low level load balancer, implemented on the network layer. The scalability is proved with series of experiments. The experiments showed that it adds small latency of several milliseconds and thus it slightly reduces the performance when the distributed system is underutilized. Rybicki et al. demonstrate how to realize a Software-as-a-Service solution for a variety of science software using container technologies. The presented solution utilized DARIAH-DE research infrastructure based on OpenStack and UNICORE grid to deliver an extensible solution for the digital humanities domain. The paper from authors Forer et al. describe the extension of Cloudflow to support ApacheSpark without any adaptions to already implemented pipelines. The described performance evaluation demonstrates that Spark can bring an additional boost for analyzing next generation sequencing(NGS) data to the eld of genetics. The Cloudflow framework is open source and freely available at https://github.com/genepi/cloudflow . The paper by Memon et al. describes an approach for executing computational jobs across HPC and HTC resources while operating on geographically dispersed data via a global federated file system. The solution is realized as a new framework that integrates UNICORE and GFFS to provide a standards-based environment to support large scale data intensive computations frequent in today's biomedical analyses. The paper Parallel algorithm for the state space exploration, authored by L. Allal et al., proposes a new automatic verification technique based on model checking that determines whether a given system satisfies its specification. Such a technique suffers from the state explosion problem when traversing all possible states of systems. A new synchronized parallel algorithm (SPA) of exploration is proposed based on a fixed number of threads. Exhaustive comparative studies between the standard parallel exploration algorithm in SPIN and the new SPA show that the SPA performs slightly better regarding the execution time and memory complexity. Smart systems in telemedicine frequently use intelligent sensor devices at large scale. Practitioners can monitor non-stop the vital parameters of hundreds of patients in real-time. The most important pillars of remote patient monitoring services are communication and data processing. Large scale data processing is done mainly using workflows. In the paper Eszter et al. give a brief overview of the different check pointing techniques and propose two new provenance based check pointing algorithms which uses the information stored in the workflow structure to dynamically change the frequency of check pointing and can be efficiently used for dynamic health care smart systems.

In this paper, a novel switched flux permanent-magnet (SFPM) memory machine, which consists of changeable magnetized permanent magnets (CMPMs) in the stator, is developed and investigated. By changing the magnetization directions of CMPMs, the PM flux linkage can be either enhanced or weakened. When PM flux linkage is weakened at high speed, the flux density in the lamination as well as iron loss can be reduced. Thus, higher efficiency can be obtained. To evaluate the efficiency improvement of SFPM memory machine, the efficiency map is calculated and compared with that of interior PM machine by taking Toyota/Prius 2010 as benchmark. It shows that several step changes of PM flux linkage can enlarge the high-efficiency region, and also reduce the back-EMF at high speed.

Recently, use of parallel machines in reservoir simulation has received considerable attention from the petroleum industry. This paper presents parallelization of a 3D compositional, equation-of-state reservoir simulator on the CM-5 and KSR-1. To the best of our knowledge, this is the first time that the parallelization of a compositional reservoir simulator has been performed on both the CM-5 and KSR-1. For new users of the CM-5 machines, the software and hardware of CM-5 architecture is presented, as well as details of the parallelization techniques. For example, domain decomposition, I/O's, phase equilibrium computations, and well model are described. The parallelism techniques on the KSR-1 are presented with the emphasis on the porting of the phase equilibrium calculation. The performance of each machine is evaluated by showing the speedup on different sets of processing nodes. Two test problems were used to explore the capability of the parallelized version of the code; one is a waterflood problem and the other is a CO2 multiple contact miscible flood, both in a West Texas oil field. These field problems were run on 1, 2, 4, 8, 16, and 32 processors to get insight into the locations of communication bottlenecks, generally occurring in the programming with distributed memory machines. The problems of latency and bandwidth which are associated with communication efficiency of the CM-5 are also addressed.

In biology, there is a research field `bioinformatics' in which computers are used as a method for problem solving. Bioinformatics includes a topic that is related to the analysis of genetic information. To analyze genetic information, a homology search is used. The homology search detects similar parts of two base sequences. The Smith-Waterman algorithm is one of the most famous approaches for a homology search. The algorithm is sometimes executed in parallel by using a GPU. In this paper, we propose an acceleration method of a parallel homology search based on the Smith-Waterman algorithm by using a GPU. The proposed method first reduces the range of calculation of the Smith-Waterman algorithm by preprocess. Next, it applies the Smith-Waterman algorithm in parallel to the multiple sub matrices obtained after the preprocess to improve efficiency. As a result of an evaluation experiment, we have measured that our method gained at most 3.8 times in execution speed compared to a simple parallel execution of the Smith-Waterman algorithm by a GPU. The gain is caused by reduction of the calculation of the Smith-Waterman algorithm and by detecting sub sequences that can be executed asynchronously in parallel.

A number of computer scientists have contended that Linda cannot possibly be implemented efficiently on distributed memory machines because there is simply too much overhead. They believe that Linda will not be able to compete with message passing on such machines even for solving computationally intensive problems. The authors address this claim by discussing C-Linda's performance in solving a particular scientific computing problem, the shallow water equations. They have implemented and evaluated the performance of the Linda program on a variety of machines. They present results for shared memory machines (Sequent Symmetry and the Encore Multimax), for distributed memory machines (iPSC/2 and iPSC/860 hypercubes), and for a network of Sparcstations connected by an Ethernet. The same Linda program was executed on all these machines and its performance was evaluated and compared to that of implementations using alternative methods available on all machines. In the authors' experience, the Linda program has generally been easier and more convenient to write than the native versions for each machine. >

We present a system for functional parallel computing on distributed memory machines, which does dynamic load balancing and is totally symmetric. This means that every node can perform any computation and is client and server at the same time. Furthermore, the calling convention is similar to threads on shared memory machines to allow a uniform usage of parallel and distributed procedure calls. Finally the communication and computation is strictly separated for easy maintenance of the user program.