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Scalable Parallel Computing on Many/Multicore Systems This set of lectures will review the application and programming model issues that will one must address when one gets chips with 32-1024 cores and “scalable” approaches will be needed to make good use of such systems. We will not discuss bit-level and instruction-level parallelism i.e. what happens on a possibly special purpose core, even though this is clearly important. We will use science and engineering applications to drive the discussion as we have substantial experience in these cases but we are interested in the lessons for commodity client and server applications that will be broadly used 5-10 years from now. We start with simple applications and algorithms from a variety of fields and identify features that makes it “obvious” that “all” science and engineering run well and scalably in parallel. We explain why unfortunately it is equally obvious that there is no straightforward way of expressing this parallelism. Parallel hardware architectures are described in enough detail to understand performance and algorithm issues and need for cross-architecture compatibility; however in these lectures we will just be users of hardware. We must understand what features of multicore chips we can and should exploit. We can explicitly use the shared memory between cores or just enjoy its implications for very fast inter-core control and communication linkage. We note that parallel algorithm research is hugely successful although this success has reduced activity in an area that deserves new attention for the next generation of architectures. The parallel software environment is discussed at several levels including programming paradigm, runtime and operating system. The importance of libraries, templates, kernels (dwarfs) and benchmarks is stressed. The programming environment has various tools including compilers with possible parallelism hints like OpenMP; tuners like Atlas; messaging models; parallelism and distribution support as in HPF, HPCS Languages, co-array Fortran, Global arrays and UPC. We also discuss the relevance of important general ideas like object-oriented paradigms (as in for example Charm++), functional languages and Software Transactional Memories. Streaming, pipelining, co-ordination, services and workflow are placed in context. Examples discussed in the last category include CCR/DSS from Microsoft and the Common Component Architecture CCA from DoE. Domain Specific environments like Matlab and Mathematica are important as there is no universal silver programming bullet; one will need interoperable focused environments. We discuss performance analysis including speedup, efficiency, scaled speedup and Amdahl's law. We show how to relate performance to algorithm/application structure and the hardware characteristics. Applications will not get scalable parallelism accidentally but only if there is an understandable performance model. We review some of the many pitfalls for both performance and correctness; these include deadlocks, race conditions, nodes that are busy doing something else and the difficulty of second-guessing automatic parallelization methods. We describe the formal sources of overhead; load imbalance and the communication/control overhead and the ways to reduce them. We relate the blocking used in caching to that used in parallel computation. We note that load balancing was the one part of parallel computing that was easier than expected. We will mix both simple idealized applications with “real problems” noting that usually it is simple problems that are the hardest as they have poor computation to control/communication ratios. We will explain the parallelism in several application classes including for science and engineering: Finite Difference, Finite Elements, FFT/Spectral, Meshes of all sorts, Particle Dynamics, Particle-Mesh, and Monte Carlo methods. Some applications like Image Processing, Graphics, Cryptography and Media coding/decoding have features similar to well understood science and engineering problems. We emphasize that nearly all applications are built hierarchically from more “basic applications” with a variety of different structures and natural programming models. Such application composition (co-ordination, workflow) must be supported with a common run-time. We contrast the difference between decomposition needed in most “basic parallel applications” to the composition supported in workflow and Web 2.0 mashups. Looking at broader application classes we should cover; Internet applications and services; artificial intelligence, optimization, machine learning; divide and conquer algorithms; tree structured searches like computer chess; applications generated by the data deluge including access, search, and the assimilation of data into simulations. There has been a growing interest in Complex Systems whether it be for critical infrastructure like energy and transportation, the Internet itself, commodity gaming, computational epidemiology or the original war games. We expect Discrete Event Simulations (such as DoD’s High Level Architecture HLA) to grow in importance as they naturally describe complex systems and because they can clearly benefit from multicore architectures. We will discuss the innovative Sequential Dynamical Systems approach used in the EpiSims, TransSims and other critical infrastructure simulation environments. In all applications we need to identify the intrinsic parallelism and the degrees of freedom that can be parallelized and distinguish small parallelism (local to core) compared to large parallelism (scalable across many cores) We will not forget many critical non-technical Issues including “Who programs – everybody or just the marine corps?”; “The market for science and engineering was small but it will be large for general multicore”; “The program exists and can’t be changed”; “What features will next hardware/software release support and how should I protect myself from change?” We will summarize lessons and relate them to application and programming model categories. In last lecture or at end of all lectures we encourage the audience to bring their own multicore application or programming model so we can discuss examples that interest you. ©2007 Microsoft Corporation. All rights reserved.

Scalable Parallel Computing on Many/Multicore Systems This set of lectures will review the application and programming model issues that will one must address when one gets chips with 32-1024 cores and “scalable” approaches will be needed to make good use of such systems. We will not discuss bit-level and instruction-level parallelism i.e. what happens on a possibly special purpose core, even though this is clearly important. We will use science and engineering applications to drive the discussion as we have substantial experience in these cases but we are interested in the lessons for commodity client and server applications that will be broadly used 5-10 years from now. We start with simple applications and algorithms from a variety of fields and identify features that makes it “obvious” that “all” science and engineering run well and scalably in parallel. We explain why unfortunately it is equally obvious that there is no straightforward way of expressing this parallelism. Parallel hardware architectures are described in enough detail to understand performance and algorithm issues and need for cross-architecture compatibility; however in these lectures we will just be users of hardware. We must understand what features of multicore chips we can and should exploit. We can explicitly use the shared memory between cores or just enjoy its implications for very fast inter-core control and communication linkage. We note that parallel algorithm research is hugely successful although this success has reduced activity in an area that deserves new attention for the next generation of architectures. The parallel software environment is discussed at several levels including programming paradigm, runtime and operating system. The importance of libraries, templates, kernels (dwarfs) and benchmarks is stressed. The programming environment has various tools including compilers with possible parallelism hints like OpenMP; tuners like Atlas; messaging models; parallelism and distribution support as in HPF, HPCS Languages, co-array Fortran, Global arrays and UPC. We also discuss the relevance of important general ideas like object-oriented paradigms (as in for example Charm++), functional languages and Software Transactional Memories. Streaming, pipelining, co-ordination, services and workflow are placed in context. Examples discussed in the last category include CCR/DSS from Microsoft and the Common Component Architecture CCA from DoE. Domain Specific environments like Matlab and Mathematica are important as there is no universal silver programming bullet; one will need interoperable focused environments. We discuss performance analysis including speedup, efficiency, scaled speedup and Amdahl's law. We show how to relate performance to algorithm/application structure and the hardware characteristics. Applications will not get scalable parallelism accidentally but only if there is an understandable performance model. We review some of the many pitfalls for both performance and correctness; these include deadlocks, race conditions, nodes that are busy doing something else and the difficulty of second-guessing automatic parallelization methods. We describe the formal sources of overhead; load imbalance and the communication/control overhead and the ways to reduce them. We relate the blocking used in caching to that used in parallel computation. We note that load balancing was the one part of parallel computing that was easier than expected. We will mix both simple idealized applications with “real problems” noting that usually it is simple problems that are the hardest as they have poor computation to control/communication ratios. We will explain the parallelism in several application classes including for science and engineering: Finite Difference, Finite Elements, FFT/Spectral, Meshes of all sorts, Particle Dynamics, Particle-Mesh, and Monte Carlo methods. Some applications like Image Processing, Graphics, Cryptography and Media coding/decoding have features similar to well understood science and engineering problems. We emphasize that nearly all applications are built hierarchically from more “basic applications” with a variety of different structures and natural programming models. Such application composition (co-ordination, workflow) must be supported with a common run-time. We contrast the difference between decomposition needed in most “basic parallel applications” to the composition supported in workflow and Web 2.0 mashups. Looking at broader application classes we should cover; Internet applications and services; artificial intelligence, optimization, machine learning; divide and conquer algorithms; tree structured searches like computer chess; applications generated by the data deluge including access, search, and the assimilation of data into simulations. There has been a growing interest in Complex Systems whether it be for critical infrastructure like energy and transportation, the Internet itself, commodity gaming, computational epidemiology or the original war games. We expect Discrete Event Simulations (such as DoD’s High Level Architecture HLA) to grow in importance as they naturally describe complex systems and because they can clearly benefit from multicore architectures. We will discuss the innovative Sequential Dynamical Systems approach used in the EpiSims, TransSims and other critical infrastructure simulation environments. In all applications we need to identify the intrinsic parallelism and the degrees of freedom that can be parallelized and distinguish small parallelism (local to core) compared to large parallelism (scalable across many cores) We will not forget many critical non-technical Issues including “Who programs – everybody or just the marine corps?”; “The market for science and engineering was small but it will be large for general multicore”; “The program exists and can’t be changed”; “What features will next hardware/software release support and how should I protect myself from change?” We will summarize lessons and relate them to application and programming model categories. In last lecture or at end of all lectures we encourage the audience to bring their own multicore application or programming model so we can discuss examples that interest you. ©2007 Microsoft Corporation. All rights reserved.

Scalable Parallel Computing on Many/Multicore Systems This set of lectures will review the application and programming model issues that will one must address when one gets chips with 32-1024 cores and “scalable” approaches will be needed to make good use of such systems. We will not discuss bit-level and instruction-level parallelism i.e. what happens on a possibly special purpose core, even though this is clearly important. We will use science and engineering applications to drive the discussion as we have substantial experience in these cases but we are interested in the lessons for commodity client and server applications that will be broadly used 5-10 years from now. We start with simple applications and algorithms from a variety of fields and identify features that makes it “obvious” that “all” science and engineering run well and scalably in parallel. We explain why unfortunately it is equally obvious that there is no straightforward way of expressing this parallelism. Parallel hardware architectures are described in enough detail to understand performance and algorithm issues and need for cross-architecture compatibility; however in these lectures we will just be users of hardware. We must understand what features of multicore chips we can and should exploit. We can explicitly use the shared memory between cores or just enjoy its implications for very fast inter-core control and communication linkage. We note that parallel algorithm research is hugely successful although this success has reduced activity in an area that deserves new attention for the next generation of architectures. The parallel software environment is discussed at several levels including programming paradigm, runtime and operating system. The importance of libraries, templates, kernels (dwarfs) and benchmarks is stressed. The programming environment has various tools including compilers with possible parallelism hints like OpenMP; tuners like Atlas; messaging models; parallelism and distribution support as in HPF, HPCS Languages, co-array Fortran, Global arrays and UPC. We also discuss the relevance of important general ideas like object-oriented paradigms (as in for example Charm++), functional languages and Software Transactional Memories. Streaming, pipelining, co-ordination, services and workflow are placed in context. Examples discussed in the last category include CCR/DSS from Microsoft and the Common Component Architecture CCA from DoE. Domain Specific environments like Matlab and Mathematica are important as there is no universal silver programming bullet; one will need interoperable focused environments. We discuss performance analysis including speedup, efficiency, scaled speedup and Amdahl's law. We show how to relate performance to algorithm/application structure and the hardware characteristics. Applications will not get scalable parallelism accidentally but only if there is an understandable performance model. We review some of the many pitfalls for both performance and correctness; these include deadlocks, race conditions, nodes that are busy doing something else and the difficulty of second-guessing automatic parallelization methods. We describe the formal sources of overhead; load imbalance and the communication/control overhead and the ways to reduce them. We relate the blocking used in caching to that used in parallel computation. We note that load balancing was the one part of parallel computing that was easier than expected. We will mix both simple idealized applications with “real problems” noting that usually it is simple problems that are the hardest as they have poor computation to control/communication ratios. We will explain the parallelism in several application classes including for science and engineering: Finite Difference, Finite Elements, FFT/Spectral, Meshes of all sorts, Particle Dynamics, Particle-Mesh, and Monte Carlo methods. Some applications like Image Processing, Graphics, Cryptography and Media coding/decoding have features similar to well understood science and engineering problems. We emphasize that nearly all applications are built hierarchically from more “basic applications” with a variety of different structures and natural programming models. Such application composition (co-ordination, workflow) must be supported with a common run-time. We contrast the difference between decomposition needed in most “basic parallel applications” to the composition supported in workflow and Web 2.0 mashups. Looking at broader application classes we should cover; Internet applications and services; artificial intelligence, optimization, machine learning; divide and conquer algorithms; tree structured searches like computer chess; applications generated by the data deluge including access, search, and the assimilation of data into simulations. There has been a growing interest in Complex Systems whether it be for critical infrastructure like energy and transportation, the Internet itself, commodity gaming, computational epidemiology or the original war games. We expect Discrete Event Simulations (such as DoD’s High Level Architecture HLA) to grow in importance as they naturally describe complex systems and because they can clearly benefit from multicore architectures. We will discuss the innovative Sequential Dynamical Systems approach used in the EpiSims, TransSims and other critical infrastructure simulation environments. In all applications we need to identify the intrinsic parallelism and the degrees of freedom that can be parallelized and distinguish small parallelism (local to core) compared to large parallelism (scalable across many cores) We will not forget many critical non-technical Issues including “Who programs – everybody or just the marine corps?”; “The market for science and engineering was small but it will be large for general multicore”; “The program exists and can’t be changed”; “What features will next hardware/software release support and how should I protect myself from change?” We will summarize lessons and relate them to application and programming model categories. In last lecture or at end of all lectures we encourage the audience to bring their own multicore application or programming model so we can discuss examples that interest you. ©2007 Microsoft Corporation. All rights reserved.

Perma.cc archive of https://en.wikipedia.org/wiki/Parallel_computing created on 2022-08-13 07:53:19.464194+00:00.

In this paper, we implemented both sequential and parallel version of fractal image compression algorithms using CUDA (Compute Unified Device Architecture) programming model for parallelizing the program in Graphics Processing Unit for medical images, as they are highly similar within the image itself. There are several improvement in the implementation of the algorithm as well. Fractal image compression is based on the self similarity of an image, meaning an image having similarity in majority of the regions. We take this opportunity to implement the compression algorithm and monitor the effect of it using both parallel and sequential implementation. Fractal compression has the property of high compression rate and the dimensionless scheme. Compression scheme for fractal image is of two kind, one is encoding and another is decoding. Encoding is very much computational expensive. On the other hand decoding is less computational. The application of fractal compression to medical images would allow obtaining much higher compression ratios. While the fractal magnification an inseparable feature of the fractal compression would be very useful in presenting the reconstructed image in a highly readable form. However, like all irreversible methods, the fractal compression is connected with the problem of information loss, which is especially troublesome in the medical imaging. A very time consuming encoding pro- cess, which can last even several hours, is another bothersome drawback of the fractal compression.

In this paper, we implemented both sequential and parallel version of fractal image compression algorithms using CUDA (Compute Unified Device Architecture) programming model for parallelizing the program in Graphics Processing Unit for medical images, as they are highly similar within the image itself. There are several improvement in the implementation of the algorithm as well. Fractal image compression is based on the self similarity of an image, meaning an image having similarity in majority of the regions. We take this opportunity to implement the compression algorithm and monitor the effect of it using both parallel and sequential implementation. Fractal compression has the property of high compression rate and the dimensionless scheme. Compression scheme for fractal image is of two kind, one is encoding and another is decoding. Encoding is very much computational expensive. On the other hand decoding is less computational. The application of fractal compression to medical images would allow obtaining much higher compression ratios. While the fractal magnification an inseparable feature of the fractal compression would be very useful in presenting the reconstructed image in a highly readable form. However, like all irreversible methods, the fractal compression is connected with the problem of information loss, which is especially troublesome in the medical imaging. A very time consuming encoding pro- cess, which can last even several hours, is another bothersome drawback of the fractal compression.

This software computes the tomographic reconstruction of spatial-spectral data from raw detector images of the Computed-Tomography Imaging Spectrometer (CTIS), which enables transient-level, multi-spectral imaging by capturing spatial and spectral information in a single snapshot.

An algorithm is proposed for computing equilibrium averages of Markov chains which suffer from metastability -- the tendency to remain in one or more subsets of state space for long time intervals. The algorithm, called the parallel replica method (or ParRep), uses many parallel processors to explore these subsets more efficiently. Numerical simulations on a simple model demonstrate consistency of the method. A proof of consistency is given in an idealized setting. The parallel replica method can be considered a generalization of A.F. Voter's parallel replica dynamics, originally developed to efficiently simulate metastable Langevin stochastic dynamics.

IPython: A New Architecture for Interactive and Parallel Computing Fernando Perez

We propose a form of parallel computing on classical computers that is based on matrix product states. The virtual parallelization is accomplished by representing bits with matrices and by evolving these matrices from an initial product state that encodes multiple inputs. Matrix evolution follows from the sequential application of gates, as in a logical circuit. The action by classical probabilistic one-bit and deterministic two-bit gates such as NAND are implemented in terms of matrix operations and, as opposed to quantum computing, it is possible to copy bits. We present a way to explore this method of computation to solve search problems and count the number of solutions. We argue that if the classical computational cost of testing solutions (witnesses) requires less than $O(n^2)$ local two-bit gates acting on $n$ bits, the search problem can be fully solved in subexponential time. Therefore, for this restricted type of search problem, the virtual parallelization scheme is faster than Grover's quantum algorithm

We summarize the results of a survey on reproducibility in parallel computing, which was conducted during the Euro-Par conference in August 2015. The survey form was handed out to all participants of the conference and the workshops. The questionnaire, which specifically targeted the parallel computing community, contained questions in four different categories: general questions on reproducibility, the current state of reproducibility, the reproducibility of the participants' own papers, and questions about the participants' familiarity with tools, software, or open-source software licenses used for reproducible research.

Parallel Computing 1988: Volume 6 , Issue Index. Digitized from IA1652917-03 . Previous issue: sim_parallel-computing_1987-11_5_3 . Next issue: sim_parallel-computing_1988-01_6_1 .

Parallel Computing 1988: Volume 7 , Issue Index. Digitized from IA1652917-03 . Previous issue: sim_parallel-computing_1988-03_6_3 . Next issue: sim_parallel-computing_1988-04_7_1 .

We propose a parallel quantum computing mode for ensemble quantum computer. In this mode, some qubits can be in pure states while other qubits in mixed states. It enables a single ensemble quantum computer to perform $"$single-instruction-multi-data" type of parallel computation. In Grover's algorithm and Shor's algorithm, parallel quantum computing can provide additional speedup. In addition, it also makes a fuller use of qubit resources in an ensemble quantum computer. As a result, some qubits discarded in the preparation of an effective pure state in the Schulman-Varizani, and the Cleve-DiVincenzo algorithms can be re-utilized.

Scalable Parallel Computing on Many/Multicore Systems This set of lectures will review the application and programming model issues that will one must address when one gets chips with 32-1024 cores and “scalable” approaches will be needed to make good use of such systems. We will not discuss bit-level and instruction-level parallelism i.e. what happens on a possibly special purpose core, even though this is clearly important. We will use science and engineering applications to drive the discussion as we have substantial experience in these cases but we are interested in the lessons for commodity client and server applications that will be broadly used 5-10 years from now. We start with simple applications and algorithms from a variety of fields and identify features that makes it “obvious” that “all” science and engineering run well and scalably in parallel. We explain why unfortunately it is equally obvious that there is no straightforward way of expressing this parallelism. Parallel hardware architectures are described in enough detail to understand performance and algorithm issues and need for cross-architecture compatibility; however in these lectures we will just be users of hardware. We must understand what features of multicore chips we can and should exploit. We can explicitly use the shared memory between cores or just enjoy its implications for very fast inter-core control and communication linkage. We note that parallel algorithm research is hugely successful although this success has reduced activity in an area that deserves new attention for the next generation of architectures. The parallel software environment is discussed at several levels including programming paradigm, runtime and operating system. The importance of libraries, templates, kernels (dwarfs) and benchmarks is stressed. The programming environment has various tools including compilers with possible parallelism hints like OpenMP; tuners like Atlas; messaging models; parallelism and distribution support as in HPF, HPCS Languages, co-array Fortran, Global arrays and UPC. We also discuss the relevance of important general ideas like object-oriented paradigms (as in for example Charm++), functional languages and Software Transactional Memories. Streaming, pipelining, co-ordination, services and workflow are placed in context. Examples discussed in the last category include CCR/DSS from Microsoft and the Common Component Architecture CCA from DoE. Domain Specific environments like Matlab and Mathematica are important as there is no universal silver programming bullet; one will need interoperable focused environments. We discuss performance analysis including speedup, efficiency, scaled speedup and Amdahl's law. We show how to relate performance to algorithm/application structure and the hardware characteristics. Applications will not get scalable parallelism accidentally but only if there is an understandable performance model. We review some of the many pitfalls for both performance and correctness; these include deadlocks, race conditions, nodes that are busy doing something else and the difficulty of second-guessing automatic parallelization methods. We describe the formal sources of overhead; load imbalance and the communication/control overhead and the ways to reduce them. We relate the blocking used in caching to that used in parallel computation. We note that load balancing was the one part of parallel computing that was easier than expected. We will mix both simple idealized applications with “real problems” noting that usually it is simple problems that are the hardest as they have poor computation to control/communication ratios. We will explain the parallelism in several application classes including for science and engineering: Finite Difference, Finite Elements, FFT/Spectral, Meshes of all sorts, Particle Dynamics, Particle-Mesh, and Monte Carlo methods. Some applications like Image Processing, Graphics, Cryptography and Media coding/decoding have features similar to well understood science and engineering problems. We emphasize that nearly all applications are built hierarchically from more “basic applications” with a variety of different structures and natural programming models. Such application composition (co-ordination, workflow) must be supported with a common run-time. We contrast the difference between decomposition needed in most “basic parallel applications” to the composition supported in workflow and Web 2.0 mashups. Looking at broader application classes we should cover; Internet applications and services; artificial intelligence, optimization, machine learning; divide and conquer algorithms; tree structured searches like computer chess; applications generated by the data deluge including access, search, and the assimilation of data into simulations. There has been a growing interest in Complex Systems whether it be for critical infrastructure like energy and transportation, the Internet itself, commodity gaming, computational epidemiology or the original war games. We expect Discrete Event Simulations (such as DoD’s High Level Architecture HLA) to grow in importance as they naturally describe complex systems and because they can clearly benefit from multicore architectures. We will discuss the innovative Sequential Dynamical Systems approach used in the EpiSims, TransSims and other critical infrastructure simulation environments. In all applications we need to identify the intrinsic parallelism and the degrees of freedom that can be parallelized and distinguish small parallelism (local to core) compared to large parallelism (scalable across many cores) We will not forget many critical non-technical Issues including “Who programs – everybody or just the marine corps?”; “The market for science and engineering was small but it will be large for general multicore”; “The program exists and can’t be changed”; “What features will next hardware/software release support and how should I protect myself from change?” We will summarize lessons and relate them to application and programming model categories. In last lecture or at end of all lectures we encourage the audience to bring their own multicore application or programming model so we can discuss examples that interest you. ©2007 Microsoft Corporation. All rights reserved.

Scalable Parallel Computing on Many/Multicore Systems This set of lectures will review the application and programming model issues that will one must address when one gets chips with 32-1024 cores and “scalable” approaches will be needed to make good use of such systems. We will not discuss bit-level and instruction-level parallelism i.e. what happens on a possibly special purpose core, even though this is clearly important. We will use science and engineering applications to drive the discussion as we have substantial experience in these cases but we are interested in the lessons for commodity client and server applications that will be broadly used 5-10 years from now. We start with simple applications and algorithms from a variety of fields and identify features that makes it “obvious” that “all” science and engineering run well and scalably in parallel. We explain why unfortunately it is equally obvious that there is no straightforward way of expressing this parallelism. Parallel hardware architectures are described in enough detail to understand performance and algorithm issues and need for cross-architecture compatibility; however in these lectures we will just be users of hardware. We must understand what features of multicore chips we can and should exploit. We can explicitly use the shared memory between cores or just enjoy its implications for very fast inter-core control and communication linkage. We note that parallel algorithm research is hugely successful although this success has reduced activity in an area that deserves new attention for the next generation of architectures. The parallel software environment is discussed at several levels including programming paradigm, runtime and operating system. The importance of libraries, templates, kernels (dwarfs) and benchmarks is stressed. The programming environment has various tools including compilers with possible parallelism hints like OpenMP; tuners like Atlas; messaging models; parallelism and distribution support as in HPF, HPCS Languages, co-array Fortran, Global arrays and UPC. We also discuss the relevance of important general ideas like object-oriented paradigms (as in for example Charm++), functional languages and Software Transactional Memories. Streaming, pipelining, co-ordination, services and workflow are placed in context. Examples discussed in the last category include CCR/DSS from Microsoft and the Common Component Architecture CCA from DoE. Domain Specific environments like Matlab and Mathematica are important as there is no universal silver programming bullet; one will need interoperable focused environments. We discuss performance analysis including speedup, efficiency, scaled speedup and Amdahl's law. We show how to relate performance to algorithm/application structure and the hardware characteristics. Applications will not get scalable parallelism accidentally but only if there is an understandable performance model. We review some of the many pitfalls for both performance and correctness; these include deadlocks, race conditions, nodes that are busy doing something else and the difficulty of second-guessing automatic parallelization methods. We describe the formal sources of overhead; load imbalance and the communication/control overhead and the ways to reduce them. We relate the blocking used in caching to that used in parallel computation. We note that load balancing was the one part of parallel computing that was easier than expected. We will mix both simple idealized applications with “real problems” noting that usually it is simple problems that are the hardest as they have poor computation to control/communication ratios. We will explain the parallelism in several application classes including for science and engineering: Finite Difference, Finite Elements, FFT/Spectral, Meshes of all sorts, Particle Dynamics, Particle-Mesh, and Monte Carlo methods. Some applications like Image Processing, Graphics, Cryptography and Media coding/decoding have features similar to well understood science and engineering problems. We emphasize that nearly all applications are built hierarchically from more “basic applications” with a variety of different structures and natural programming models. Such application composition (co-ordination, workflow) must be supported with a common run-time. We contrast the difference between decomposition needed in most “basic parallel applications” to the composition supported in workflow and Web 2.0 mashups. Looking at broader application classes we should cover; Internet applications and services; artificial intelligence, optimization, machine learning; divide and conquer algorithms; tree structured searches like computer chess; applications generated by the data deluge including access, search, and the assimilation of data into simulations. There has been a growing interest in Complex Systems whether it be for critical infrastructure like energy and transportation, the Internet itself, commodity gaming, computational epidemiology or the original war games. We expect Discrete Event Simulations (such as DoD’s High Level Architecture HLA) to grow in importance as they naturally describe complex systems and because they can clearly benefit from multicore architectures. We will discuss the innovative Sequential Dynamical Systems approach used in the EpiSims, TransSims and other critical infrastructure simulation environments. In all applications we need to identify the intrinsic parallelism and the degrees of freedom that can be parallelized and distinguish small parallelism (local to core) compared to large parallelism (scalable across many cores) We will not forget many critical non-technical Issues including “Who programs – everybody or just the marine corps?”; “The market for science and engineering was small but it will be large for general multicore”; “The program exists and can’t be changed”; “What features will next hardware/software release support and how should I protect myself from change?” We will summarize lessons and relate them to application and programming model categories. In last lecture or at end of all lectures we encourage the audience to bring their own multicore application or programming model so we can discuss examples that interest you. ©2007 Microsoft Corporation. All rights reserved.

http://uf.catalog.fcla.edu/uf.jsp?st=UF030003142&ix=pm&I=0&V=D&pm=1

In this paper, we propose algorithms and software for parallel implementation of conversion of VLSI Layout Data from CAD format Gerber and MEBES into an internal representation and then into format of automatic mask inspection system T29. The software is developed on basis of OpenMP technology to work on PC with 4-core processor. It is shown that using parallel computing speeds up a conversion process. In the future we are planning to develop similar tools for data conversion from CIF and DFX formats into the internal format, and further into format GDS-II. These tools allow developing a program complex of topological data processing to work with automatic mask inspection system made by R&D Company “KBTEM-OMO” of “Planar” Corporatio

In this paper, we propose algorithms and software for parallel implementation of conversion of VLSI Layout Data from CAD format Gerber and MEBES into an internal representation and then into format of automatic mask inspection system T29. The software is developed on basis of OpenMP technology to work on PC with 4-core processor. It is shown that using parallel computing speeds up a conversion process. In the future we are planning to develop similar tools for data conversion from CIF and DFX formats into the internal format, and further into format GDS-II. These tools allow developing a program complex of topological data processing to work with automatic mask inspection system made by R&D Company “KBTEM-OMO” of “Planar” Corporatio

This article is from PLoS ONE , volume 9 . Abstract The metagenomic method directly sequences and analyses genome information from microbial communities. The main computational tasks for metagenomic analyses include taxonomical and functional structure analysis for all genomes in a microbial community (also referred to as a metagenomic sample). With the advancement of Next Generation Sequencing (NGS) techniques, the number of metagenomic samples and the data size for each sample are increasing rapidly. Current metagenomic analysis is both data- and computation- intensive, especially when there are many species in a metagenomic sample, and each has a large number of sequences. As such, metagenomic analyses require extensive computational power. The increasing analytical requirements further augment the challenges for computation analysis. In this work, we have proposed Parallel-META 2.0, a metagenomic analysis software package, to cope with such needs for efficient and fast analyses of taxonomical and functional structures for microbial communities. Parallel-META 2.0 is an extended and improved version of Parallel-META 1.0, which enhances the taxonomical analysis using multiple databases, improves computation efficiency by optimized parallel computing, and supports interactive visualization of results in multiple views. Furthermore, it enables functional analysis for metagenomic samples including short-reads assembly, gene prediction and functional annotation. Therefore, it could provide accurate taxonomical and functional analyses of the metagenomic samples in high-throughput manner and on large scale.

This article is from PLoS ONE , volume 9 . Abstract The metagenomic method directly sequences and analyses genome information from microbial communities. The main computational tasks for metagenomic analyses include taxonomical and functional structure analysis for all genomes in a microbial community (also referred to as a metagenomic sample). With the advancement of Next Generation Sequencing (NGS) techniques, the number of metagenomic samples and the data size for each sample are increasing rapidly. Current metagenomic analysis is both data- and computation- intensive, especially when there are many species in a metagenomic sample, and each has a large number of sequences. As such, metagenomic analyses require extensive computational power. The increasing analytical requirements further augment the challenges for computation analysis. In this work, we have proposed Parallel-META 2.0, a metagenomic analysis software package, to cope with such needs for efficient and fast analyses of taxonomical and functional structures for microbial communities. Parallel-META 2.0 is an extended and improved version of Parallel-META 1.0, which enhances the taxonomical analysis using multiple databases, improves computation efficiency by optimized parallel computing, and supports interactive visualization of results in multiple views. Furthermore, it enables functional analysis for metagenomic samples including short-reads assembly, gene prediction and functional annotation. Therefore, it could provide accurate taxonomical and functional analyses of the metagenomic samples in high-throughput manner and on large scale.

The objective of this paper is to accelerate the existing incremental and parallel subgradient methods for constrained nonsmooth convex optimization to solve the problem of minimizing the sum of nonsmooth, convex functionals over a constraint set in a Hilbert space. Our approach to accelerate the existing algorithms is to develop line search methods that can determine a more adequate step-size than the ones used in the existing methods at each iteration. The proposed line search method can determine step-sizes to satisfy weaker conditions than the ones used in the existing methods. This implies that the incremental and parallel subgradient methods based on the line search approach are generalizations of the existing ones. We show that the whole sequence generated by each of the two proposed methods weakly converges to a solution to the problem. The main contribution of this paper is provision of numerical examples showing that the two proposed methods perform better than the existing ones. The numerical results are evaluated with a multi-core computer and show that our parallel method reduces the running time and iterations needed to find an optimal solution compared with other ones.

The objective of this paper is to accelerate the existing incremental and parallel subgradient methods for constrained nonsmooth convex optimization to solve the problem of minimizing the sum of nonsmooth, convex functionals over a constraint set in a Hilbert space. Our approach to accelerate the existing algorithms is to develop line search methods that can determine a more adequate step-size than the ones used in the existing methods at each iteration. The proposed line search method can determine step-sizes to satisfy weaker conditions than the ones used in the existing methods. This implies that the incremental and parallel subgradient methods based on the line search approach are generalizations of the existing ones. We show that the whole sequence generated by each of the two proposed methods weakly converges to a solution to the problem. The main contribution of this paper is provision of numerical examples showing that the two proposed methods perform better than the existing ones. The numerical results are evaluated with a multi-core computer and show that our parallel method reduces the running time and iterations needed to find an optimal solution compared with other ones.

SciPy 2010 Day 1 Cloud Track 6 Parallel Computing with IPython: an Application to Air Pollution Modeling B.E. Granger and Josh Hemann

SciPy 2010 Day 1 Cloud Track 6 Parallel Computing with IPython: an Application to Air Pollution Modeling B.E. Granger and Josh Hemann

SciPy 2010 Day 1 Cloud Track 6 Parallel Computing with IPython: an Application to Air Pollution Modeling B.E. Granger and Josh Hemann

Parallel Computing is an active peer-reviewed academic journal covering the theory and use of parallel computer systems, including vector, pipeline, array and fifth-generation computers, as well as high-speed computing. It was established in 1984 and is published 10 times a year (monthly until 2014) by Elsevier. The journal serves as a platform for researchers, computer scientists, engineers, and practitioners to publish original research findings, methodologies, and innovations in the field of parallel computing. It covers a wide range of topics, including parallel algorithms and programming models, parallel architectures and systems, parallel software and tools, performance analysis and evaluation, parallel applications in various domains, and emerging trends in parallel computing. The journal encourages submissions that address both theoretical foundations and practical aspects of parallel computing, including scalability, fault tolerance, load balancing, and efficient resource utilisation as well as studies that explore parallel computing in areas such as scientific simulations, data analytics, machine learning, image and signal processing, and computational biology. The Internet Archive Collection contains microfilm published between 1984 and 1994 Parallel Computing can be found online at: www.sciencedirect.com/journal/parallel-computing The ISSN is: 0167-8191

This report summarizes work on parallel computations for NASA Grant NAG-1-1529 for the period 1 Jan. - 30 June 1994. Short summaries on highly parallel preconditioners, target-specific parallel reductions, and simulation of delta-cache protocols are provided.

Parallel Computing 1989: Volume 12 , Issue Index. Digitized from IA1652917-03 . Previous issue: sim_parallel-computing_1989-08-28_11_3 . Next issue: sim_parallel-computing_1989-10_12_1 .

In this grant, we have proposed a three-year research effort focused on developing High Performance Computation and Communication (HPCC) methodologies for structural analysis on parallel processors and clusters of workstations, with emphasis on reducing the structural design cycle time. Besides consolidating and further improving the FETI solver technology to address plate and shell structures, we have proposed to tackle the following design related issues: (a) parallel coupling and assembly of independently designed and analyzed three-dimensional substructures with non-matching interfaces, (b) fast and smart parallel re-analysis of a given structure after it has undergone design modifications, (c) parallel evaluation of sensitivity operators (derivatives) for design optimization, and (d) fast parallel analysis of mildly nonlinear structures. While our proposal was accepted, support was provided only for one year.

In this grant, we have proposed a three-year research effort focused on developing High Performance Computation and Communication (HPCC) methodologies for structural analysis on parallel processors and clusters of workstations, with emphasis on reducing the structural design cycle time. Besides consolidating and further improving the FETI solver technology to address plate and shell structures, we have proposed to tackle the following design related issues: (a) parallel coupling and assembly of independently designed and analyzed three-dimensional substructures with non-matching interfaces, (b) fast and smart parallel re-analysis of a given structure after it has undergone design modifications, (c) parallel evaluation of sensitivity operators (derivatives) for design optimization, and (d) fast parallel analysis of mildly nonlinear structures. While our proposal was accepted, support was provided only for one year.

The idea of upgrading performance and utility of computer systems by incorporating parallel processing has been around since at least the 1940s. A significant investment in parallel processing in the 1980s and 1990s has led to an abundance of parallel architectures that due to technical constraints at the time had to rely on multi-chip multi-processing. Unfortunately, their impact on mainstream computing was quite limited. 'Tribal lore' suggests the following reason: while programming for parallelism tends to be easy, turning this parallelism into the 'coarse-grained' type, needed to optimize performance for multi-chip multi-processing (with their high coordination overhead), has been quite hard. The mainstream computing paradigm has always relied on serial code. However, commercially successful processors are entering a second decade of near stagnation in the maximum number of instructions they can issue towards a single computational task in one clock. Alas, the multi-decade reliance on advancing the clock is also coming to an end. The PRAM-On-Chip research project at UMD is reviewed. The project is guided by a fact, an old insight, a recent one and a premise. The fact: Billion transistor chips are here, up from less than 30,000 circa 1980. The older insight: Using a very simple parallel computation model, the parallel random access model (PRAM), the parallel algorithms research community succeeded in developing a general-purpose theory of parallel algorithms that was much richer than any competing approach and is second in magnitude only to serial algorithmics. However, since it did not offer an effective abstraction for multi-chip multi-processors this elegant algorithmic theory remained in the ivory towers of theorists. The PRAM-On-Chip insight: The Billion transistor chip era allows for the first time low-overhead on-chip multi-processors so that the PRAM abstraction becomes effective. The premise: Were the architecture component of PRAM-On-Chip feasible in the 1990s, its parallel programming component would become the mainstream standard. In 1988-90 standard algorithms textbooks chose to include significant PRAM chapters (some still have them). Arguably nothing could stand in the way of teaching them to every student at every computer science program. Programming for concurrency/parallelism is quickly becoming an integral part of mainstream computing. Yet, industry and academia leaders in system software and general-purpose application software have maintained a passive posture: their attention tends to focus too much on getting the best performance out of architectures that originated from a hardware centric approach, or very specific applications, and too little on trying to impact the evolving generation of multi-core and/or multi-threaded general-purpose architectures. We argue, perhaps provocatively, that: (i) limiting programming for parallelism to fit hardware-centric architectures imports the epidemic of programmability problems that has plagued parallel computing into mainstream computing, (ii) it is only a matter of time until the industry will seek convergence based on parallel programmability: the difference in the bottom line between a successful and a less successful strategy on parallel programmability will be too big to ignore, (iii) a more assertive position by such leaders is necessary, and (iv) the PRAM-On-Chip approach offers a more balanced way that avoids these problems. URL: http://www.umiacs.umd.edu/~vishkin/XMT ©2005 Microsoft Corporation. All rights reserved.

The development of implicit schemes for obtaining steady state solutions to the Euler and Navier-Stokes equations on unstructured grids is outlined. Applications are presented that compare the convergence characteristics of various implicit methods. Next, the development of explicit and implicit schemes to compute unsteady flows on unstructured grids is discussed. Next, the issues involved in parallelizing finite volume schemes on unstructured meshes in an MIMD (multiple instruction/multiple data stream) fashion are outlined. Techniques for partitioning unstructured grids among processors and for extracting parallelism in explicit and implicit solvers are discussed. Finally, some dynamic load balancing ideas, which are useful in adaptive transient computations, are presented.

{\sc top-c} (Task Oriented Parallel C) is a freely available package for parallel computing. It is designed to be easy to learn and to have good tolerance for the high latencies that are common in commodity networks of computers. It has been successfully used in a wide range of examples, providing linear speedup with the number of computers. A brief overview of {\sc top-c} is provided, along with recent experience with cosmic ray physics simulations.

We present a computational algorithm for computing short range forces between particles. The algorithm has two distinguishing features. First, it is optimized for multi-processor computers, and will use as many processors as are available. Second, it is optimized for inhomogeneous, dynamic particle distributions; for any distribution the computational load is distributed evenly to all processors, and the communication time is less than 15\% of the total run time. In this talk we present our new algorithm. We developed the program for a grand-challenge problem in cosmology, simulation of the formation of large-scale structure in the universe. This simulation, run on the Thinking Machines Corporation CM-5, uses the particle-particle/particle-mesh (PPPM) \cite{hock_east} algorithm. The particle-particle phase is computed using the algorithm we describe in this paper. We discuss this and other applications.

We present a computational algorithm for computing short range forces between particles. The algorithm has two distinguishing features. First, it is optimized for multi-processor computers, and will use as many processors as are available. Second, it is optimized for inhomogeneous, dynamic particle distributions; for any distribution the computational load is distributed evenly to all processors, and the communication time is less than 15\% of the total run time. In this talk we present our new algorithm. We developed the program for a grand-challenge problem in cosmology, simulation of the formation of large-scale structure in the universe. This simulation, run on the Thinking Machines Corporation CM-5, uses the particle-particle/particle-mesh (PPPM) \cite{hock_east} algorithm. The particle-particle phase is computed using the algorithm we describe in this paper. We discuss this and other applications.

The Microsoft .NET Framework 4 and Visual Studio 2010 include new technologies for expressing, debugging, and tuning parallelism in managed applications. Dive into key areas of support, including Parallel Language Integrated Query (PLINQ), cutting-edge concurrency views in the Visual Studio profiler, and debugger tool windows for analyzing the state of concurrent code. In addition to exploring such features, we will examine some common parallel patterns prevalent in technical computing and how these features can be used to best implement such patterns. ©2010 Microsoft Corporation. All rights reserved.

In this paper, we describe work in which we are evaluating how the evolving properties of nano-electronic devices could best be utilized in highly parallel computing structures. Because of their combination of high performance, low power, and extreme compactness, such structures would have obvious applications in spaceborne environments, both for general mission control and for on-board data analysis. However, the anticipated properties of nano-devices mean that the optimum architecture for such systems is by no means certain. Candidates include single instruction multiple datastream (SIMD) arrays, neural networks, and multiple instruction multiple datastream (MIMD) assemblies.

In this paper, we describe work in which we are evaluating how the evolving properties of nano-electronic devices could best be utilized in highly parallel computing structures. Because of their combination of high performance, low power, and extreme compactness, such structures would have obvious applications in spaceborne environments, both for general mission control and for on-board data analysis. However, the anticipated properties of nano-devices mean that the optimum architecture for such systems is by no means certain. Candidates include single instruction multiple datastream (SIMD) arrays, neural networks, and multiple instruction multiple datastream (MIMD) assemblies.

In this paper, we describe work in which we are evaluating how the evolving properties of nano-electronic devices could best be utilized in highly parallel computing structures. Because of their combination of high performance, low power, and extreme compactness, such structures would have obvious applications in spaceborne environments, both for general mission control and for on-board data analysis. However, the anticipated properties of nano-devices mean that the optimum architecture for such systems is by no means certain. Candidates include single instruction multiple datastream (SIMD) arrays, neural networks, and multiple instruction multiple datastream (MIMD) assemblies.

In this paper, we describe work in which we are evaluating how the evolving properties of nano-electronic devices could best be utilized in highly parallel computing structures. Because of their combination of high performance, low power, and extreme compactness, such structures would have obvious applications in spaceborne environments, both for general mission control and for on-board data analysis. However, the anticipated properties of nano-devices mean that the optimum architecture for such systems is by no means certain. Candidates include single instruction multiple datastream (SIMD) arrays, neural networks, and multiple instruction multiple datastream (MIMD) assemblies.

Parallel Computing 1988 - 1989: Volume 9 , Issue Index. Digitized from IA1652917-03 . Previous issue: sim_parallel-computing_1988-10_8_1-3 . Next issue: sim_parallel-computing_1988-12_9_1 .

Parallel Computing 1989: Volume 10 , Issue Index. Digitized from IA1652917-03 . Previous issue: sim_parallel-computing_1989-02_9_3 . Next issue: sim_parallel-computing_1989-03_10_1 .

Parallel Computing 1989: Volume 10 , Issue Index. Digitized from IA1652917-03 . Previous issue: sim_parallel-computing_1989-02_9_3 . Next issue: sim_parallel-computing_1989-03_10_1 .

Parallel Computing 1989: Volume 10 , Issue Index. Digitized from IA1652917-03 . Previous issue: sim_parallel-computing_1989-02_9_3 . Next issue: sim_parallel-computing_1989-03_10_1 .

Parallel Computing 1989: Volume 10 , Issue Index. Digitized from IA1652917-03 . Previous issue: sim_parallel-computing_1989-02_9_3 . Next issue: sim_parallel-computing_1989-03_10_1 .

First Class

Massively parallel desktop computing capabilities now well within the reach of individual academics modify the environment for posterior simulation in fundamental and potentially quite advantageous ways. But to fully exploit these benefits algorithms that conform to parallel computing environments are needed. Sequential Monte Carlo comes very close to this ideal whereas other approaches like Markov chain Monte Carlo do not. This paper presents a sequential posterior simulator well suited to this computing environment. The simulator makes fewer analytical and programming demands on investigators, and is faster, more reliable and more complete than conventional posterior simulators. The paper extends existing sequential Monte Carlo methods and theory to provide a thorough and practical foundation for sequential posterior simulation that is well suited to massively parallel computing environments. It provides detailed recommendations on implementation, yielding an algorithm that requires only code for simulation from the prior and evaluation of prior and data densities and works well in a variety of applications representative of serious empirical work in economics and finance. The algorithm is robust to pathological posterior distributions, generates accurate marginal likelihood approximations, and provides estimates of numerical standard error and relative numerical efficiency intrinsically. The paper concludes with an application that illustrates the potential of these simulators for applied Bayesian inference.

Massively parallel desktop computing capabilities now well within the reach of individual academics modify the environment for posterior simulation in fundamental and potentially quite advantageous ways. But to fully exploit these benefits algorithms that conform to parallel computing environments are needed. Sequential Monte Carlo comes very close to this ideal whereas other approaches like Markov chain Monte Carlo do not. This paper presents a sequential posterior simulator well suited to this computing environment. The simulator makes fewer analytical and programming demands on investigators, and is faster, more reliable and more complete than conventional posterior simulators. The paper extends existing sequential Monte Carlo methods and theory to provide a thorough and practical foundation for sequential posterior simulation that is well suited to massively parallel computing environments. It provides detailed recommendations on implementation, yielding an algorithm that requires only code for simulation from the prior and evaluation of prior and data densities and works well in a variety of applications representative of serious empirical work in economics and finance. The algorithm is robust to pathological posterior distributions, generates accurate marginal likelihood approximations, and provides estimates of numerical standard error and relative numerical efficiency intrinsically. The paper concludes with an application that illustrates the potential of these simulators for applied Bayesian inference.

Massively parallel desktop computing capabilities now well within the reach of individual academics modify the environment for posterior simulation in fundamental and potentially quite advantageous ways. But to fully exploit these benefits algorithms that conform to parallel computing environments are needed. Sequential Monte Carlo comes very close to this ideal whereas other approaches like Markov chain Monte Carlo do not. This paper presents a sequential posterior simulator well suited to this computing environment. The simulator makes fewer analytical and programming demands on investigators, and is faster, more reliable and more complete than conventional posterior simulators. The paper extends existing sequential Monte Carlo methods and theory to provide a thorough and practical foundation for sequential posterior simulation that is well suited to massively parallel computing environments. It provides detailed recommendations on implementation, yielding an algorithm that requires only code for simulation from the prior and evaluation of prior and data densities and works well in a variety of applications representative of serious empirical work in economics and finance. The algorithm is robust to pathological posterior distributions, generates accurate marginal likelihood approximations, and provides estimates of numerical standard error and relative numerical efficiency intrinsically. The paper concludes with an application that illustrates the potential of these simulators for applied Bayesian inference.