Thomas James Christopher Ward

IBM · Systems

This is a complete screensaver as per the developerWorks article. Download it, unzip it, and either run the 'autorun.bat' file or burn all the files to a CD/DVD and insert it into a Microsoft Windows box whereupon it should autorun, offering to install the screensaver and giving an instant demo of what the screensaver will look like. I refer you to...

An information processing system for performing a transform of a multidimensional matrix in a distributed memory network. The method includes storing a multidimensional matrix of side N in a distributed memory network with a plurality of nodes and distributing work associated with a calculation of a transform of the matrix among N.sup.2 of the plur...

The Blue Gene®/L supercomputer provides scientists with the cutting-edge computing power and complex data-visualization tools they need to stay at the forefront of their disciplines. Learn how this technology lets computational molecular biologists create protein folding and misfolding simulations to better understand these complex molecules. In...

Storage class memory is receiving increasing attention for use in HPC systems for the acceleration of intensive IO operations. We report a particular instance using SLC FLASH memory integrated with an IBM BlueGene/Q supercomputer at scale (Blue Gene Active Storage, BGAS). We describe two principle modes of operation of the non-volatile memory: 1) b...

This paper describes a parallel strategy to extend the scalability of a small 3D FFT on thousands of Blue Gene/L processors. The approach is to execute the intermediate phases of the 3D FFT on smaller processor subsets. Performance measurements of the standalone 3D FFT on two communication protocols, MPI and BG/L ADE are presented. While the perfor...

github repo for screensavers as at date of Linux Foundation blog article

Construct and package a Linux® Live DVD to install using the standard Microsoft® Windows® install process and operate as a classic Windows screensaver.

Source code to enable high-performance indexed access to data which changes infrequently, originally developed to work with IBM TXSeries CICS, but capable of more general usage.

Complex problems can often only be solved with a workflow of different applications whose progress depends also on the need of shared data. There are different challenges that developers must overcome when sharing data in a workflow; each application may have very different requirements in how they access and consume shared data. For example, data...

This is BlueMatter, the IBM-written molecular dynamics package for the BlueGene/L and BlueGene/P supercomputers. IBM has published this as open source software here https://github.com/IBM/BlueMatter .

This software is related to https://github.com/gpudirect ; it is to facilitate communication beween NVIDIA GPUs and Mellanox Infiniband adapters without requiring intervention from the host CPU in the time-critical path.

Almost all of the world’s top 500 supercomputers today run Linux®. Mostly they have batch job submission systems, which partition the supercomputer as required for the applications, and run the applications in sequence in their allocated partitions in an attempt to keep the expensive supercomputer at maximum utilization. It is also possible to run...

Testimonial for effort on the CORAL project

This tutorial explains how to set up an x86 system to build and package software to run on an IBM POWER processor-based system running the Linux operating system. This is useful if you want to develop and build software on your x86 notebook or desktop, but your customers want to use the software you develop on their IBM POWER hardware running Linux...

Scientific workflows are often composed of compute-intensive simulations and data-intensive analysis and visualization, both equally important for productivity. High-performance computers run the compute-intensive phases efficiently, but data-intensive processing is still getting less attention. Dense non-volatile memory integrated into supercomput...

SDL, seabios, syslinux, vgabios, and zlib , taken as source code snapshots from their respective repositories. Filed here for completeness.

Source code for the Windows-side middleware is available on the public Internet, and for convenience is repeated here. Source code and build instructions for Damn Small Linux are available at http://damnsmalllinux.org/ . Source code for One Laptop Per Child is available via http://www.laptop.org/ . The OFSET material is available to download in bin...

Source code for the Windows-side middleware is available on the public Internet, and for convenience is repeated here. Source code and build instructions for Damn Small Linux are available at http://damnsmalllinux.org/. Source code for One Laptop Per Child is available via http://www.laptop.org/. The OFSET material is available to download in binar...

Integrate knowins-3.60-en.iso into the Web_Interactive_Math_Screensaver directory to get another screensaver, this one with a math theme. A current WIMS seems available here https://sourcesup.renater.fr/frs/?group_id=379 and the old ISO image is here http://wims.univ-mrs.fr/knowims/ .

Open source source code for scalable key-value store, snapshot on 12 May 2015 . Public code on 'github.com' at https://github.com/Scalable-Key-Value/code .

Some documents about BlueMatter, the molecular dynamics package developed for BlueGene

Add 'freeduc-games-1-6.iso' from the OFSET material on sourceforge to the 'qemusaver' directory, and you will have another screensaver. From here http://sourceforge.net/projects/ofset/files/freeduc-cd/games-1.6/ .

Open source source code for scalable key-value store, snapshot on 1 May 2015. Public code on 'github.com' at https://github.com/Scalable-Key-Value/code .

This is the software used on the IBM System BlueGene in this IBM Developerworks article http://www.ibm.com/developerworks/library/l-bluegene/index.html "Protein modeling with Blue Gene/L".

'avi' file which was uploaded to YouTube as https://www.youtube.com/watch?v=sqhXsoP7ddU in support of the IBM DeveloperWorks article http://www.ibm.com/developerworks/library/l-bluegene/

An information processing system for performing a transform of a multidimensional matrix in a distributed memory network. The method includes storing a multidimensional matrix of side N in a distributed memory network with a plurality of nodes and distributing work associated with a calculation of a transform of the matrix among N2 of the plurality...

Source code supplementary to https://www.research.ibm.com/bluegene/jrd_2005/cust_math/cust-math-secure.pdf , originally published on IBM Alphaworks but no longer available there

Source code supplementary to https://www.research.ibm.com/bluegene/jrd_2005/cust_math/cust-math-secure.pdf , originally published on IBM Alphaworks but no longer available there

A method and arrangements for increased precision in the computation of a reciprocal square root is disclosed. In accordance with the present invention, it is possible to achieve fifty three (53) bits of precision in less processing time than previously possible.

A method and system for evaluating a call to a library function at compile time. A first call included in a program being compiled by a compiler is identified. The first call is a call to a library function included in a pre-defined list of library functions external to the program. The first call includes one or more arguments associated with one...

The IBM System BlueGene/P comes from the factory with IBM's Compute Node Kernel, which is well-suited to running supercomputer applications. But it is also possible to run Linux in the compute fabric. This standard programming environment broadens the set of applications which can run on the leadership hardware, and makes it easy to put the superco...

This needs knosciences-1-0.iso adding into the 'qemusaver' directory to become a screensaver as described in the article. This ISO is currently for download here http://download.tuxfamily.org/knosciences/ .

This needs freeduc-cd-1.4.1.iso adding into the 'qemusaver' directory to become a screensaver as described in the article. freeduc-cd-1.4.1.iso is available on sourceforge here http://sourceforge.net/projects/ofset/files/freeduc-cd/1.4.1/ .

A method, information processing system and computer readable medium for performing a transform of a multidimensional matrix in a distributed memory network. The method includes storing a multidimensional matrix of side N in a distributed memory network comprising a plurality of nodes and distributing work associated with a calculation of a transfo...

Device driver source code contributed by IBM to Argonne National Laboratory for their ZeptoOS project. The complete modified Linux is available for public download with "git clone http://git.anl-external.org/bg-linux.repos/linux-2.6.29.1-BGP.git/" as described in the ANL wiki http://bg-linux.anl-external.org/wiki/index.php/2.6.29_based_ZeptoOS_Linu...

We present the Active Storage Fabrics (ASF) model for storage embedded parallel processing as a way to ad-dress petascale data intensive challenges. ASF is aimed at emerging scalable system-on-a-chip, storage class mem-ory architectures, but may be realized in prototype form on current parallel systems. ASF can be used to trans-parently accelerate...

N-body simulations present some of the most interesting challenges in the area of massively parallel computing, especially when the object is to improve the total time to solution for a fixed size problem. The Blue Matter molecular simulation framework has been developed specifically to address these challenges in order to explore programming model...

N-body simulations present some of the most interesting challenges in the area of massively parallel computing, especially when the object is to improve the time to solution for a fixed-size problem. The Blue Matter molecular simulation framework was developed specifically to address these challenges, to explore programming models for massively par...

This needs a file 'olpc.img' adding in to the 'qemusaver' directory to become a screensaver. '.img' files are XO images (disk images) from the One Laptop Per Child project at http://www.laptop.org/ .

Integrate knowins-3.60-en.iso into the Web_Interactive_Math_Screensaver directory to get another screensaver, this one with a math theme. WIMS seems available here https://sourcesup.renater.fr/frs/?group_id=379 but I can't currently find the old ISO image.

This needs games-knoppix-3-7-0-1.iso adding into the 'qemusaver' directory to become a screensaver as described in the article. This live linux distribution is no longer being distributed, but may be available via 'knopper.net' if there is sufficient demand. One of Klaus Knopper's students coordinated the development.

This paper describes a novel spatial-force decomposition for N-body simulations for which we observe O(sqrt(p)) communication scaling. This has enabled Blue Matter to approach the effective limits of concurrency for molecular dynamics using particle-mesh (FFT-based) methods for handling electrostatic interactions. Using this decomposition, Blue Mat...

This paper describes some of the issues involved with scaling biomolecular simulations onto massively parallel machines drawing on the Blue Matter application team’s experiences with Blue Gene/L. Our experiences in scaling biomolecular simulation to one atom/node on BG/L should be relevant to scaling biomolecular simulations onto larger peta-scale...

This paper presents strong scaling performance data for the Blue Mat- ter molecular dynamics framework using a novel n-body spatial decomposition and a collective communications technique implemented on both MPI and low level hardware interfaces. Using Blue Matter on Blue Gene/L, we have measured scalability through 16,384 nodes with measured time...

This paper describes a novel spatial-force decomposition for N-body simulations for which we observe O(sqrt(p)) communication scaling. This has enabled Blue Matter to approach the effective limits of concurrency for molecular dynamics using particle-mesh (FFT-based) methods for handling electrostatic interactions. Using this decomposition, Blue Mat...

Construct and package a Linux® LiveCD so that it will install using the standard Microsoft® Windows® install process and will operate as a standard Windows screensaver. Answering the most common concern about open source software, this article shows that, yes, Linux will run under Windows. So why should you read this article? Why, indeed, should...

This paper provides an overview of the Blue Matter application development effort within the Blue Gene project that supports our scientific simulation efforts in the areas of protein folding and membrane-protein systems. The design philosophy of the Blue Gene/L architecture relies on large numbers of power efficient nodes (whose technology is deriv...

Blue Gene/L uses a large number of low power processors, together with multiple integrated interconnection networks, to build a supercomputer with low cost, space and power consumption. It uses a novel system software architecture designed with application scalability in mind. However, whether real applications will scale to tens of thousands of pr...

This paper presents performance characteristics of a communications- intensive kernel, the complex data 3D FFT, running on the Blue Gene/L architec- ture. Two implementations of the volumetric FFT algorithm were characterized, one built on the MPI library using an optimized collective all-to-all operation (2) and another built on a low-level System...

While developing the protein folding application for the IBM Blue Gene®/L supercomputer, some frequently executed computational kernels were encountered. These were significantly more complex than the linear algebra kernels that are normally provided as tuned libraries with modern machines. Using regular library functions for these would have resul...

Blue Matter is the application framework being developed in conjunction with the scientific portion of the IBM Blue Gene® project. We describe the parallel decomposition currently being used to target the Blue Gene/L machine and discuss the application-based trace tools used to analyze the performance of the application. We also present the results...

This paper presents results on a communications-intensive kernel, the three-dimensional fast Fourier transform (3D FFT), running on the 2,048-node Blue Gene®/L (BG/L) prototype. Two implementations of the volumetric FFT algorithm were characterized, one built on the Message Passing Interface library and another built on an active packet Application...

We describe the design of a dual-issue single-instruction, multiple-data-like (SIMD-like) extension of the IBM PowerPC® 440 floating-point unit (FPU) core and the compiler and algorithmic techniques to exploit it. This extended FPU is targeted at both the IBM massively parallel Blue Gene®/L machine and the more pervasive embedded platforms. We disc...

In this work we demonstrate the use of a rigorous formalism for the extraction of state-to-state transition functions as a way to study the kinetics of protein folding in the context of a Markov chain. The approach is illustrated by its application to two different systems: a blocked alanine dipeptide in a vacuum and the C-terminal -hairpin motif f...

We describe the design, implementation, and evaluation of a dual-issue SIMD-like extension of the PowerPC 440 floating-point unit (FPU) core. This extended FPU is targeted at both IBM's massively parallel Blue-Gene/L machine as well as more pervasive embedded platforms. It has several novel features, such as a computational crossbar and cross-load/...

We describe the design, implementation, and evaluation of a dual-issue SIMD-like extension of the PowerPC 440 floating-point unit (FPU) core. This extended FPU is targeted at both IBM's massively parallel BlueGene/L machine as well as more pervasive embedded platforms. It has several novel features, such as a computational crossbar and cross-load/s...

In this paper we describe the context, architecture, and challenges of Blue Matter, the application framework being developed in conjunction with the science effort within IBM's Blue Gene project. The study of the mechanisms behind protein folding and related topics can require long time simulations on systems with a wide range of sizes and the app...

This paper gives an overview of the BlueGene/L Supercomputer. This is a jointly funded research partnership between IBM and the Lawrence Livermore National Laboratory as part of the United States Department of Energy ASCI Advanced Architecture Research Program. Application performance and scaling studies have recently been initiated with partners a...

This paper gives an overview of the BlueGene/L Supercomputer. This is a jointly funded research partnership between IBM and the Lawrence Livermore National Laboratory as part of the United States Department of Energy ASCI Advanced Architecture Research Program. Application performance and scaling studies have recently been initiated with partners a...

System-on-a-chip technology allows a level of integration that can be leveraged to develop inexpensive high-performance, low-power computing nodes. When used in aggregate, this approach promises to challenge conventional supercomputer architectures in the high-performance computing arena. Systems under consideration reach into the hundreds of thous...

Summary form only given. Large powerful networks coupled to state-of-the-art processors have traditionally dominated supercomputing. As technology advances, this approach is likely to be challenged by a more cost-effective System-On-A-Chip approach, with higher levels of system integration. The scalability of applications to architectures with tens...

This paper gives an overview of the BlueGene/L Supercomputer. This is a jointly funded research partnership between IBM and the Lawrence Livermore National Laboratory as part of the United States Department of Energy ASCI Advanced Architecture Research Program. Application performance and scaling studies have recently been initiated with partners a...

Large powerful networks coupled to state-of-the-art processors have traditionally dominated supercomputing. As technology advances, this approach is likely to be challenged by a more cost-effective System-On-A-Chip approach, with higher levels of system integration. The scalability of applications to architectures with tens to hundreds of thousands...

System-on-a-chip technology allows a level of integration that can be leveraged to develop inexpensive high-performance, low-power computing nodes. When used in aggregate, this approach promises to challenge conventional supercomputer architectures in the high-performance computing arena. Systems under consideration reach into the hundreds of thous...

In December 1999,IBM announced the start of a five-year effort to build a massively parallel computer, to be applied to the study of biomolecular phenomena such as protein folding. The project has two main goals: to advance our understanding of the mechanisms behind protein folding via large-scale simulation, and to explore novel ideas in massively...

An asynchronous data channel for a disk drive reads fields of data synchronized at a bit frequency which are separated by adjustment regions having two different patterns of control signals. Each pattern repeats at a different submultiple of the bit frequency. The channel derives two clock signals at the two submultiple frequencies, and produces a...

This paper describes a novel decomposition for N-body simulations that has enabled Blue Matter to approach the effective limits of concurrency for molecular dynamics using particle-mesh (FFT-based) methods for han- dling electrostatic interactions. Using this decomposition, Blue Matter run- ning on Blue Gene/L has achieved simulation rates in exces...

We propose an architecture for a General Parallel Operating System (GPOS) to make the task of efficiently exploiting Massively Parallel Processing (MPP) machines easier.