Lecture 15-16: Parallel Programming with Cilk
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Other Apis What’S Wrong with Openmp?
Threaded Programming Other APIs What’s wrong with OpenMP? • OpenMP is designed for programs where you want a fixed number of threads, and you always want the threads to be consuming CPU cycles. – cannot arbitrarily start/stop threads – cannot put threads to sleep and wake them up later • OpenMP is good for programs where each thread is doing (more-or-less) the same thing. • Although OpenMP supports C++, it’s not especially OO friendly – though it is gradually getting better. • OpenMP doesn’t support other popular base languages – e.g. Java, Python What’s wrong with OpenMP? (cont.) Can do this Can do this Can’t do this Threaded programming APIs • Essential features – a way to create threads – a way to wait for a thread to finish its work – a mechanism to support thread private data – some basic synchronisation methods – at least a mutex lock, or atomic operations • Optional features – support for tasks – more synchronisation methods – e.g. condition variables, barriers,... – higher levels of abstraction – e.g. parallel loops, reductions What are the alternatives? • POSIX threads • C++ threads • Intel TBB • Cilk • OpenCL • Java (not an exhaustive list!) POSIX threads • POSIX threads (or Pthreads) is a standard library for shared memory programming without directives. – Part of the ANSI/IEEE 1003.1 standard (1996) • Interface is a C library – no standard Fortran interface – can be used with C++, but not OO friendly • Widely available – even for Windows – typically installed as part of OS – code is pretty portable • Lots of low-level control over behaviour of threads • Lacks a proper memory consistency model Thread forking #include <pthread.h> int pthread_create( pthread_t *thread, const pthread_attr_t *attr, void*(*start_routine, void*), void *arg) • Creates a new thread: – first argument returns a pointer to a thread descriptor. -
Analysis of GPU-Libraries for Rapid Prototyping Database Operations
Analysis of GPU-Libraries for Rapid Prototyping Database Operations A look into library support for database operations Harish Kumar Harihara Subramanian Bala Gurumurthy Gabriel Campero Durand David Broneske Gunter Saake University of Magdeburg Magdeburg, Germany fi[email protected] Abstract—Using GPUs for query processing is still an ongoing Usually, library operators for GPUs are either written by research in the database community due to the increasing hardware experts [12] or are available out of the box by device heterogeneity of GPUs and their capabilities (e.g., their newest vendors [13]. Overall, we found more than 40 libraries for selling point: tensor cores). Hence, many researchers develop optimal operator implementations for a specific device generation GPUs each packing a set of operators commonly used in one involving tedious operator tuning by hand. On the other hand, or more domains. The benefits of those libraries is that they are there is a growing availability of GPU libraries that provide constantly updated and tested to support newer GPU versions optimized operators for manifold applications. However, the and their predefined interfaces offer high portability as well as question arises how mature these libraries are and whether they faster development time compared to handwritten operators. are fit to replace handwritten operator implementations not only w.r.t. implementation effort and portability, but also in terms of This makes them a perfect match for many commercial performance. database systems, which can rely on GPU libraries to imple- In this paper, we investigate various general-purpose libraries ment well performing database operators. Some example for that are both portable and easy to use for arbitrary GPUs such systems are: SQreamDB using Thrust [14], BlazingDB in order to test their production readiness on the example of using cuDF [15], Brytlyt using the Torch library [16]. -
8A. Going Parallel
2019/2020 UniPD - T. Vardanega 02/06/2020 Terminology /1 • Program = static piece of text 8a. Going parallel – Instructions + link-time data • Processor = resource that can execute a program – In a “multi-processor,” processors may – Share uniformly one common address space for main memory – Have non-uniform access to shared memory – Have unshared parts of memory – Share no memory as in “Shared Nothing” (distributed memory) Where we take a bird’s eye look at what architectures changes (again!) when jobs become • Process = instance of program + run-time data parallel in response to the quest for best – Run-time data = registers + stack(s) + heap(s) use of (massively) parallel hardware Parallel Lang Support 505 Terminology /2 Terms in context: LWT within LWP • No uniform naming of threads of control within process –Thread, Kernel Thread, OS Thread, Task, Job, Light-Weight Process, Virtual CPU, Virtual Processor, Execution Agent, Executor, Server Thread, Worker Thread –Taskgenerally describes a logical piece of work – Element of a software architecture –Threadgenerally describes a virtual CPU, a thread of control within a process –Jobin the context of a real-time system generally describes a single execution consequent to a task release Lightweight because OS • No uniform naming of user-level lightweight threads does not schedule threads –Task, Microthread, Picothread, Strand, Tasklet, Fiber, Lightweight Thread, Work Item – Called “user-level” in that scheduling is done by code outside of Exactly the same logic applies to user-level lightweight the kernel/operating-system threads (aka tasklets), which do not need scheduling Parallel Lang Support 506 Parallel Lang Support 507 Real-Time Systems 1 2019/2020 UniPD - T. -
Opencl on Shared Memory Multicore Cpus
OpenCL on shared memory multicore CPUs Akhtar Ali, Usman Dastgeer and Christoph Kessler Book Chapter N.B.: When citing this work, cite the original article. Part of: Proceedings of the 5th Workshop on MULTIPROG -2012. E. Ayguade, B. Gaster, L. Howes, P. Stenström, O. Unsal (eds), 2012. Copyright: HiPEAC Network of Excellence Available at: Linköping University Electronic Press http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-93951 Published in: Proc. Fifth Workshop on Programmability Issues for Multi-Core Computers (MULTIPROG-2012) at HiPEAC-2012 conference, Paris, France, Jan. 2012. OpenCL for programming shared memory multicore CPUs Akhtar Ali, Usman Dastgeer, and Christoph Kessler PELAB, Dept. of Computer and Information Science, Linköping University, Sweden [email protected] {usman.dastgeer,christoph.kessler}@liu.se Abstract. Shared memory multicore processor technology is pervasive in mainstream computing. This new architecture challenges programmers to write code that scales over these many cores to exploit the full compu- tational power of these machines. OpenMP and Intel Threading Build- ing Blocks (TBB) are two of the popular frameworks used to program these architectures. Recently, OpenCL has been defined as a standard by Khronos group which focuses on programming a possibly heteroge- neous set of processors with many cores such as CPU cores, GPUs, DSP processors. In this work, we evaluate the effectiveness of OpenCL for programming multicore CPUs in a comparative case study with OpenMP and Intel TBB for five benchmark applications: matrix multiply, LU decomposi- tion, 2D image convolution, Pi value approximation and image histogram generation. The evaluation includes the effect of compiler optimizations for different frameworks, OpenCL performance on different vendors’ plat- forms and the performance gap between CPU-specific and GPU-specific OpenCL algorithms for execution on a modern GPU. -
Heterogeneous Task Scheduling for Accelerated Openmp
Heterogeneous Task Scheduling for Accelerated OpenMP ? ? Thomas R. W. Scogland Barry Rountree† Wu-chun Feng Bronis R. de Supinski† ? Department of Computer Science, Virginia Tech, Blacksburg, VA 24060 USA † Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA [email protected] [email protected] [email protected] [email protected] Abstract—Heterogeneous systems with CPUs and computa- currently requires a programmer either to program in at tional accelerators such as GPUs, FPGAs or the upcoming least two different parallel programming models, or to use Intel MIC are becoming mainstream. In these systems, peak one of the two that support both GPUs and CPUs. Multiple performance includes the performance of not just the CPUs but also all available accelerators. In spite of this fact, the models however require code replication, and maintaining majority of programming models for heterogeneous computing two completely distinct implementations of a computational focus on only one of these. With the development of Accelerated kernel is a difficult and error-prone proposition. That leaves OpenMP for GPUs, both from PGI and Cray, we have a clear us with using either OpenCL or accelerated OpenMP to path to extend traditional OpenMP applications incrementally complete the task. to use GPUs. The extensions are geared toward switching from CPU parallelism to GPU parallelism. However they OpenCL’s greatest strength lies in its broad hardware do not preserve the former while adding the latter. Thus support. In a way, though, that is also its greatest weak- computational potential is wasted since either the CPU cores ness. To enable one to program this disparate hardware or the GPU cores are left idle. -
Correct and Efficient Work-Stealing for Weak Memory Models
Correct and Efficient Work-Stealing for Weak Memory Models Nhat Minh Lê Antoniu Pop Albert Cohen Francesco Zappa Nardelli INRIA and ENS Paris Abstract Lev’s deque for the ARM architectures, and prove its correctness Chase and Lev’s concurrent deque is a key data structure in shared- against the memory semantics defined in [12] and [7]. Our second memory parallel programming and plays an essential role in work- contribution is a systematic study of the performance of several stealing schedulers. We provide the first correctness proof of an implementations of Chase–Lev on relaxed hardware. In detail, we optimized implementation of Chase and Lev’s deque on top of the compare our optimized ARM implementation against a standard POWER and ARM architectures: these provide very relaxed mem- implementation for the x86 architecture and two portable variants ory models, which we exploit to improve performance but consider- expressed in C11: a reference sequentially consistent translation ably complicate the reasoning. We also study an optimized x86 and of the algorithm, and an aggressively optimized version making a portable C11 implementation, conducting systematic experiments full use of the release–acquire and relaxed semantics offered by to evaluate the impact of memory barrier optimizations. Our results C11 low-level atomics. These implementations of the Chase–Lev demonstrate the benefits of hand tuning the deque code when run- deque are evaluated in the context of a work-stealing scheduler. We ning on top of relaxed memory models. consider diverse worker/thief configurations, including a synthetic benchmark with two different workloads and standard task-parallel Categories and Subject Descriptors D.1.3 [Programming Tech- kernels. -
AMD Accelerated Parallel Processing Opencl Programming Guide
AMD Accelerated Parallel Processing OpenCL Programming Guide November 2013 rev2.7 © 2013 Advanced Micro Devices, Inc. All rights reserved. AMD, the AMD Arrow logo, AMD Accelerated Parallel Processing, the AMD Accelerated Parallel Processing logo, ATI, the ATI logo, Radeon, FireStream, FirePro, Catalyst, and combinations thereof are trade- marks of Advanced Micro Devices, Inc. Microsoft, Visual Studio, Windows, and Windows Vista are registered trademarks of Microsoft Corporation in the U.S. and/or other jurisdic- tions. Other names are for informational purposes only and may be trademarks of their respective owners. OpenCL and the OpenCL logo are trademarks of Apple Inc. used by permission by Khronos. The contents of this document are provided in connection with Advanced Micro Devices, Inc. (“AMD”) products. AMD makes no representations or warranties with respect to the accuracy or completeness of the contents of this publication and reserves the right to make changes to specifications and product descriptions at any time without notice. The information contained herein may be of a preliminary or advance nature and is subject to change without notice. No license, whether express, implied, arising by estoppel or other- wise, to any intellectual property rights is granted by this publication. Except as set forth in AMD’s Standard Terms and Conditions of Sale, AMD assumes no liability whatsoever, and disclaims any express or implied warranty, relating to its products including, but not limited to, the implied warranty of merchantability, fitness for a particular purpose, or infringement of any intellectual property right. AMD’s products are not designed, intended, authorized or warranted for use as compo- nents in systems intended for surgical implant into the body, or in other applications intended to support or sustain life, or in any other application in which the failure of AMD’s product could create a situation where personal injury, death, or severe property or envi- ronmental damage may occur. -
Implementing FPGA Design with the Opencl Standard
Implementing FPGA Design with the OpenCL Standard WP-01173-3.0 White Paper Utilizing the Khronos Group’s OpenCL™ standard on an FPGA may offer significantly higher performance and at much lower power than is available today from hardware architectures such as CPUs, graphics processing units (GPUs), and digital signal processing (DSP) units. In addition, an FPGA-based heterogeneous system (CPU + FPGA) using the OpenCL standard has a significant time-to-market advantage compared to traditional FPGA development using lower level hardware description languages (HDLs) such as Verilog or VHDL. 1 OpenCL and the OpenCL logo are trademarks of Apple Inc. used by permission by Khronos. Introduction The initial era of programmable technologies contained two different extremes of programmability. As illustrated in Figure 1, one extreme was represented by single core CPU and digital signal processing (DSP) units. These devices were programmable using software consisting of a list of instructions to be executed. These instructions were created in a manner that was conceptually sequential to the programmer, although an advanced processor could reorder instructions to extract instruction-level parallelism from these sequential programs at run time. In contrast, the other extreme of programmable technology was represented by the FPGA. These devices are programmed by creating configurable hardware circuits, which execute completely in parallel. A designer using an FPGA is essentially creating a massively- fine-grained parallel application. For many years, these extremes coexisted with each type of programmability being applied to different application domains. However, recent trends in technology scaling have favored technologies that are both programmable and parallel. Figure 1. -
Concurrent Cilk: Lazy Promotion from Tasks to Threads in C/C++
Concurrent Cilk: Lazy Promotion from Tasks to Threads in C/C++ Christopher S. Zakian, Timothy A. K. Zakian Abhishek Kulkarni, Buddhika Chamith, and Ryan R. Newton Indiana University - Bloomington, fczakian, tzakian, adkulkar, budkahaw, [email protected] Abstract. Library and language support for scheduling non-blocking tasks has greatly improved, as have lightweight (user) threading packages. How- ever, there is a significant gap between the two developments. In previous work|and in today's software packages|lightweight thread creation incurs much larger overheads than tasking libraries, even on tasks that end up never blocking. This limitation can be removed. To that end, we describe an extension to the Intel Cilk Plus runtime system, Concurrent Cilk, where tasks are lazily promoted to threads. Concurrent Cilk removes the overhead of thread creation on threads which end up calling no blocking operations, and is the first system to do so for C/C++ with legacy support (standard calling conventions and stack representations). We demonstrate that Concurrent Cilk adds negligible overhead to existing Cilk programs, while its promoted threads remain more efficient than OS threads in terms of context-switch overhead and blocking communication. Further, it enables development of blocking data structures that create non-fork-join dependence graphs|which can expose more parallelism, and better supports data-driven computations waiting on results from remote devices. 1 Introduction Both task-parallelism [1, 11, 13, 15] and lightweight threading [20] libraries have become popular for different kinds of applications. The key difference between a task and a thread is that threads may block|for example when performing IO|and then resume again. -
Scalable and High Performance MPI Design for Very Large
SCALABLE AND HIGH-PERFORMANCE MPI DESIGN FOR VERY LARGE INFINIBAND CLUSTERS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Sayantan Sur, B. Tech ***** The Ohio State University 2007 Dissertation Committee: Approved by Prof. D. K. Panda, Adviser Prof. P. Sadayappan Adviser Prof. S. Parthasarathy Graduate Program in Computer Science and Engineering c Copyright by Sayantan Sur 2007 ABSTRACT In the past decade, rapid advances have taken place in the field of computer and network design enabling us to connect thousands of computers together to form high-performance clusters. These clusters are used to solve computationally challenging scientific problems. The Message Passing Interface (MPI) is a popular model to write applications for these clusters. There are a vast array of scientific applications which use MPI on clusters. As the applications operate on larger and more complex data, the size of the compute clusters is scaling higher and higher. Thus, in order to enable the best performance to these scientific applications, it is very critical for the design of the MPI libraries be extremely scalable and high-performance. InfiniBand is a cluster interconnect which is based on open-standards and gaining rapid acceptance. This dissertation presents novel designs based on the new features offered by InfiniBand, in order to design scalable and high-performance MPI libraries for large-scale clusters with tens-of-thousands of nodes. Methods developed in this dissertation have been applied towards reduction in overall resource consumption, increased overlap of computa- tion and communication, improved performance of collective operations and finally designing application-level benchmarks to make efficient use of modern networking technology. -
Opencl SYCL 2.2 Specification
SYCLTM Provisional Specification SYCL integrates OpenCL devices with modern C++ using a single source design Version 2.2 Revision Date: – 2016/02/15 Khronos OpenCL Working Group — SYCL subgroup Editor: Maria Rovatsou Copyright 2011-2016 The Khronos Group Inc. All Rights Reserved Contents 1 Introduction 13 2 SYCL Architecture 15 2.1 Overview . 15 2.2 The SYCL Platform and Device Model . 15 2.2.1 Platform Mixed Version Support . 16 2.3 SYCL Execution Model . 17 2.3.1 Execution Model: Queues, Command Groups and Contexts . 18 2.3.2 Execution Model: Command Queues . 19 2.3.3 Execution Model: Mapping work-items onto an nd range . 21 2.3.4 Execution Model: Execution of kernel-instances . 22 2.3.5 Execution Model: Hierarchical Parallelism . 24 2.3.6 Execution Model: Device-side enqueue . 25 2.3.7 Execution Model: Synchronization . 25 2.4 Memory Model . 26 2.4.1 Access to memory . 27 2.4.2 Memory consistency . 28 2.4.3 Atomic operations . 28 2.5 The SYCL programming model . 28 2.5.1 Basic data parallel kernels . 30 2.5.2 Work-group data parallel kernels . 30 2.5.3 Hierarchical data parallel kernels . 30 2.5.4 Kernels that are not launched over parallel instances . 31 2.5.5 Synchronization . 31 2.5.6 Error handling . 32 2.5.7 Scheduling of kernels and data movement . 32 2.5.8 Managing object lifetimes . 34 2.5.9 Device discovery and selection . 35 2.5.10 Interfacing with OpenCL . 35 2.6 Anatomy of a SYCL application . -
DNA Scaffolds Enable Efficient and Tunable Functionalization of Biomaterials for Immune Cell Modulation
ARTICLES https://doi.org/10.1038/s41565-020-00813-z DNA scaffolds enable efficient and tunable functionalization of biomaterials for immune cell modulation Xiao Huang 1,2, Jasper Z. Williams 2,3, Ryan Chang1, Zhongbo Li1, Cassandra E. Burnett4, Rogelio Hernandez-Lopez2,3, Initha Setiady1, Eric Gai1, David M. Patterson5, Wei Yu2,3, Kole T. Roybal2,4, Wendell A. Lim2,3 ✉ and Tejal A. Desai 1,2 ✉ Biomaterials can improve the safety and presentation of therapeutic agents for effective immunotherapy, and a high level of control over surface functionalization is essential for immune cell modulation. Here, we developed biocompatible immune cell-engaging particles (ICEp) that use synthetic short DNA as scaffolds for efficient and tunable protein loading. To improve the safety of chimeric antigen receptor (CAR) T cell therapies, micrometre-sized ICEp were injected intratumorally to present a priming signal for systemically administered AND-gate CAR-T cells. Locally retained ICEp presenting a high density of priming antigens activated CAR T cells, driving local tumour clearance while sparing uninjected tumours in immunodeficient mice. The ratiometric control of costimulatory ligands (anti-CD3 and anti-CD28 antibodies) and the surface presentation of a cytokine (IL-2) on ICEp were shown to substantially impact human primary T cell activation phenotypes. This modular and versatile bio- material functionalization platform can provide new opportunities for immunotherapies. mmune cell therapies have shown great potential for cancer the specific antibody27, and therefore a high and controllable den- treatment, but still face major challenges of efficacy and safety sity of surface biomolecules could allow for precise control of ligand for therapeutic applications1–3, for example, chimeric antigen binding and cell modulation.