Alice Koniges, Berkeley Lab, NERSC
Katherine Yelick, UC Berkeley and Berkeley Lab, NERSC
Rolf Rabenseifner, High Performance Computing Center Stuttgart
Reinhold Bader, Leibniz Supercomputing Center Munich
David Eder, Lawrence Livermore National Laboratory
A full-day tutorial at SC12
PGAS (Partitioned Global Address Space) languages offer both an alternative to traditional parallelization approaches (MPI and OpenMP), and the possibility of improved performance on heterogeneous and modern architectures. In this tutorial we cover general PGAS concepts and give an in depth presentation of two commonly used PGAS languages, Coarray Fortran (CAF) and Unified Parallel C (UPC). Hands-on exercises to illustrate important concepts are interspersed with the lectures. Basic PGAS features, syntax for data distribution, intrinsic functions and synchronization primitives are discussed. Advanced topics include optimization and correctness checking of PGAS codes with an emphasis on emerging and planned PGAS language extensions targeted at scalability and usability improvement. A section on migration of MPI codes using performance improvements from both CAF and UPC is given in a hybrid programming section. Longer examples, tools and performance data on the latest petascale systems round out the presentations.
This tutorial represents a unique collaboration between the Berkeley PGAS/UPC group and experienced hands-on PGAS and hybrid instructors. Participants will be provided with the technical foundations necessary to write library or application codes using CAF or UPC, and an introduction to experimental techniques for combining MPI with PGAS languages.
The tutorial will stress some of the advantages of PGAS programming models including
· potentially easier programmability and therefore higher productivity than with purely MPI-based programming due to one-sided communication semantics, integration of the type system and other language features included with the parallel facilities
· optimization potential for the language processor (compiler + runtime system)
· improved scalability compared to OpenMP at the same level of usage complexity due to better locality control
· flexibility with respect to architectures – PGAS may be deployed on shared memory multi-core systems as well as (with some care required) on large-scale MPP architectures
The tutorial's strategy to provide an integrated view of both CAF and UPC will allow the audience to get a clear picture of similarities and differences between these two approaches to PGAS programming. Hybrid programming using both OpenMP and PGAS will be illustrated and compared.
The PGAS base is growing and targets a wide range of SC attendees. Application programmers, vendors and library designers coming from both C and Fortran backgrounds, will attend this tutorial. Multicore architectures are the norm now, from high end systems to desktops. This tutorial therefore addresses computer professionals with access to a very wide variety of programming platforms. This tutorial attracts more participants than tutorials specialized to only one PGAS language. In HPC, many applications are multi-language applications, e.g., with parts in Fortran, C and C++. The tutorial does cover general PGAS aspects (30%), as well as the more specific UPC implementation (35%) and CAF implementation (35%). In the exercises, the participants can concentrate on their preferred language or use both.
Participants should have knowledge of at least one of the Fortran 95 and C programming languages, and should be comfortable with running example programs in a Linux environment. Technical assistants (TA) and other personnel will be available for help with the exercises. In addition, a basic knowledge of traditional parallel programming models (MPI and OpenMP) is useful but not essential for the more advanced parts of the tutorial. Attendees are paired in groups of two or with a TA if/when we need to accommodate attendees without laptops. On laptops, a secure shell for SSH should be installed to be able to login to the compute nodes that are provided for the exercises, and we have alternate servers available both in the US and Germany if there were any problems with outages. See also http://www.nersc.gov/users/data-and-networking/connecting-to-nersc/ .
After an introduction to general PGAS concepts as well as to the status of the standardization efforts, the basic syntax for declaration and use of shared data is presented; the requirements and rules for synchronization of accesses to shared data are explained (PGAS memory model). This is followed by the topic of dynamic memory management for shared entities. Then, advanced synchronizations mechanisms like locks, atomic procedures as well as collective procedures are discussed, as well as their usefulness for implementation of certain parallel programming patterns. The section on hybrid programming explains the way MPI makes allowances for hybrid models, and how this can be matched with PGAS-based implementations. Finally, still existing deficiencies in the present language definitions of CAF and UPC will be indicated; an outlook will be provided for possible future extensions, which are presently still under discussion among language developers, and should allow to overcome most of the above-mentioned deficiencies.
The hands-on sessions are interspersed with the presentations such that approximately one hour of presentation is followed by 30 minutes of exercises. The exercises will come from a pool of exercises that have been tested on courses given throughout Europe, as well as additional exercises for the newest material.
The NERSC computer center will make available a special partition of their Cray XT machines and a set of accounts to accommodate the hands-on exercises. This model has already been successfully deployed at the previous SC10 and SC11 PGAS tutorials. In the event that a natural disaster or a system crash takes this planned system down, the users will have access to the same exercises on an SGI UltraViolet system at LRZ. Attendees will use laptops that can open a ssh window; they will be grouped in pairs to accommodate people without a laptop, and also to handle any other account issues that come up. Attendees may do the exercises in pairs in both UPC and CAF, to allow comparison of both languages. When possible, C programmers will be paired with Fortran programmers. For advanced programmers or those who want to stay in one language, additional exercise material will be provided for efficient use of the exercise time. UC Berkeley teaching assistants from the course CS 267, “Applications of Parallel Computers,” may be available as needed to help with the hands-on exercises.
Presently planned examples include
and this list will be updated as the tutorial material is finalized.
[-- Coffee break --]
[-- Lunch break --]
[-- Coffee break --]
[-- End --]
Dr. Alice Koniges is a Physicist and Computer Scientist at the National Energy Research Scientific Computing Center (NERSC) at the Berkeley Lab, where she leads the Petascale Computing Initiative and various science research projects including preparing codes for exascale. Her current research interests include programming models, benchmarking and optimization, applications in plasma physics, material science, energy research, and arbitrary Lagrange Eulerian methods for time-dependent PDE’s. Previous to working at the Berkeley Lab, she held various positions at the Lawrence Livermore National Laboratory, including management of the Lab’s institutional computing. She recently led the effort to develop a new code that is used predict the impacts of target shrapnel and debris on the operation of the National Ignition Facility (NIF), the world’s most powerful laser. She was the first woman to receive a PhD in Applied and Computational Mathematics at Princeton University and also has MSE and MA degrees from Princeton and a BA in Applied Mechanics from the University of California, San Diego. She is editor and lead author of the book “Industrial Strength Parallel Computing,” (Morgan Kaufmann Publishers 2000) and has published more than 80 refereed technical papers.
Dr. Katherine Yelick is the Associate Laboratory Director for Computing Sciences at Lawrence Berkeley National Laboratory, Director of the National Energy Research Scientific Computing (NERSC) Center and a Professor of Electrical Engineering and Computer Sciences at the University of California at Berkeley. She is the author or co-author of two books and more than 100 refereed technical papers on parallel languages, compilers, algorithms, libraries, architecture, and storage. She co-invented the UPC and Titanium languages and demonstrated their applicability across architectures through the use of novel runtime and compilation methods. She also co-developed techniques for self-tuning numerical libraries, including the first self-tuned library for sparse matrix kernels which automatically adapt the code to properties of the matrix structure and machine. Her work includes performance analysis and modeling as well as optimization techniques for memory hierarchies, multicore processors, communication libraries, and processor accelerators. She earned her Ph.D. in Electrical Engineering and Computer Science from MIT and has been a professor of Electrical Engineering and Computer Sciences at UC Berkeley since 1991 with a joint research appointment at Berkeley Lab since 1996. She has received multiple research and teaching awards and is a member of the California Council on Science and Technology and a member of the National Academies committee on Sustaining Growth in Computing Performance.
Dr. Rolf Rabenseifner studied mathematics and physics at the University of Stuttgart. Since 1984, he has worked at the High-Performance Computing-Center Stuttgart (HLRS). He led the projects DFN-RPC, a remote procedure call tool, and MPI-GLUE, the first metacomputing MPI combining different vendor's MPIs without losses to full MPI functionality. In his dissertation, he developed a controlled logical clock as global time for trace-based profiling of parallel and distributed applications. Since 1996, he has been a member of the MPI-2 Forum and since Dec. 2007 he is in the steering committee of the MPI-3 Forum. From January to April 1999, he was an invited researcher at the Center for High-Performance Computing at Dresden University of Technology. Currently, he is head of Parallel Computing - Training and Application Services at HLRS. He is involved in MPI profiling and benchmarking e.g., in the HPC Challenge Benchmark Suite. In recent projects, he studied parallel I/O, parallel programming models for clusters of SMP nodes, and optimization of MPI collective routines. In workshops and summer schools, he teaches parallel programming models in many universities and labs in Germany. In January 2012, the Gauss Center of Supercomputing (GCS), with HLRS, LRZ in Garching and the Jülich Supercomputing Center as members, was selected as one of six PRACE Advanced Training Centers (PATCs) and he was appointed as GCS' PATC director.
Dr. Reinhold Bader studied physics and mathematics at the Ludwigs-Maximilians University in Munich, completing his studies with a PhD (“Electronic Properties of Boron Nitride and Gallium Arsenide under hydrostatic pressure and tetragonal deformation”) in theoretical solid-state physics in 1998. Since the beginning of 1999, he has worked at Leibniz Supercomputing Centre (LRZ) as a member of the scientific staff, being involved in HPC user support, procurements of new systems, benchmarking of prototypes in the context of the PRACE project, courses for parallel programming, and configuration management for the HPC systems deployed at LRZ. Since May 2012, he is leader of the HPC services group at LRZ, which is responsible for operation of all HPC-related systems and system software packages at LRZ. As a member of the German delegation to WG5, the international Fortran Standards Committee, he has contributed to the further development of the Fortran language, in particular the Technical Specification TS 29113 (Further Interoperability of Fortran with C), and a future Technical Specification of extended coarray facilities. In connection with the work on TS 29113, he has participated in the discussion and proofreading of the new MPI-3.0 Fortran interfaces, which is presently being finalized under the auspices of the MPI Forum. He has published a number of contributions to ACMs Fortran Forum and is responsible for development and maintenance of the Fortran interface to the GNU Scientific Library.
Dr. David Eder is a computational physicist and group leader at the Lawrence Livermore National Laboratory in California. He has extensive experience with application codes for the study of multiphysics problems, including codes in various programming languages. His latest endeavors include ALE (Arbitrary Lagrange Eulerian) on unstructured and block-structured grids for simulations that span many orders of magnitude. He was awarded a research prize in 2000 for use of advanced codes to design the National Ignition Facility (NIF) 192 beam laser that is now in operational mode. He is currently designing and performing large-scale simulation efforts to predict performance of the NIF. He has a track record of giving SC tutorials to a broad audience and with a particular emphasis on real applications and performance issues. He has a PhD in Astrophysics from Princeton University and a BS in Mathematics and Physics from the Univ. of Colorado. He has published approximately 80 research papers.
· Parallel Programming
URL of this page (shortened):