Programs as Diagrams: From Categorical Computability to Computable Categories

This is a draft of the textbook/monograph that presents computability theory using string diagrams. The introductory chapters have been taught as graduate and undergraduate courses and evolved through 8 years of lecture notes. The later chapters contain new ideas and results about categorical computability and some first steps into computable category theory. The underlying categorical view of computation is based on monoidal categories with program evaluators, called *monoidal computers*. This categorical structure can be viewed as a single-instruction diagrammatic programming language called Run, whose only instruction is called RUN. This version: improved text, moved the final chapter to the next volume. (The final version will continue lots of exercises and workouts, but already this version has severely degraded graphics to meet the size bounds.)Comment: 150 pages, 81 figure

Scalable Interactive Volume Rendering Using Off-the-shelf Components

This paper describes an application of a second generation implementation of the Sepia architecture (Sepia-2) to interactive volu-metric visualization of large rectilinear scalar fields. By employingpipelined associative blending operators in a sort-last configuration a demonstration system with 8 rendering computers sustains 24 to 28 frames per second while interactively rendering large data volumes (1024x256x256 voxels, and 512x512x512 voxels). We believe interactive performance at these frame rates and data sizes is unprecedented. We also believe these results can be extended to other types of structured and unstructured grids and a variety of GL rendering techniques including surface rendering and shadow map-ping. We show how to extend our single-stage crossbar demonstration system to multi-stage networks in order to support much larger data sizes and higher image resolutions. This requires solving a dynamic mapping problem for a class of blending operators that includes Porter-Duff compositing operators

Investigating SRAM PUFs in large CPUs and GPUs

Physically unclonable functions (PUFs) provide data that can be used for cryptographic purposes: on the one hand randomness for the initialization of random-number generators; on the other hand individual fingerprints for unique identification of specific hardware components. However, today's off-the-shelf personal computers advertise randomness and individual fingerprints only in the form of additional or dedicated hardware. This paper introduces a new set of tools to investigate whether intrinsic PUFs can be found in PC components that are not advertised as containing PUFs. In particular, this paper investigates AMD64 CPU registers as potential PUF sources in the operating-system kernel, the bootloader, and the system BIOS; investigates the CPU cache in the early boot stages; and investigates shared memory on Nvidia GPUs. This investigation found non-random non-fingerprinting behavior in several components but revealed usable PUFs in Nvidia GPUs.Comment: 25 pages, 6 figures. Code in appendi

A bibliometric analysis of the Journal of Molecular Graphics and Modelling

This paper reviews the articles published in Volumes 2-24 of the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics), focusing on the changes that have occurred in the subject over the years, and on the most productive and most cited authors and institutions. The most cited papers are those describing systems or algorithms, but the proportion of these types of article is decreasing as more applications of molecular graphics and molecular modelling are reported

PC-CUBE: A Personal Computer Based Hypercube

PC-CUBE is an ensemble of IBM PCs or close compatibles connected in the hypercube topology with ordinary computer cables. Communication occurs at the rate of 115.2 K-band via the RS-232 serial links. Available for PC-CUBE is the Crystalline Operating System III (CrOS III), Mercury Operating System, CUBIX and PLOTIX which are parallel I/O and graphics libraries. A CrOS performance monitor was developed to facilitate the measurement of communication and computation time of a program and their effects on performance. Also available are CXLISP, a parallel version of the XLISP interpreter; GRAFIX, some graphics routines for the EGA and CGA; and a general execution profiler for determining execution time spent by program subroutines. PC-CUBE provides a programming environment similar to all hypercube systems running CrOS III, Mercury and CUBIX. In addition, every node (personal computer) has its own graphics display monitor and storage devices. These allow data to be displayed or stored at every processor, which has much instructional value and enables easier debugging of applications. Some application programs which are taken from the book Solving Problems on Concurrent Processors (Fox 88) were implemented with graphics enhancement on PC-CUBE. The applications range from solving the Mandelbrot set, Laplace equation, wave equation, long range force interaction, to WaTor, an ecological simulation