On Designing Multicore-aware Simulators for Biological Systems

The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to speed it up on multi-core platforms, which pose new challenges for parallelisation techniques. These opportunities are developed in two general families of solutions involving both the single simulation and a bulk of independent simulations (either replicas of derived from parameter sweep). Proposed solutions are tested on the parallelisation of the CWC simulator (Calculus of Wrapped Compartments) that is carried out according to proposed solutions by way of the FastFlow programming framework making possible fast development and efficient execution on multi-cores.Comment: 19 pages + cover pag

10191 Abstracts Collection -- Program Composition and Optimization : Autotuning, Scheduling, Metaprogramming and Beyond

From May 9 to 12, 2010, the Dagstuhl Seminar 10191 ``Program Composition and Optimization: Autotuning, Scheduling, Metaprogramming and Beyond\u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Challenging the abstraction penalty in parallel patterns libraries

In the last years, pattern-based programming has been recognized as a good practice for efficiently exploiting parallel hardware resources. Following this approach, multiple libraries have been designed for providing such high-level abstractions to ease the parallel programming. However, those libraries do not share a common interface. To pave the way, GrPPI has been designed for providing an intermediate abstraction layer between application developers and existing parallel programming frameworks like OpenMP, Intel TBB or ISO C++ threads. On the other hand, FastFlow has been adopted as an efficient object-based programming framework that may benefit from being supported as an additional GrPPI backend. However, the object-based approach presents some major challenges to be incorporated under the GrPPI type safe functional programming style. In this paper, we present the integration of FastFlow as a new GrPPI backend to demonstrate that structured parallel programming frameworks perfectly fit the GrPPI design. Additionally, we also demonstrate that GrPPI does not incur in additional overheads for providing its abstraction layer, and we study the programmability in terms of lines of code and cyclomatic complexity. In general, the presented work acts as reciprocal validation of both FastFlow (as an efficient, native structured parallel programming framework) and GrPPI (as an efficient abstraction layer on top of existing parallel programming frameworks).This work has been partially supported by the European Commission EU H2020-ICT-2014-1 Project RePhrase (No. 644235) and by the Spanish Ministry of Economy and Competitiveness through TIN2016-79637-P “Towards Unification of HPC and Big Data Paradigms”

Autonomic behavioural framework for structural parallelism over heterogeneous multi-core systems.

With the continuous advancement in hardware technologies, significant research has been devoted to design and develop high-level parallel programming models that allow programmers to exploit the latest developments in heterogeneous multi-core/many-core architectures. Structural programming paradigms propose a viable solution for e ciently programming modern heterogeneous multi-core architectures equipped with one or more programmable Graphics Processing Units (GPUs). Applying structured programming paradigms, it is possible to subdivide a system into building blocks (modules, skids or components) that can be independently created and then used in di erent systems to derive multiple functionalities. Exploiting such systematic divisions, it is possible to address extra-functional features such as application performance, portability and resource utilisations from the component level in heterogeneous multi-core architecture. While the computing function of a building block can vary for di erent applications, the behaviour (semantic) of the block remains intact. Therefore, by understanding the behaviour of building blocks and their structural compositions in parallel patterns, the process of constructing and coordinating a structured application can be automated. In this thesis we have proposed Structural Composition and Interaction Protocol (SKIP) as a systematic methodology to exploit the structural programming paradigm (Building block approach in this case) for constructing a structured application and extracting/injecting information from/to the structured application. Using SKIP methodology, we have designed and developed Performance Enhancement Infrastructure (PEI) as a SKIP compliant autonomic behavioural framework to automatically coordinate structured parallel applications based on the extracted extra-functional properties related to the parallel computation patterns. We have used 15 di erent PEI-based applications (from large scale applications with heavy input workload that take hours to execute to small-scale applications which take seconds to execute) to evaluate PEI in terms of overhead and performance improvements. The experiments have been carried out on 3 di erent Heterogeneous (CPU/GPU) multi-core architectures (including one cluster machine with 4 symmetric nodes with one GPU per node and 2 single machines with one GPU per machine). Our results demonstrate that with less than 3% overhead, we can achieve up to one order of magnitude speed-up when using PEI for enhancing application performance

Refactoring software to heterogeneous parallel platforms

In summary, the papers included in this special issue are representative of the progress achieved by the research community at various levels from the very high level using parallel patterns to lower levels using, for example, transactional software memory. Also the integration of GPUs and FPGAs in the landscape is essential to achieve better performance in different categories of applications. All these innovative research directions will contribute to better achieve the long-term goal of better refactoring of existing applications to new and evolving parallel heterogeneous architectures

FastFlow: Efficient Parallel Streaming Applications on Multi-core

Shared memory multiprocessors come back to popularity thanks to rapid spreading of commodity multi-core architectures. As ever, shared memory programs are fairly easy to write and quite hard to optimise; providing multi-core programmers with optimising tools and programming frameworks is a nowadays challenge. Few efforts have been done to support effective streaming applications on these architectures. In this paper we introduce FastFlow, a low-level programming framework based on lock-free queues explicitly designed to support high-level languages for streaming applications. We compare FastFlow with state-of-the-art programming frameworks such as Cilk, OpenMP, and Intel TBB. We experimentally demonstrate that FastFlow is always more efficient than all of them in a set of micro-benchmarks and on a real world application; the speedup edge of FastFlow over other solutions might be bold for fine grain tasks, as an example +35% on OpenMP, +226% on Cilk, +96% on TBB for the alignment of protein P01111 against UniProt DB using Smith-Waterman algorithm.Comment: 23 pages + cove

HitFlow: A Dataflow Programming Model for Hybrid Distributed- and Shared-Memory Systems

Producción CientíficaDataflow programming consists in developing a program by describing its sequential stages and the interactions between them. The runtime systems supporting this kind of programming are responsible for exploiting the parallelism by concurrently executing the different stages as soon as their dependencies are met. In this paper we introduce a new parallel programming model and framework based on the dataflow paradigm. It presents a new combination of features that allows to easily map programs to shared or distributed memory, exploiting data locality and affinity to obtain the same performance than optimized coarse-grain MPI programs. These features include: It is a unique one-tier model that supports hybrid shared- and distributed-memory systems with the same abstractions; it can express activities arbitrarily linked, including non-nested cycles; it uses internally a distributed work-stealing mechanism to allow Multiple-Producer/Multiple-Consumer configurations; and it has a runtime mechanism for the reconfiguration of the dependences and communication channels which also allows the creation of task-to-task data affinities. We present an evaluation using examples of different classes of applications. Experimental results show that programs generated using this framework deliver good performance in hybrid distributed- and shared-memory environments, with a similar development effort as other dataflow programming models oriented to shared-memory.2019-01-01MICINN (Spain) and ERDF program of the European Union: HomProg-HetSys project (TIN2014-58876- P), PCAS project (TIN2017-88614-R), CAPAP-H6 (TIN2016-81840-REDT), and COST Program Action IC1305: Network for Sustainable Ultrascale Com- puting (NESUS). By Junta de Castilla y Le on, project PROPHET (VA082P17). And by the computing facilities of Extremadura Research Centre for Advanced Technologies (CETA- CIEMAT), funded by the European Regional Develop- ment Fund (ERDF). CETA-CIEMAT belongs to CIEMAT and the Govern- ment of Spain