No.075 Putting Heterogeneous High-Performance Computing at the Fingertips of Domain Experts


NII Shonan Meeting Seminar 075

Topics of Presentations

Below are the tentative titles and abstracts for presentations we have received so far, in no particular order.

Opening Cilk up for Heterogeneous Many-Cores.

Prof. Michael Philippsen,?University of Erlangen-Nuremberg

Cilk is a well-known programming model for task parallel programs that?was originally designed for homogeneous shared memory systems with a?few cores. To open up Cilk for heterogeneous many-core platforms there?are both technical obstacles to overcome and proceeds to yield.

The IBM Cell processor is a heterogeneous architecture consisting of a?front-end PowerPC and eight SPE co-processors that do the work. Each?SPE is equipped with a small scratch-pad memory (256kB) for both?instructions and data while the main memory has to be accessed with?explicit DMA transfers. Here Cilk’s work stealing mechanism is the?central issue. It allows to continue the execution of a function?somewhere in its body on a different core. We show how the resulting?distributed lists are cleaned up with garbage collection techniques at?local barriers.

On GPUs thousands of threads are orchestrated into warps/groups that?share a single program counter. The main issue is the performance?penalty of divergence, i.e., if control flow diverges within a warp,?the execution of the threads is sequentialized. To reduce divergence,?we create device functions for each “un-interruptible” code sequence?and sort continuations accordingly. To have enough threads of the same?type ready for ?execution, task execution order must be changed from?from depth first to breadth first.

The Intel MIC is a shared-memory many-core architecture with 60?cores. Due to the number of cores, speculative execution can be used?to parallelize recursive code for which a static analysis cannot prove?the absence of data-dependences and races. To gain performance we?generate a parallel Cilk version of the recursion and spawn it?speculatively and simultaneously to the sequential code. There is?speedup if neither the underlying software transactional memory nor?the race detection system causes an abort.

Bridging the gap between the atmospheric scales: Atmospheric modeling by coupling NWP and CDF models

Prof. Tetsuya Takemi,?Kyoto University

The atmospheric motions has a wide range in their temporal and spatial?scales. With the continuing advances in computational resources,?numerical weather prediction (NWP) models can resolve the scales on the?order of 1-10 km, while computational fluid dynamics (CFD) models can?cover the spatial scales on the order of 1-10 km. Therefore, there is an?overlap in the scales that can be represented in both NWP and CFD models,?which enhances the collaboration between atmospheric scientists and?fluid engineers. In this talk, we will present our recent efforts in?simulating microscale atmospheric flows over complex topography?including urban districts by coupling NWP and CFD models. Specifically,?turbulent flow and dispersion over complex topography was simulated with?a large-eddy simulation (LES) technique in the CFD model. A special care?was made to represent turbulent motions in connecting the NWP model?outputs into an LES model.

Optically reconfigurable gate array for heterogeneous high-performance computing

Prof. Minoru Watanabe

Optically reconfigurable gate array (ORGA) can support a high-speed dynamic reconfiguration.?The reconfiguration time of ORGAs reaches over 100 MHz. Its programmable gate array can dynamically be reconfigured at every 10 ns. ?Using such high-speed dynamically reconfigurable devices, single-instruction-set-computer (SISC) can be implemented. ?The SISC can work on dynamically reconfigurable device just like RISCs while such SISC can increase the performance of programmable gate arrays due to its simple architecture. In the first presentation, I will introduce the SISC implementation on ORGA which maybe can be applied for heterogeneous high-performance computing.

Multiparty Session Types and their applications to HPC

Prof. Nobuko Yoshida

We give a summary of our recent research developments on multiparty session types for verifying distributed and concurrent programs, and our collaborations with industry partners.

We shall first talk how Robin Milner, Kohei Honda and Yoshida started collaborations with industry to develop a web service protocol description language called Scribble and discovered the theory of multiparty session types through the collaborations. We then talk about the recent developments in Scribble (which is a protocol description language for multiparty session types), the runtime session monitoring framework and applications to generate MPI programs from Scribble.

Climbing Mont Blanc – A Training Site for Energy Efficient Programming on Heterogeneous Multicore Processors

Prof. Lasse Natvig,?Norwegian University of Science and Technology

Climbing Mont Blanc (CMB) is an open online judge used for training in energy efficient programming of state-of-the-art heterogeneous multicores. It uses an Odroid-XU3 board with an Exynos Octa processor and integrated power sensors. This processor is three-way heterogeneous containing 14 different cores of three different types. The board currently accepts C and C++ programs, with support for OpenCL v1.1, OpenMP 4.0 and Pthreads. Programs submitted using the graphical user interface are evaluated with respect to time and energy used, and energy-efficiency (EDP). A small and varied set of problems are available, and the system is currently in use in a medium sized course on parallel computing at NTNU. Other online programming judges exist, but we are not aware of any similar system that also reports energy-efficiency. The talk will present some early experience from using the CMB system and explain how fellow researchers can collaborate and contribute by uploading new problems and solve existing problems. ?Our long term goal is to enhance the body of knowledge in the area of energy-efficient computing on handheld devices from submissions to the system.

Towards a HPC Research Roadmap Beyond Exascale

Prof. Dr. Theo Ungerer,?University of Augsburg

The goal of EuroLab-4-HPC, a European Community funded CSA (Coordination and Support Action), is to create the foundation for a European Research Center of Excellence in High Performance Computing Systems. One of the principal objectives of the project is to align the agendas of the best research groups on a roadmap for long-term HPC system research.

The HPC research roadmap of EuroLab-4-HPC targets a long-term research vision beyond exascale (2020 to 2030). This roadmap will include all layers of the HPC stack, from applications to hardware, as well as the vertical challenges of Green ICT, energy and resiliency, and the convergence of HPC, embedded HPC, and data centres for big data. We are currently forming cross-cutting working groups to address the problem from these diverse perspectives.

A roadmap that targets five to fifteen years in the future will naturally contain parts that are highly speculative. We are therefore identifying disruptive technologies that could be technologically feasible within the next decade, in order to assess how they would affect future architectures and the research roadmap.

The talk will focus on disruptive technologies and will discuss our initial directions with the audience. The roadmapping efforts started Sept 2015; a preliminary roadmap is due August 2016 and the final roadmap will be delivered on August 2017. The HPC research roadmap is coordinated by Theo Ungerer, University of Augsburg.

Safe embedding and optimizing of EDSL

Prof. Oleg Kiselyov,?Tohoku University

We outline a framework for embedding of typed domain-specific?languages that ensures that only well-typed DSL expressions are?embeddable. The framework lets the user write a wide range of?transformations. They typically convert a DSL expression to a form?from which an efficient target code can easily be generated. The?transformations preserve typing and hygiene by the very construction,?and hence make it more difficult for the transformation writers to?shoot themselves in the foot. We have used the framework for compiling?language-integrated queries to efficient SQL.

Performance-portable HPC code from single source code

Dr. Mark Govett, NOAA

I would like to talk about our experience developing code that is performance?portable with a single source code, and runs efficiently on CPU, GPU and MIC?systems. It has been run on over 130,000 CPU cores, 15000 GPUs, and over?1000 MIC processors. I will show scalabiliy and performance results for our?Weather model. But I am most interested in learning and having a conversation where we share our collective knowledge on techniques, code design, algorithms,?etc that are necessary elements toward achieving performance portability with a single source.

Practical abstract machine models for heterogeneous multi-cores

Dr. Raphael ‘kena’ Poss, University of Amsterdam

It is 2015 and yet we are still subject to a 1980-era?diversity of frameworks and programming languages each with their own?abstractions for programmers. One supports GPU-like parallelism, another?can offload certain streaming operations (eg. crypto), another offers?on-chip message passing… But what is the underlying structure behind??In this talk I will highlight commonalities and differences and present?our current research direction with AM3, a general-purpose model for?heterogeneous platforms.

Building blocks for domain experts: a compiler and runtime system perspective

Prof. Albert Cohen, INRIA

Performance portability is always important, but the needs of domain?experts go beyond achieving decent performance at a reasonable?cost. Our research aims at helping tool designers rather than?providing multi-purpose or specialized tools for domain experts?themselves. In particular, we are interested in improving the?productivity of programming language engineers who are also interested?in a specific domain, and domain engineers interested in developing?programming language tools. Eventually, ninja domain programmers being?the most influential in defining the software practices in?high-performance computing, they tend to also determine the success or?demise of a computing platform. We are thus helping computing platform?engineers increase their ability to provide great tools for their?ninja users.

We will take concrete examples from polyhedral compilation,?task-parallel runtimes, and cyberphysical systems with a strong?computational component, raising open questions towards the adoption?of such techniques and looking for collaborations.

High level programming in heterogeneous cluster environments

Dr. Oren Segal, University of Massachusetts Lowell

The strength of heterogeneous systems is also their Achilles heel, i.e. the diversity of the devices and ecosystems needed to maintain them present major technological challenges. Some of the biggest challenges are in the realm of system programing. We believe that for heterogeneous systems to become a mainstream design choice, high level and standard software design flows need to be adopted in order to achieve transparency when dealing with diverse devices and architectures. We present two open source frameworks meant to assist in transparency when dealing with accelerators in common data center environments. The first is Aparapi-UCores which allows automatic Java to OpenCL translation and targeting of CPUs/GPUs/APUs and FPGAs using a single Java code base. The second is Spark-UCores (SparkCL) which allows running Java/OpenCL accelerator code on heterogeneous cluster nodes running as part of an Apache Spark cluster. We describe the current status of these frameworks and performance results across different architectures. We will also discuss, caching, scheduling and challenges related to achieving good performance and performance per watt on heterogeneous clusters using a high level programming framework such as SparkCL.

Chapel: A Programming Language for Productive, Future-Proof Parallel Computing

Dr. Brad Chamberlain, Cray Inc

In this talk, I will describe some of Chapel’s core features for productivity and flexibility, such as the ability for end-users to define their own parallel loop schedules and array distributions within the language. I’ll provide status and future plans for the language and will call out ways in which we hope that applied scientists and other computer scientists might work with us to increase the chances of productive exascale computing with Chapel.

Theories and Optimization of Nonuniform Locality and Heterogeneous Memory

Prof. Chen Ding,?University of?Rochester

Formal definitions of locality at program, trace, and machine levels.

The higher-order theory of locality (HOTL) and its use in cache performance optimization especially for multicore/manycore shared cache.

(Exploring with others) Formalization and theoretical implications of locality optimization in parallel applications, languages, compilers and run-time systems.

The safe parallelization of a scripting language, in particular Ruby, and a demonstration of safe (hint-based) parallel programming.

Acceleration of Global Atmospheric Model by Heterogeneous Computing with OpenACC

Prof. Ryuji Yoshida, RIKEN

1. an example of the leading edge global atmospheric simulation

2. climate simulation needs more computational performance?- it’s a motivation for using heterogeneous HPC.

3. an example of applying heterogeneous computing for global atmospheric model (NICAM-DC)?- the model is implemented by using OpenACC, and I’ll talk about a tuning strategy.

4. an another example: accelerator would be effective for physical schemes (radiation scheme)

5. current difficulties in heterogeneous computing

6. As a discussion topics; what is the most effective heterogeneous computing??- I would like to introduce a project trying to use DSL on the global model.

Homogeneous Software for Heterogeneous Architectures

Dr. Dan Ghica, University of Birmingham

The increasing complexity of hardware (e.g. GPU and FPGA) and OS-level software (e.g. containers) is reflected in a proliferation of new programming languages and idioms. Even though many such languages enjoy all the syntactic trappings of modern programming languages they are essentially system-specific languages which exhibit most of their typical problems (extreme complexity, fragility, lack of portability) and impose a tremendous burden on the programmer. It is not an exaggeration to say that many such emerging computational platforms are inaccessible to all but a few highly trained specialists. There is a clear danger that we will repeat the mistakes of the pioneering days of computing (1950s and 1960s) when each computer model came with its own distinct OS and programming language. We need to re-establish machine-independent programming as the default and dominant programming model, for the same reasons that it was first established in the 1960s with the advent of Fortran, Algol and LISP. In this talk I will explain how the programmer can be relieved of the burden of programming heterogeneous architectures by creating better type systems, more powerful compilers and smarter linkers. I will illustrate the theory with two concrete case studies: compiling an Algol-like programming language for the heterogeneous Zinq architecture from Xilinx, and an ML-like programming language for a generic deployment-independent distributed platform.

Present and future projections of urban climate based on downscaling techniques

Prof. Satoru Iizuka,?Nagoya University

Present and future (2030s, 2050s, and 2070s) projections of urban climate in the third biggest metropolitan area in Japan (Nagoya?metropolitan area) based on downscaling techniques are presented.?Downscaling is a computer simulation technique to systematically?analyze/project present or future climate from global scale to urban?scale in a step-by-step manner. In this presentation, first, the?prediction accuracy of the downscaling simulations is verified by?comparing observation data and the results of the present climate?analyses, and the advantages and disadvantages are studied. Next, the?future climate change in the Nagoya metropolitan area is examined?through the results of the future climate projections. In future?climate projections, it is necessary to assume various future?scenarios such as global climate scenario (greenhouse gas emissions?scenario), urban structure scenario, and city-block/building structure?scenario. The effects of the future scenarios on the future climate?projections and the uncertainties of the projections are also?discussed.

The Heterogeneous Programming Stack: Architectures, Performance Monitoring, Scheduling, and Virtualization

Prof. Lesley Shannon,?Simon Fraser University

As we move into a heterogeneous computing world, it?introduces changes to all aspects of the computing hierarchy. While we work to make changes to the individual components?there is also significant potential to improve computing?performance, power efficiency, and programmability by working?on the interactions and integration of the various components of?the computing stack. ?This talk discusses the some of the questions?that should be addressed to frame this next generation of?computing design.

Heterogeneous Computing without Heterogeneous Programming?

Dr. Clemens Grelck, ?University of Amsterdam

Heterogeneous computing systems offer unprecedented performance at the
expense of unprecedented programming complexity. A range of programming
paradigms need to be mastered and carefully integrated with each other
to harness at least some of the compute power theoretically offered by
such systems. This may be a challenge for some brave, but hardly more
than a nuisance for the vast majority of programmers.

I will talk about our work in the context of the functional array language
SAC (Single Assignment C) to make heterogeneous systems effectively
usable without any sort of heterogeneous programming. From a uniform source
code that is highly abstract, but does expose fine-grained concurrency,
we aim at compiling down to heterogeneous systems in a completely automatic
way. While this may not achieve the highest possible performance, we open
up a door for non-expert programmers in a world of ever more complex
computing systems.



Dr. Wim Vanderbauwhede

Dr. Wim A. Vanderbauwhede received his PhD in Electrotechnical Engineering from the University of Gent, Belgium in 1996. Before returning to academic research in 2001, Dr Vanderbauwhede worked as an IC Design Engineer and Senior Technology R&D Engineer. From 2001-2004 he was Research Fellow at Strathclyde University.?Currently he is a Senior Lecturer in Computing Science at the University of Glasgow.

Dr Vanderbauwhede’s research focuses on improving the efficiency in High-Performance Computing, both in terms of application development — making parallel programming on heterogeneous systems easier for the end user — and in terms of computational efficiency: reducing the energy consumption per computation to improve the scalability.?He is an expert in FPGA, GPU and multicore parallel programming and in compilers and machine?architectures for heterogeneous manycore systems. His book High-Performance Computing using FPGAs?was published by Springer in March 2013. He has active collaborations on acceleration of Numerical Weather Predictions with Kyoto University and Aizu University (Japan) and Manchester University (UK) and on FPGA computing with University of Massachusetts (US). He currently leads a 2 Million GBP EPSRC project between Glasgow University, Heriot-Watt University and Imperial College London on compilation for heterogeneous manycore systems.

Dr Vanderbauwhede has published more than a hundred refereed conference and journal papers. He is an editorial board member for
IJRC and program committee member/reviewer for several international?conferences/journals.

Prof. Tetsuya Takemi

Prof. Tetsuya Takemi received his PhD and MSc from Kyoto University in 1999 and 1994 respectively.?From 1999-2004 he was Assistant Professor at Osaka University, from 2004-2007 Lecturer at Tokyo Institute of Technology and from 2007 Associate Professor at the Disaster Prevention Research Institute of Kyoto University.?From 2001-2002 he was a visiting scientist at National Center for Atmospheric Research in the United States.

His research interests include mesoscale and microscale meteorology, environmental fluid dynamics, atmospheric convection and mesoscale meteorological modeling, in particular of severe local storms and heavy rain.?He is also studying on numerical simulations of atmospheric turbulence and dispersion over complex terrain and complex building configuration by developing an approach to couple mesoscale meteorological model and large-eddy simulation model.

Prof. Takemi has published more than eighty refereed conference and journal papers. He is a member of the Meteorological Society of Japan, Japan Geoscience Union, Japan Association for Wind Engineering, American Meteorological Society and the American Geophysical Union. He is the Chief Editor of SOLA, an online letter journal of the Meteorological Society of Japan, and the Co-Chief Editor of Journal of the Meteorological Society of Japan.

Prof. Sven-Bodo Scholz

Sven-Bodo Scholz received his Dr.rer.nat. and a German Habilitation from?the University of Kiel in 1996 and in 2004, respectively.
From 2004 – 2011 he was Senior Lecturer and later Reader at the University of Hertfordshire in England.?Currently, he is Professor at Heriot-Watt University, Scotland.

Sven-Bodo Scholz’s research is driven by the desire to bridge the gap?between high-productivity programming tools and high-performance,
heterogeneous many-core systems by means of compilation technology. He has?made various contributions in the area of programming languages and?compilation technology including novel type systems, partial evaluation?techniques, memory management techniques and novel approaches to generic?programming. He has initiated and led several research projects that?focused around the design and implementation of programming systems, all of?which contributed to several ready-to-use systems in the public domain.

He was Co-I and P-I on several grants, nationally-funded, as well as EU-funded totalling?in excess of 3 Million GBP. He has authored over 100 publications, was editor of books?and special journal issues, and member of various program committees. He is a member?of the ACM and of IFIP working group 2.11. He has organised several workshops, symposia?and tutorial presentations and is member of the IFL steering committee.


First name Family name Affiliation Country URL Research Interest
Mark Govett NOAA ESRL USA Weather Forecasting, High performance computing
Lesley Shannon Simon Fraser University Canda Computing system design and programming models,?Operating Systems for asymmetric/heterogeneous multicore systems
Satoru Iizuka Nagoya University Japan Sustainable Urban Development
Ryuji Yoshida RIKEN Advanced Institute for Computational Science Japan NWP, HPC, OpenACC
Nobuko Yoshida Imperial College London UK Concurrent Programming
Albert Cohen INRIA France Compiler technology, Data-Flow
Clemens Grelck University of Amsterdam The Netherlands Compiler technology, Dynamic Adaptation
Bradford Chamberlain Cray Inc. USA Compiler technology Chapel
Chen Ding University of Rochester USA Compiler technology for HPC
Oleg Kiselyov Tohoku University Japan Programm Generation
Martin Elsman University of Copenhagen Denmark Compiler Technology
Theo Ungerer University of Augsburg Germany Compiler Technology
Michael Philippsen University of Erlangen-Nuremberg Germany Compiler Technology
Yukiyoshi Kameyama University of Tsukuba Japan Programming Logic
Oren Segal University of Massachusetts Lowell USA FPGA Programming, OpenCL
Minoru Watanabe Shizuoka University Japan FPGA Architectures
Lilia Georgieva Heriot-Wattt University UK Proof Theory
Christian Fensch Heriot-Watt University UK Compiler Technology
Mary Sheeran Chalmers University of Technology Sweden Compiler Technology
Lasse Natvig IDI, NTNU Norway Compiler Technology
Raphael ‘kena’ Poss University of Amsterdam The Netherlands Compiler Technology
Dan Ghica University of Birmingham UK Programming languages type systems and semantics
Cosmin Oancea University of Copenhagen Denmark Programming Languages, Parallel programming
Hisashi Yashiro RIKEN Advanced Institute for Computational Science Japan Development of global/regional climate model towards to Exa-scale HPC system


The meeting runs from?Monday 16 November (check-in day, welcome reception) to Friday 20 November noon.?There is one half-day excursion planned on the Thursday.

The program has not been finalised but?the schedule will be similar to?NII-Shonan-MeetingTime-Table-4daysSAMPLE-201404171.


You can find the?overview?of the meeting on the Shonan?Seminars page.