A Policy-Based Optimization Library
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CHERI C/C++ Programming Guide
UCAM-CL-TR-947 Technical Report ISSN 1476-2986 Number 947 Computer Laboratory CHERI C/C++ Programming Guide Robert N. M. Watson, Alexander Richardson, Brooks Davis, John Baldwin, David Chisnall, Jessica Clarke, Nathaniel Filardo, Simon W. Moore, Edward Napierala, Peter Sewell, Peter G. Neumann June 2020 15 JJ Thomson Avenue Cambridge CB3 0FD United Kingdom phone +44 1223 763500 https://www.cl.cam.ac.uk/ c 2020 Robert N. M. Watson, Alexander Richardson, Brooks Davis, John Baldwin, David Chisnall, Jessica Clarke, Nathaniel Filardo, Simon W. Moore, Edward Napierala, Peter Sewell, Peter G. Neumann, SRI International This work was supported by the Defense Advanced Research Projects Agency (DARPA) and the Air Force Research Laboratory (AFRL), under contracts FA8750-10-C-0237 (“CTSRD”) and HR0011-18-C-0016 (“ECATS”). The views, opinions, and/or findings contained in this report are those of the authors and should not be interpreted as representing the official views or policies of the Department of Defense or the U.S. Government. This work was supported in part by the Innovate UK project Digital Security by Design (DSbD) Technology Platform Prototype, 105694. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 789108), ERC Advanced Grant ELVER. We also acknowledge the EPSRC REMS Programme Grant (EP/K008528/1), Arm Limited, HP Enterprise, and Google, Inc. Approved for Public Release, Distribution Unlimited. Technical reports published by the University of Cambridge Computer Laboratory are freely available via the Internet: https://www.cl.cam.ac.uk/techreports/ ISSN 1476-2986 3 Abstract This document is a brief introduction to the CHERI C/C++ programming languages. -
Optimizing the Use of High Performance Software Libraries
Optimizing the Use of High Performance Software Libraries Samuel Z. Guyer and Calvin Lin The University of Texas at Austin, Austin, TX 78712 Abstract. This paper describes how the use of software libraries, which is preva- lent in high performance computing, can benefit from compiler optimizations in much the same way that conventional computer languages do. We explain how the compilation of these informal languages differs from the compilation of more conventional computer languages. In particular, such compilation requires precise pointer analysis, requires domain-specific information about the library’s seman- tics, and requires a configurable compilation scheme. Finally, we show that the combination of dataflow analysis and pattern matching form a powerful tool for performing configurable optimizations. 1 Introduction High performance computing, and scientific computing in particular, relies heavily on software libraries. Libraries are attractive because they provide an easy mechanism for reusing code. Moreover, each library typically encapsulates a particular domain of ex- pertise, such as graphics or linear algebra, and the use of such libraries allows program- mers to think at a higher level of abstraction. In many ways, libraries are simply in- formal domain-specific languages whose only syntactic construct is the procedure call. This procedural interface is significant because it couches these informal languages in a familiar form, which is less imposing than a new computer language that introduces new syntax. Unfortunately, while libraries are not viewed as languages by users, they also are not viewed as languages by compilers. With a few exceptions, compilers treat each invocation of a library routine the same as any other procedure call. -
SSC Reference Manual SDK 2017-1-17, Version 170
SSC Reference Manual SDK 2017-1-17, Version 170 Aron Dobos and Paul Gilman January 13, 2017 The SSC (SAM Simulation Core) software library is the collection of simu- lation modules used by the National Renewable Energy Laboratory’s System Advisor Model (SAM). The SSC application programming interface (API) al- lows software developers to integrate SAM’s modules into web and desktop applications. The API includes mechanisms to set input variable values, run simulations, and retrieve values of output variables. The SSC modules are available in pre-compiled binary dynamic libraries minimum system library de- pendencies for Windows, OS X, and Linux operating systems. The native API language is ISO-standard C, and language wrappers are available for C#, Java, MATLAB, Python, and PHP. The API and model implementations are thread- safe and reentrant, allowing the software to be used in a parallel computing environment. This document describes the SSC software architecture, modules and data types, provides code samples, introduces SDKtool, and describes the language wrappers. Contents 2 Contents 1 Overview4 1.1 Framework Description.............................. 4 1.2 Modeling an Energy System........................... 4 2 An Example: Running PVWatts5 2.1 Write the program skeleton ........................... 6 2.2 Create the data container ............................ 6 2.3 Assign values to the module input variables.................. 7 2.4 Run the module.................................. 7 2.5 Retrieve results from the data container and display them.......... 8 2.6 Cleaning up.................................... 8 2.7 Compile and run the C program ........................ 9 2.8 Some additional comments............................ 9 3 Data Variables9 3.1 Variable Names.................................. 10 3.2 Variable Types ................................. -
UCLA Electronic Theses and Dissertations
UCLA UCLA Electronic Theses and Dissertations Title Projection algorithms for large scale optimization and genomic data analysis Permalink https://escholarship.org/uc/item/95v3t2nk Author Keys, Kevin Lawrence Publication Date 2016 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA Los Angeles Projection algorithms for large scale optimization and genomic data analysis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomathematics by Kevin Lawrence Keys 2016 c Copyright by Kevin Lawrence Keys 2016 ABSTRACT OF THE DISSERTATION Projection algorithms for large scale optimization and genomic data analysis by Kevin Lawrence Keys Doctor of Philosophy in Biomathematics University of California, Los Angeles, 2016 Professor Kenneth L. Lange, Chair The advent of the Big Data era has spawned intense interest in scalable mathematical optimiza- tion methods. Traditional approaches such as Newton’s method fall apart whenever the features outnumber the examples in a data set. Consequently, researchers have intensely developed first- order methods that rely only on gradients and subgradients of a cost function. In this dissertation we focus on projected gradient methods for large-scale constrained opti- mization. We develop a particular case of a proximal gradient method called the proximal distance algorithm. Proximal distance algorithms combine the classical penalty method of constrained min- imization with distance majorization. To optimize the loss function f(x) over a constraint set C, ρ 2 the proximal distance principle mandates minimizing the penalized loss f(x) + 2 dist(x; C) and following the solution xρ to its limit as ρ ! 1. -
Sparse Matrix Linear Models for Structured High-Throughput Data
Submitted to the Annals of Applied Statistics SPARSE MATRIX LINEAR MODELS FOR STRUCTURED HIGH-THROUGHPUT DATA BY JANE W. LIANG *,† Department of Biostatistics Harvard T.H. Chan School of Public Health 655 Huntington Ave, Boston, MA 02115-6028 [email protected] Harvard T.H. Chan School of Public Health † AND BY S´ AUNAK SEN ‡,§ Department of Preventive Medicine University of Tennessee Health Science Center 66 N. Pauline St, Memphis, TN 38163-2181 [email protected] University of Tennessee Health Science Center ‡ University of California, San Francisco § Recent technological advancements have led to the rapid generation of high-throughput biological data, which can be used to address novel scien- tific questions in broad areas of research. These data can be thought of as a large matrix with covariates annotating both rows and columns of this ma- trix. Matrix linear models provide a convenient way for modeling such data. In many situations, sparse estimation of these models is desired. We present fast, general methods for fitting sparse matrix linear models to structured high-throughput data. We induce model sparsity using an L1 penalty and consider the case when the response matrix and the covariate matrices are large. Due to data size, standard methods for estimation of these penalized regression models fail if the problem is converted to the corresponding uni- variate regression scenario. By leveraging matrix properties in the structure of our model, we develop several fast estimation algorithms (coordinate descent, FISTA, and ADMM) and discuss their trade-offs. We evaluate our method’s performance on simulated data, E. coli chemical genetic screening data, and two Arabidopsis genetic datasets with multivariate responses. -
Pygtk 2.0 Tutorial
PyGTK 2.0 Tutorial John Finlay October 7, 2012 PyGTK 2.0 Tutorial by John Finlay Published March 2, 2006 ii Contents 1 Introduction 1 1.1 Exploring PyGTK . .2 2 Getting Started 5 2.1 Hello World in PyGTK . .7 2.2 Theory of Signals and Callbacks . .9 2.3 Events . 10 2.4 Stepping Through Hello World . 11 3 Moving On 15 3.1 More on Signal Handlers . 15 3.2 An Upgraded Hello World . 15 4 Packing Widgets 19 4.1 Theory of Packing Boxes . 19 4.2 Details of Boxes . 20 4.3 Packing Demonstration Program . 22 4.4 Packing Using Tables . 27 4.5 Table Packing Example . 28 5 Widget Overview 31 5.1 Widget Hierarchy . 31 5.2 Widgets Without Windows . 34 6 The Button Widget 35 6.1 Normal Buttons . 35 6.2 Toggle Buttons . 38 6.3 Check Buttons . 40 6.4 Radio Buttons . 42 7 Adjustments 45 7.1 Creating an Adjustment . 45 7.2 Using Adjustments the Easy Way . 45 7.3 Adjustment Internals . 46 8 Range Widgets 49 8.1 Scrollbar Widgets . 49 8.2 Scale Widgets . 49 8.2.1 Creating a Scale Widget . 49 8.2.2 Methods and Signals (well, methods, at least) . 50 8.3 Common Range Methods . 50 8.3.1 Setting the Update Policy . 50 8.3.2 Getting and Setting Adjustments . 51 8.4 Key and Mouse Bindings . 51 8.5 Range Widget Example . 51 9 Miscellaneous Widgets 57 9.1 Labels . 57 9.2 Arrows . 60 9.3 The Tooltips Object . -
A Proposal for a Revision of ISO Modula-2 2
A Proposal for a Revision of ISO Modula-2 Benjamin Kowarsch, Modula-2 Software Foundation ∗ May 2020 (arXiv.org preprint) Abstract The Modula-2 language was first specified in [Wir78] by N. Wirth at ETH Z¨urich in 1978 and then revised several times. The last revision [Wir88] was published in 1988. The resulting language reports included ambiguities and lacked a comprehensive standard library. To resolve the ambiguities and specify a comprehensive standard library an ISO/IEC working group was formed and commenced work in 1987. A base standard was then ratified and published as IS 10514-1 in 1996 [JTC96]. Several conforming compilers have since been developed. At least five remain available of which at least three are actively maintained and one has been open sourced. Meanwhile, various deficiencies of the standard have become apparent but since its publication, no revision and no maintenance has been carried out. This paper discusses some of the deficiencies of IS 10514-1 and proposes a limited revision that could be carried out with moderate effort. The scope of the paper has been deliberately limited to the core language of the base standard and therefore excludes the standard library. 1 ISO/IEC Standardisation [II20] describes ISO/IEC standardisation procedures, summarised in brief below. 1.1 Organisational Overview The International Organisation for Standardisation (ISO) and the International Electrotechnical Commission (IEC) operate a joint technical committee (JTC1) to develop, publish and maintain information technology standards. JTC1 is organised into subcommittees (SC) and working groups (WG). The subcommittee for programming languages is JTC1/SC22. The working group that developed the ISO Modula-2 standard was JTC1/SC22/WG13. -
Finding What C++ Lost: Tracking Referent Objects with GCC
MEng Project Report Finding What C++ Lost: Tracking Referent Objects with GCC Alexander Lamaison Department of Computing Imperial College London <[email protected]> Supervisor: Paul H. J. Kelly <[email protected]> 16th June 2007 ii Abstract Pointer arithmetic in C and C++, though powerful, is inherently dangerous and a constant source of program flaws. Technologies exist to reduce these risks, one of which is Mudflap: an extension to GCC 4 that performs runtime bounds-checking. This has an number of weak- nesses, notably its inability to detect the case of pointers that stray between objects allocated adjacently. We have created MIRO, an improved version which uses the stricter approach of referent object tracking. As well as increasing the effectiveness of the checking, this allows us to provide more useful debugging information when violations occur. It requires no changes to existing C and C++ programs including non-compliant, but common, calculations involving invalid pointer values. Code compiled with MIRO can be mixed freely with unchecked code combining safety with performance and reducing the threshold to adoption. Acknowledgements I would like to thank, firstly, my supervisor and mentor Paul Kelly for guiding me through this project as well as the last four years of study and for always listening to my ramblings without complaint. Steven Lovegrove, my friend, in particular for helping me track down the source of the C++ STL problem but for help with many other problems too. Also John Wilander, Mariam Kamkar, Michael Zhivich, Tim Leek and Richard Lippmann for kindly donating the source code to their testbeds that were so invaluable throughout this project. -
TCG TSS 2.0 TPM Command Transmission Interface (TCTI) API Specification
TCG TSS 2.0 TPM Command Transmission Interface (TCTI) API Specification Family "2.0" Version 1.0, Revision 12 8 April 2019 Contact: [email protected] TCG PUBLISHED Copyright © TCG 2019 TCG Disclaimers, Notices, and License Terms Copyright Licenses: Trusted Computing Group (TCG) grants to the user of the source code in this specification (the “Source Code”) a worldwide, irrevocable, nonexclusive, royalty free, copyright license to reproduce, create derivative works, distribute, display and perform the Source Code and derivative works thereof, and to grant others the rights granted herein. The TCG grants to the user of the other parts of the specification (other than the Source Code) the rights to reproduce, distribute, display, and perform the specification solely for the purpose of developing products based on such documents. Source Code Distribution Conditions: Redistributions of Source Code must retain the above copyright licenses, this list of conditions and the following disclaimers. Redistributions in binary form must reproduce the above copyright licenses, this list of conditions and the following disclaimers in the documentation and/or other materials provided with the distribution. Disclaimers: THE COPYRIGHT LICENSES SET FORTH ABOVE DO NOT REPRESENT ANY FORM OF LICENSE OR WAIVER, EXPRESS OR IMPLIED, BY ESTOPPEL OR OTHERWISE, WITH RESPECT TO PATENT RIGHTS HELD BY TCG MEMBERS (OR OTHER THIRD PARTIES) THAT MAY BE NECESSARY TO IMPLEMENT THIS SPECIFICATION OR OTHERWISE. Contact TCG Administration ([email protected]) for information on specification licensing rights available through TCG membership agreements. THIS SPECIFICATION IS PROVIDED "AS IS" WITH NO EXPRESS OR IMPLIED WARRANTIES WHATSOEVER, INCLUDING ANY WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, ACCURACY, COMPLETENESS, OR NONINFRINGEMENT OF INTELLECTUAL PROPERTY RIGHTS, OR ANY WARRANTY OTHERWISE ARISING OUT OF ANY PROPOSAL, SPECIFICATION OR SAMPLE. -
Abstract Data Types (Adts), After More on the Heap Preparing for The
Preparing for the Midterm Exam • Exam logistics o Date/time: Thursday October 26 in lecture o Open books, open notes, open mind, but not open laptop/PDA Abstract Data Types (ADTs), o Covering material from lecture, precept, and reading, but not tools After More on the Heap • Preparing for the midterm o Lecture and precept materials available online o Course textbooks, plus optional books on reserve Prof. David August o Office hours and the course listserv o Old midterm exams on the course Web site COS 217 1 2 A Little More About the Heap… Example: Read a Line (or URL) • Memory layout of a C program • Write a function that reads a word from stdin o Text: code, constant data o Read from stdin until encountering a space, tab, ‘\n’, or EOF o Data: initialized global & static variables o Output a pointer to the sequence of characters, ending with ‘\0’ BSS: uninitialized global & static variables 0 o Text • Example code (very, very buggy) o Heap: dynamic memory Stack: local variables Data o #include <stdio.h> • Purpose of the heap BSS o Memory allocated explicitly by the programmer Heap int main(void) { o Using the functions malloc and free char* buf; • But, why would you ever do this??? scanf(“%s”, buf); o Glutton for punishment??? printf(“Hello %s\n”, buf); return 0; } Stack 0xffffffff 3 4 Problem: Need Storage for String Problem: Input Longer Than Array • Improving the code • Improving the code o Allocate storage space for the string o Don’t allow input that exceeds the array size Example: define an array o • Example (better, but not perfect) -
CPSC 213: Assignment 7
CPSC 213: Assignment 7 Due: Monday, March 12, 2012 at 6pm. Late assignments are accepted until Wednesday, March 14 at 6pm with a 25% penalty per day (or fraction of a day) past the due date. This rule is strictly applied and there are no exceptions. Goal In this assignment you will investigate interrupts and asynchronous programming by reading and modifying a program that uses signals to trigger asynchronous actions. This assignment is closely modeled on the asynchronous disk read example discussed in the lecture and gives you a chance to experience this sort of programming first hand, using a software environment that mimics hardware interrupts. Interrupts, Signals and Asynchronous Programming Included with this assignment is a small C program called async.c. This program uses a Unix OS feature called “signals” to mimic hardware interrupts. In the boot procedure, the program registers interruptServiceRoutine as a signal handler for the SIGALRM signal and then tells the OS to deliver this signal to the program once every second. The program includes a method called doAsync that schedules an asynchronous event, sort of like a disk-read request. These events complete in order, one at a time, each time the SIGALRM is delivered to the program. The doAsync procedure enqueues events on a circular completion queue and interruptServiceRoutine dequeues these completion events when SIGALRMs arrive and delivers the completion by calling the completion routine with two parameters, a pointer and an int, whose meaning is determined by the completion routine. You will note the use of the type void*. This type is called an “opaque pointer” and is used to store pointers of any type. -
Arxiv:1803.01621V4 [Eess.SP] 27 Jan 2020
Proximal gradient algorithms: Applications in signal processing a, b c Niccol`oAntonello ∗, Lorenzo Stella , Panagiotis Patrinos , Toon van Waterschootc,d a Idiap Research Institute, Rue Marconi 19, 1920 Martigny Switzerland b Amazon Research, Krausenstraße 38, 10117 Berlin, Germany c KU Leuven, ESAT{STADIUS, Stadius Center for Dynamical Systems, Signal Processing and Data Analytics, Kasteelpark Arenberg 10, 3001 Leuven, Belgium d KU Leuven, ESAT{ETC, e-Media Research Lab, Andreas Vesaliusstraat 13, 1000 Leuven, Belgium Abstract Advances in numerical optimization have supported breakthroughs in several areas of signal processing. This paper focuses on the recent enhanced variants of the proximal gradient numerical optimization algorithm, which combine quasi- Newton methods with forward-adjoint oracles to tackle large-scale problems and reduce the computational burden of many applications. These proximal gradi- ent algorithms are here described in an easy-to-understand way, illustrating how they are able to address a wide variety of problems arising in signal processing. A new high-level modeling language is presented which is used to demonstrate the versatility of the presented algorithms in a series of signal processing appli- cation examples such as sparse deconvolution, total variation denoising, audio de-clipping and others. Keywords: Numerical optimization; Proximal gradient algorithm; Large-scale optimization IThis research work was carried out at the ESAT Laboratory of KU Leuven, the frame of the FP7-PEOPLE Marie Curie Initial Training Network \Dereverberation and Reverberation of Audio, Music, and Speech (DREAMS)", funded by the European Commission under Grant Agreement no. 316969, European Research Council under the European Union's Horizon 2020 research and innovation program / ERC Consolidator Grant: SONORA no.