Results for “Computer programs” — Page 7

DOE OSTI2019

DEFT: a program for operators in EFT

We describe a Python-based computer program, DEFT, for manipulating operators in effective field theories (EFTs). In its current incarnation, DEFT can be applied to 4-dimensional, Poincaré invariant theories with gauge group SU(3)×SU(2)×U(1), such as the Standard Model (SM), but a variety of extensions (e.g. to lower dimensions or to an arbitrary product of unitary gauge groups) are conceptually straightforward. Amongst other features, the program is able to: (i) check whether an input list of Lagrangian operators (of a given dimension in the EFT expansion) is a basis for the space of operators contributing to S-matrix elements, once redundancies (such as Fierz-Pauli identities, integration by parts, and equations of motion) are taken into account; (ii) generate such a basis (where possible) from an input algorithm; (iii) carry out a change of basis. We describe applications to the SM (where we carry out a number of non-trivial cross-checks) and extensions thereof, and outline how the program may be of use in precision tests of the SM and in the ongoing search for new physics at the LHC and elsewhere. The code and instructions can be downloaded from http://web.physics.ucsb.edu/~dwsuth/DEFT/.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

An Efficient Algorithm for Automatic Structure Optimization in X-ray Standing-Wave Experiments

We present that x-ray standing-wave photoemission experiments involving multilayered samples are emerging as unique probes of the buried interfaces that are ubiquitous in current device and materials research. Such data require for their analysis a structure optimization process comparing experiment to theory that is not straightforward. In this work, we present a new computer program for optimizing the analysis of standing-wave data, called SWOPT, that automates this trial-and-error optimization process. The program includes an algorithm that has been developed for computationally expensive problems: so-called black-box simulation optimizations. It also includes a more efficient version of the Yang X-ray Optics Program (YXRO) [Yang, S.-H., Gray, A.X., Kaiser, A.M., Mun, B.S., Sell, B.C., Kortright, J.B., Fadley, C.S., J. Appl. Phys. 113, 1 (2013)] which is about an order of magnitude faster than the original version. Human interaction is not required during optimization. We tested our optimization algorithm on real and hypothetical problems and show that it finds better solutions significantly faster than a random search approach. The total optimization time ranges, depending on the sample structure, from minutes to a few hours on a modern laptop computer, and can be up to 100x faster than a corresponding manual optimization. Finally, these speeds make the SWOPT program a valuable tool for realtime analyses of data during synchrotron experiments.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Quantum Algorithm Implementations for Beginners

As quantum computers become available to the general public, the need has arisen to train a cohort of quantum programmers, many of whom have been developing classical computer programs for most of their careers. While currently available quantum computers have less than 100 qubits, quantum computing hardware is widely expected to grow in terms of qubit count, quality, and connectivity. This review aims at explaining the principles of quantum programming, which are quite different from classical programming, with straightforward algebra that makes understanding of the underlying fascinating quantum mechanical principles optional. We give an introduction to quantum computing algorithms and their implementation on real quantum hardware. We survey 20 different quantum algorithms, attempting to describe each in a succinct and self-contained fashion. We show how these algorithms can be implemented on IBM’s quantum computer, and in each case, we discuss the results of the implementation with respect to differences between the simulator and the actual hardware runs. This article introduces computer scientists, physicists, and engineers to quantum algorithms and provides a blueprint for their implementations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Program structure-based blocking

Embodiments relate to program structure-based blocking. An aspect includes receiving source code corresponding to a computer program by a compiler of a computer system. Another aspect includes determining a prefetching section in the source code by a marking module of the compiler. Yet another aspect includes performing, by a blocking module of the compiler, blocking of instructions located in the prefetching section into instruction blocks, such that the instruction blocks of the prefetching section only contain instructions that are located in the prefetching section.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

Program structure-based blocking

Embodiments relate to program structure-based blocking. An aspect includes receiving source code corresponding to a computer program by a compiler of a computer system. Another aspect includes determining a prefetching section in the source code by a marking module of the compiler. Yet another aspect includes performing, by a blocking module of the compiler, blocking of instructions located in the prefetching section into instruction blocks, such that the instruction blocks of the prefetching section only contain instructions that are located in the prefetching section.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Trabecula: A Random Generator of Computational Phantoms for Bone Marrow Dosimetry

This study was motivated by the efforts on evaluation of radiation risk for leukemia incidence in the Techa River Cohort, where the main bone marrow dose contributors were 89,90Sr (bone-seeking beta emitters). Energy deposition in bone marrow targets was evaluated by simulating radiation particle transport using computational phantoms. The present paper describes the computer program “Trabecula” implementing an algorithm for parametric generation of computational phantoms, which serve as the basis for calculating bone marrow doses. “Trabecula” is a user-friendly tool that automatically converts analytical models into voxelized representations that are directly compatible as input to MCNP.

Shishkina, Elena A.↗

DOE OSTI2025

The Right Time at the Right Places

In my undergraduate studies at the Massachusetts Institute of Technology (MIT), the short-lived chemical physics major allowed me to evade a number of courses required for chemistry majors. Thus, it was possible to take many physics courses and most of the advanced PhD-level courses in physical chemistry. I also took the introductory electrical engineering course in computer programming. The latter allowed me to write lots of computer code as a part of my (passing, but largely unsuccessful) senior thesis directed graciously by Professor Walter Thorson. As recommended by MIT Professor John C. Slater, I moved to Stanford University with Professor Frank Harris as my PhD supervisor. Frank was the perfect advisor for me, providing very close direction during the first year, and then allowing me to develop more and more independently. Within a few days of my twenty-fifth birthday, I became an assistant professor of chemistry at the University of California, Berkeley. Eighteen years later, I moved to the University of Georgia as director of a new research institute.

autobiography↗

DOE OSTI2014

Network support for system initiated checkpoints

A system, method and computer program product for supporting system initiated checkpoints in parallel computing systems. The system and method generates selective control signals to perform checkpointing of system related data in presence of messaging activity associated with a user application running at the node. The checkpointing is initiated by the system such that checkpoint data of a plurality of network nodes may be obtained even in the presence of user applications running on highly parallel computers that include ongoing user messaging activity.

Chen, Dong↗

DOE OSTI2015

System-wide power management control via clock distribution network

An apparatus, method and computer program product for automatically controlling power dissipation of a parallel computing system that includes a plurality of processors. A computing device issues a command to the parallel computing system. A clock pulse-width modulator encodes the command in a system clock signal to be distributed to the plurality of processors. The plurality of processors in the parallel computing system receive the system clock signal including the encoded command, and adjusts power dissipation according to the encoded command.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2017

I/O routing in a multidimensional torus network

A method, system and computer program product are disclosed for routing data packet in a computing system comprising a multidimensional torus compute node network including a multitude of compute nodes, and an I/O node network including a plurality of I/O nodes. In one embodiment, the method comprises assigning to each of the data packets a destination address identifying one of the compute nodes; providing each of the data packets with a toio value; routing the data packets through the compute node network to the destination addresses of the data packets; and when each of the data packets reaches the destination address assigned to said each data packet, routing said each data packet to one of the I/O nodes if the toio value of said each data packet is a specified value. In one embodiment, each of the data packets is also provided with an ioreturn value used to route the data packets through the compute node network.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

I/O routing in a multidimensional torus network

A method, system and computer program product are disclosed for routing data packet in a computing system comprising a multidimensional torus compute node network including a multitude of compute nodes, and an I/O node network including a plurality of I/O nodes. In one embodiment, the method comprises assigning to each of the data packets a destination address identifying one of the compute nodes; providing each of the data packets with a toio value; routing the data packets through the compute node network to the destination addresses of the data packets; and when each of the data packets reaches the destination address assigned to said each data packet, routing said each data packet to one of the I/O nodes if the toio value of said each data packet is a specified value. In one embodiment, each of the data packets is also provided with an ioreturn value used to route the data packets through the compute node network.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

I/O routing in a multidimensional torus network

A method, system and computer program product are disclosed for routing data packet in a computing system comprising a multidimensional torus compute node network including a multitude of compute nodes, and an I/O node network including a plurality of I/O nodes. In one embodiment, the method comprises assigning to each of the data packets a destination address identifying one of the compute nodes; providing each of the data packets with a toio value; routing the data packets through the compute node network to the destination addresses of the data packets; and when each of the data packets reaches the destination address assigned to said each data packet, routing said each data packet to one of the I/O nodes if the toio value of said each data packet is a specified value. In one embodiment, each of the data packets is also provided with an ioreturn value used to route the data packets through the compute node network.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Checkpointing using compute node health information

A method is disclosed, as well as an associated apparatus and computer program product, for checkpointing using a plurality of communicatively coupled compute nodes. The method comprises acquiring health information for a first node of the plurality of compute nodes, and determining a first failure probability for the first node using the health information. The first failure probability corresponds to a predetermined time interval. The method further comprises selecting a second node of the plurality of compute nodes as a partner node for the first node. The second node has a second failure probability for the time interval. A composite failure probability of the first node and the second node is less than the first failure probability. The method further comprises copying checkpoint information from the first node to the partner node.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

I/O routing in a multidimensional torus network

A method, system and computer program product are disclosed for routing data packet in a computing system comprising a multidimensional torus compute node network including a multitude of compute nodes, and an I/O node network including a plurality of I/O nodes. In one embodiment, the method comprises assigning to each of the data packets a destination address identifying one of the compute nodes; providing each of the data packets with a toio value; routing the data packets through the compute node network to the destination addresses of the data packets; and when each of the data packets reaches the destination address assigned to said each data packet, routing said each data packet to one of the I/O nodes if the toio value of said each data packet is a specified value. In one embodiment, each of the data packets is also provided with an ioreturn value used to route the data packets through the compute node network.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

I/O routing in a multidimensional torus network

A method, system and computer program product are disclosed for routing data packet in a computing system comprising a multidimensional torus compute node network including a multitude of compute nodes, and an I/O node network including a plurality of I/O nodes. In one embodiment, the method comprises assigning to each of the data packets a destination address identifying one of the compute nodes; providing each of the data packets with a toio value; routing the data packets through the compute node network to the destination addresses of the data packets; and when each of the data packets reaches the destination address assigned to said each data packet, routing said each data packet to one of the I/O nodes if the toio value of said each data packet is a specified value. In one embodiment, each of the data packets is also provided with an ioreturn value used to route the data packets through the compute node network.

Chen, Dong↗

DOE OSTI2024

Shorter function summaries for finite state machine-based high consequence systems using logic synthesis and tautologies (Final Report LDRD 24-1302)

Computer programs are often viewed as collections of functions – each function has parameters (inputs) and computes a return value, and each has potential side effects that modify program state (outputs). In this research, a Sandia symbolic execution tool designed to support “human-in-the-loop” analysis was modified to automatically create “function summaries,” and a new tool, “diaboolical,” was created to support enhancing readability of the summary using a novel approach to bit-vector simplification that leverages logic synthesis and tautologies. For this effort, students at Auburn University created several finite state machines (FSMs) to serve as exemplars for high-consequence systems. Function summaries for each of the machines were obtained, and then portions of the summaries were simplified using both diaboolical and the simplification procedure of a popular SMT solver. A comparison of the results shows that diaboolical can often produce smaller function summaries, with expression length improvements over the unsimplified function summaries ranging from 0% to 90% for diaboolical and 0% to 65% for the SMT solver, though diaboolical had a significantly greater cost in time. Diaboolical was evaluated against a collection of “arbitrary” C-code as well as FSM exemplars, and for both datasets it achieved an approximately 10% improvement in expression length compared to simplifications that could be obtained using existing techniques. Function summaries can assist assurance efforts that evaluate existing systems and their executable code. A smaller function summary is likely easier for humans to understand and could thus increase the ability and efficacy of assurance practices centered around the analysis of executable artifacts.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Non-volatile memory for checkpoint storage

A system, method and computer program product for supporting system initiated checkpoints in high performance parallel computing systems and storing of checkpoint data to a non-volatile memory storage device. The system and method generates selective control signals to perform checkpointing of system related data in presence of messaging activity associated with a user application running at the node. The checkpointing is initiated by the system such that checkpoint data of a plurality of network nodes may be obtained even in the presence of user applications running on highly parallel computers that include ongoing user messaging activity. In one embodiment, the non-volatile memory is a pluggable flash memory card.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

ProteoSign: an end-user online differential proteomics statistical analysis platform

Profiling of proteome dynamics is crucial for understanding cellular behavior in response to intrinsic and extrinsic stimuli and maintenance of homeostasis. Over the last 20 years, mass spectrometry (MS) has emerged as the most powerful tool for large-scale identification and characterization of proteins. Bottom-up proteomics, the most common MS-based proteomics approach, has always been challenging in terms of data management, processing, analysis and visualization, with modern instruments capable of producing several gigabytes of data out of a single experiment. Here, we present ProteoSign, a freely available web application, dedicated in allowing users to perform proteomics differential expression/abundance analysis in a userfriendly and self-explanatory way. Although several non-commercial standalone tools have been developed for post-quantification statistical analysis of proteomics data, most of them are not end-user appealing as they often require very stringent installation of programming environments, third-party software packages and sometimes further scripting or computer programming. To avoid this bottleneck, we have developed a user-friendly software platform accessible via a web interface in order to enable proteomics laboratories and core facilities to statistically analyse quantitative proteomics data sets in a resource-efficient manner. ProteoSign is available at http://bioinformatics.med.uoc.gr/ProteoSign and the source code at https://github.com/yorgodillo/ ProteoSign.

59 BASIC BIOLOGICAL SCIENCES↗