The designers of a new coordination interface enacting complex workflows have to tackle a dichotomy: choosing a language-independent or language-dependent approach. Language-independent approaches decouple workflow models from the host code’s business logic and advocate portability. Language-dependent approaches foster flexibility and performance by adopting the same host language for business and coordination code. Jupyter Notebooks, with their capability to describe both imperative and declarative code in a unique format, allow taking the best of the two approaches, maintaining a clear separation between application and coordination layers but still providing a unified interface to both aspects. We advocate the Jupyter Notebooks’ potential to express complex distributed workflows, identifying the general requirements for a Jupyter-based Workflow Management System (WMS) and introducing a proof-of-concept portable implementation working on hybrid Cloud-HPC infrastructures. As a byproduct, we extended the vanilla IPython kernel with workflow-based parallel and distributed execution capabilities. The proposed Jupyter-workflow (Jw) system is evaluated on common scenarios for High Performance Computing (HPC) and Cloud, showing its potential in lowering the barriers between prototypical Notebooks and production-ready implementations.

Power and energy consumption are becoming key challenges for the supercomputers' exascale race. HPC systems' processors waist active power during communication and synchronization among the MPI processes in large-scale HPC applications. However, due to the time scale at which communication happens, transitioning into low-power states while waiting for the completion of each communication may introduce unacceptable overhead. In this article, we present COUNTDOWN, a run-time library for identifying and automatically reducing the power consumption of the CPUs during communication and synchronization. COUNTDOWN saves energy without penalizing the time-to-completion by lowering CPUs power consumption only during idle times for which power state transition overhead is negligible. This is done transparently to the user, without requiring labor-intensive and error-prone application code modifications, nor requiring recompilation of the application. We test our methodology on a production Tier-1 system. For the NAS benchmarks, COUNTDOWN saves between 6 and 50 percent energy, with a time-to-solution penalty lower than 5 percent. In a complete production-Quantum ESPRESSO-for a 3.5K cores run, COUNTDOWN saves 22.36 percent energy, with a performance penalty below 3 percent. Energy saving increases to 37 percent with a performance penalty of 6.38 percent, if the application is executed without communication tuning.

Complex computing platforms such as High Performance Computers and Data Centers are critical systems from the energy sustainability viewpoint, due to their high computational power and demanding thermal stability specifications. In this context, cooling is a crucial component to operate such systems efficiently. Adavanced solutions, based on liquid and hybrid topologies are available today, but they come with a twofold challenge. On one hand, as widely recognized in the literature, the cooling devices need to be operated in a coordinated and energy-efficient fashion. In addition, after design and deployment, the cooling system has to be dynamically managed to efficiently adapt to workload, and environmental conditions. On the other hand, at design time, the cooling hardware architecture has to be selected in order to fit in the best way the needs of the computing facility, also depending on the environmental conditions characterizing its location. This work presents a flexible, low-complexity modeling tool to describe the overall thermal behavior of complex computational platforms, as well as the effect of the diverse cooling components, and the corresponding energy consumption. Analytical modeling equations, stemming from physical first principles, are used, thus providing a compact and computationally manageable tool. This can be then exploited to explore the design space, choosing the correct cooling configuration, and/or define energy-optimal holistic cooling strategies, for complex, multidimensional, and hard constrained systems such as today SuperComputers. The proposed method is presented in general terms, then validated on a case study of a real-life HPC system with a hybrid cooling architecture.

The power consumption of supercomputers is a major challenge for system owners, users, and society. It limits the capacity of system installations, it requires large cooling infrastructures, and it is the cause of a large carbon footprint. Reducing power during application execution without changing the application source code or increasing time-to-completion is highly desirable in real-life high-performance computing scenarios. The power management run-time frameworks proposed in the last decade are based on the assumption that the duration of communication and application phases in an MPI application can be predicted and used at run-time to trade-off communication slack with power consumption. In this article, we first show that this assumption is too general and leads to mispredictions, slowing down applications, thereby jeopardizing the claimed benefits. We then propose a new approach based on (i) the separation of communication phases and slack during MPI calls and (ii) a timeout algorithm to cope with the hardware power management latency, which jointly makes it possible to achieve performance-neutral power saving in MPI applications without requiring labor-intensive and risky application source code modifications. We validate our approach in a tier-1 production environment with widely adopted scientific applications. Our approach has a time-to-completion overhead lower than 1 percent, while it successfully exploits slack in communication phases to achieve an average energy saving of 10 percent. If we focus on a large-scale application runs, the proposed approach achieves 22 percent energy saving with an overhead of only 0.4 percent. With respect to state-of-the-art approaches, COUNTDOWN Slack is the only that always leads to an energy saving with negligible overhead (<; 3 percent).

Molecular Docking is a crucial task in the process of Drug Discovery. This task consists in the estimation of the position of a molecule inside the docking site. It is used in the early stages of the drug discovery process to perform a virtual screening of a large library of molecule candidates. This task is usually performed using High Performance Computing platforms, due to sheer number of candidates and due to complexity of the docking problem. In this work we ported and optimized a Molecular Docking Module to an heterogeneous system with one or more GPGPU accelerators, leveraging the directive languages OpenMP and OpenACC. We show that with the proposed approach, we are able to reach a better utilization of the available resources compared to the usual CPU/GPU data splitting, reaching a 25% throughput improvement within the single node.

The ANTAREX project developed an approach to the performance tuning of High Performance applications based on an Aspect-oriented Domain Specific Language (DSL), with the goal to simplify the enforcement of extra-functional properties in large scale applications. The project aims at demonstrating its tools and techniques on two relevant use cases, one in the domain of computational drug discovery, the other in the domain of online vehicle navigation. In this paper, we present an overview of the project and of its main achievements, as well as of the large scale experiments that have been planned to validate the approach.

Designing and optimizing applications for energy-efficient High Performance Computing systems up to the Exascale era is an extremely challenging problem. This paper presents the toolbox developed in the ANTAREX European project for autotuning and adaptivity in energy efficient HPC systems. In particular, the modules of the ANTAREX toolbox are described as well as some preliminary results of the application to two target use cases. 1

The ANTAREX project relies on a Domain Specific Language (DSL) based on Aspect Oriented Programming (AOP) concepts to allow applications to enforce extra functional properties such as energy-efficiency and performance and to optimize Quality of Service (QoS) in an adaptive way. The DSL approach allows the definition of energy-efficiency, performance, and adaptivity strategies as well as their enforcement at runtime through application autotuning and resource and power management. In this paper, we present an overview of the ANTAREX DSL and some of its capabilities through a number of examples, including how the DSL is applied in the context of one of the project use cases.

Supercomputers, nowadays, aggregate a large number of nodes featuring the same nominal HW components (e.g., processors and GPGPUS). In real-life machines, the chips populating each node are subject to a wide range of variability sources, related to performance and temperature operating points (i.e., ACPI p-states) as well as process variations and die binning. Eurora is a fully operational supercomputer prototype that topped July 2013 Green500 and it represents a unique 'living lab' for next-generation ultra-green supercomputers. In this paper we evaluate and quantify the impact of variability on Eurora's energy-performance tradeoffs under a wide range of workloads intensity. Our experiments demonstrate that variability comes from hardware component mismatches as well as from the interplay between run-time energy management and workload variations. Thus, variability has a significant impact on energy efficiency even at the moderate scale of the Eurora machine, thereby substantiating the critical importance of variability management in future green supercomputers.

Exascale computing represents the next leap in the HPC race. Reaching this level of performance is subject to several engineering challenges such as energy consumption, equipment-cooling, reliability and massive parallelism. Model-based optimization is an essential tool in the design process and control of energy efficient, reliable and thermally constrained systems. However, in the Exascale domain, model learning techniques tailored to the specific supercomputer require real measurements and must therefore handle and analyze a massive amount of data coming from the HPC monitoring infrastructure. This becomes rapidly a “big data” scale problem. The common approach where measurements are first stored in large databases and then processed is no more affordable due to the increasingly storage costs and lack of real-time support. Nowadays instead, cloud-based machine learning techniques aim to build on-line models using real-time approaches such as “stream processing” and “in-memory” computing, that avoid storage costs and enable fastdata processing. Moreover, the fast delivery and adaptation of the models to the quick data variations, make the decision stage of the optimization loop more effective and reliable. In this paper we leverage scalable, lightweight and flexible IoT technologies, such as the MQTT protocol, to build a highly scalable HPC monitoring infrastructure able to handle the massive sensor data produced by next-gen HPC components. We then show how state-of-the art tools for big data computing and analysis, such as Apache Spark, can be used to manage the huge amount of data delivered by the monitoring layer and to build adaptive models in real-time using on-line machine learning techniques.

Density Functional Theory calculations with plane waves and pseudopotentials represent one of the most important simulation techniques in high performance computing. Together with parallel linear algebra (ZGEMM and matrix diagonalization), the most important bottleneck results from the Fast Fourier Transform (FFT), required, for example, when the local potential is applied to the wavefunction. In these calculations, the existence of a cutoff on the plane waves is reflected on a spherical domain for the FFT. After a 1D FFT is performed on pencils distributed among processors, data is transposed with a MPI_Alltoall and a 2D FFT is executed [2].

Advanced cooling systems and optimization strategies are critical to operate modern supercomputers and high-performance computing systems in an energy-efficient fashion. Hybrid architectures combining emerging liquid cooling with traditional air cooling are a promising solution. Standard management techniques maintain these systems at fixed operating points, typically without coordination between the diverse cooling knobs. In this paper, we propose an energy-aware optimization strategy exploiting heterogeneous cooling systems in a holistic fashion with the goal of minimizing the overall cooling system power consumption, while at the same time meeting the system thermal constraints. To this purpose, we developed a modeling approach to build a low-order analytical model, which captures the overall thermal behavior of the system. Then, this compact and computationally manageable model is exploited to set and solve a treatable optimization problem, leading to definition of an energy-optimal cooling strategy. The proposed method is presented taking Galileo as real-life case study. Galileo is a high-performance computing system with hybrid cooling architecture recently installed at CINECA (a supercomputing facility located in Italy). The cooling strategy resulting from the proposed approach is compared with common strategies in order to assess the efficiency advantages.

Eurora (EURopean many integrated cORe Architecture) is today the most energy efficient supercomputer in the world. Ranked 1st in the Green500 in July 2013, is a prototype built from Eurotech and Cineca toward next-generation Tier-0 systems in the PRACE 2IP EU project. Eurora's outstanding energy-efficiency is achieved by adopting a direct liquid cooling solution and a heterogeneous architecture with best-in-class general purpose HW components (Intel Xeon E5, Intel Xeon Phi and NVIDIA Kepler K20). In this paper we present a novel, low-overhead monitoring infrastructure capable to track in detail and in real-time the thermal and power characteristics of Eurora's components with fine-grained resolution. Our experiments give insights on Eurora's thermal/power trade-offs and highlight opportunities for run-time power/thermal management and optimization.

Supercomputers, nowadays, aggregate a large number of nodes sharing the same nominal HW components (eg. processors and GPGPUS). In real-life machines, the chips populating each node are subject to a wide range of variability sources, related to performance and temperature operating points (i.e. ACPI p-states) as well as process variations and die binning. Eurora is a fully operational supercomputer prototype that topped July 2013 Green500 and it represents a unique 'living lab' for next-generation ultra-green supercomputers. In this paper we evaluate and quantify the impact of variability on Eurora's energy-performance tradeoffs under a wide range of workload intensity.