PC Operating Research Articles

Swan: A tool for porting CUDA programs to OpenCL

The use of modern, high-performance graphical processing units (GPUs) for acceleration of scientific computation has been widely reported. The majority of this work has used the CUDA programming model supported exclusively by GPUs manufactured by NVIDIA. An industry standardisation effort has recently produced the OpenCL specification for GPU programming. This offers the benefits of hardware-independence and reduced dependence on proprietary tool-chains. Here we describe a source-to-source translation tool, “Swan” for facilitating the conversion of an existing CUDA code to use the OpenCL model, as a means to aid programmers experienced with CUDA in evaluating OpenCL and alternative hardware. While the performance of equivalent OpenCL and CUDA code on fixed hardware should be comparable, we find that a real-world CUDA application ported to OpenCL exhibits an overall 50% increase in runtime, a reduction in performance attributable to the immaturity of contemporary compilers. The ported application is shown to have platform independence, running on both NVIDIA and AMD GPUs without modification. We conclude that OpenCL is a viable platform for developing portable GPU applications but that the more mature CUDA tools continue to provide best performance. Program summary Program title: Swan Catalogue identifier: AEIH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEIH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public License version 2 No. of lines in distributed program, including test data, etc.: 17 736 No. of bytes in distributed program, including test data, etc.: 131 177 Distribution format: tar.gz Programming language: C Computer: PC Operating system: Linux RAM: 256 Mbytes Classification: 6.5 External routines: NVIDIA CUDA, OpenCL Nature of problem: Graphical Processing Units (GPUs) from NVIDIA are preferentially programed with the proprietary CUDA programming toolkit. An alternative programming model promoted as an industry standard, OpenCL, provides similar capabilities to CUDA and is also supported on non-NVIDIA hardware (including multicore ×86 CPUs, AMD GPUs and IBM Cell processors). The adaptation of a program from CUDA to OpenCL is relatively straightforward but laborious. The Swan tool facilitates this conversion. Solution method: Swan performs a translation of CUDA kernel source code into an OpenCL equivalent. It also generates the C source code for entry point functions, simplifying kernel invocation from the host program. A concise host-side API abstracts the CUDA and OpenCL APIs. A program adapted to use Swan has no dependency on the CUDA compiler for the host-side program. The converted program may be built for either CUDA or OpenCL, with the selection made at compile time. Restrictions: No support for CUDA C++ features Running time: Nominal

S-states of helium-like ions

A simple Mathematica (version 7) code for computing S-state energies and wave functions of two-electron (helium-like) ions is presented. The elegant technique derived from the classical papers of Pekeris (1958, 1959, 1962, 1965, 1971) [1–3] is applied. The basis functions are composed of the Laguerre functions. The method is based on the perimetric coordinates and specific properties of the Laguerre polynomials. Direct solution of the generalized eigenvalues and eigenvectors problem is used, distinct from the Pekeris works. No special subroutines were used, only built-in objects supported by Mathematica. The accuracy of the results and computation times depend on the basis size. The ground state and the lowest triplet state energies can be computed with a precision of 12 and 14 significant figures, respectively. The accuracy of the higher excited states calculations is slightly worse. The resultant wave functions have a simple analytical form, that enables calculation of expectation values for arbitrary physical operators without any difficulties. Only three natural parameters are required in the input. The above Mathematica code is simpler than the earlier version (Liverts and Barnea, 2010 [4]). At the same time, it is faster and more accurate. Program summary Program title: TwoElAtomSL(SH) Catalogue identifier: AEHY_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHY_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 11 434 No. of bytes in distributed program, including test data, etc.: 540 063 Distribution format: tar.gz Programming language: Mathematica 7.0 Computer: Any PC Operating system: Any which supports Mathematica; tested under Microsoft Windows XP and Linux SUSE 11.0 RAM: ⩾ 10 9 bytes Classification: 2.1, 2.2, 2.7, 2.9 Nature of problem: The Schrödinger equation for atoms (ions) with more than one electron has not been solved analytically. Approximate methods must be applied in order to obtain the wave functions or another physical attributes from quantum mechanical calculations. Solution method: The S-wave function is expanded into a triple set of basis functions which are composed of the exponentials combined with the Laguerre polynomials in the perimetric coordinates. Using specific properties of the Laguerre polynomials, solution of the two-electron Schrödinger equation reduces to solving the generalized eigenvalues and eigenvector problem for the proper Hamiltonian. The unknown exponential parameter is determined by means of minimization of the corresponding eigenvalue (energy). Restrictions: First, the too large length of expansion (basis size) takes the too large computation time and operative memory giving no perceptible improvement in accuracy. Second, the number of shells Ω in the wave function expansion enables one to calculate the excited nS-states up to n = Ω + 1 inclusive. Running time: 2–60 minutes (depends on basis size and computer speed).

Fast pulse detection algorithms for digitized waveforms from scintillators

Advanced C++ programming methods as well as fast Pulse Detection Algorithms (PDA) have been implemented in order to increase the computing speed of a LabVIEW™ data processing software developed for a Digital Pulse Shape Discrimination (DPSD) system for liquid scintillators. The newly implemented PDAs are described and compared: the most efficient method has been implemented in the data processing software, which has also been ported into C++. The comparison of the computing speeds of the new and old versions of the PDAs are presented. Program summary Program title: DPDS – Digital Pulse Detection Software Catalogue identifier: AEHQ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEHQ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 454 070 No. of bytes in distributed program, including test data, etc.: 20 987 104 Distribution format: tar.gz Programming language: C++ (Borland Visual C++) Computer: IBM PC Operating system: MS Windows 2000 and later… RAM: <50 Mbytes, highly depends on settings Classification: 4.12 External routines: Only standard Borland Visual C++ libraries Nature of problem: A very slow pulse detection algorithm, used as standard in LABView, is preventing the ability to process achieved data during the pause between plasma discharges in modern tokamaks. Solution method: Simple yet precise pulse detection algorithms implemented and the whole data processing software translated from LABView into C++. This speeded up the elaboration up to 30 times. Restrictions: Windows system decimal separator must be “.”, not “,”. Additional comments: Processing 300 MB data file should not take longer then 10 minutes. Running time: From 1 minute to 1 hour.

Greenhouse Gas Emissions and Operational Electricity Use in the ICT and Entertainment &amp; Media Sectors

SummaryThe positive and negative environmental impacts of information and communication technology (ICT) are widely debated. This study assesses the electricity use and greenhouse gas (GHG) emissions related to the ICT and entertainment &amp; media (E&amp;M) sectors at sector level, including end users, and thus complements information on the product level. GHGs are studied in a life cycle perspective, but for electricity use, only the operational use is considered. The study also considers which product groups or processes are major contributors. Using available data and extrapolating existing figures to the global scale for 2007 reveals that the ICT sector produced 1.3% of global GHG emissions in 2007 and the E&amp;M sector 1.7%. The corresponding figures for global electricity use were 3.9% and 3.2%, respectively. The results indicate that for the ICT sector, operation leads to more GHG emissions than manufacture, although impacts from the manufacture of some products are significant. For the E&amp;M sector, operation of TVs and production of printed media are the main reasons for overall GHG emissions. TVs as well as printed media, with the estimations made here, led to more GHG emissions on a global level in 2007 than PCs (manufacture and operation). A sector study of this type provides information on a macro scale, a perspective easily lost when considering, for example, the product‐related results of life cycle assessments. The macro scale is essential to capture changes in total consumption and use. However, the potential of the ICT sector to help decrease environmental impacts from other sectors was not included in the assessment.

Code OK3 – An upgraded version of OK2 with beam wobbling function

For computer simulations on heavy ion beam (HIB) irradiation onto a target with an arbitrary shape and structure in heavy ion fusion (HIF), the code OK2 was developed and presented in Computer Physics Communications 161 (2004). Code OK3 is an upgrade of OK2 including an important capability of wobbling beam illumination. The wobbling beam introduces a unique possibility for a smooth mechanism of inertial fusion target implosion, so that sufficient fusion energy is released to construct a fusion reactor in future. New version program summary Program title: OK3 Catalogue identifier: ADST_v3_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADST_v3_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 221 517 No. of bytes in distributed program, including test data, etc.: 2 471 015 Distribution format: tar.gz Programming language: C++ Computer: PC (Pentium 4, 1 GHz or more recommended) Operating system: Windows or UNIX RAM: 2048 MBytes Classification: 19.7 Catalogue identifier of previous version: ADST_v2_0 Journal reference of previous version: Comput. Phys. Comm. 161 (2004) 143 Does the new version supersede the previous version?: Yes Nature of problem: In heavy ion fusion (HIF), ion cancer therapy, material processing, etc., a precise beam energy deposition is essentially important [1]. Codes OK1 and OK2 have been developed to simulate the heavy ion beam energy deposition in three-dimensional arbitrary shaped targets [2, 3]. Wobbling beam illumination is important to smooth the beam energy deposition nonuniformity in HIF, so that a uniform target implosion is realized and a sufficient fusion output energy is released. Solution method: OK3 code works on the base of OK1 and OK2 [2, 3]. The code simulates a multi-beam illumination on a target with arbitrary shape and structure, including beam wobbling function. Reasons for new version: The code OK3 is based on OK2 [3] and uses the same algorithm with some improvements, the most important one is the beam wobbling function. Summary of revisions: 1. In the code OK3, beams are subdivided on many bunches. The displacement of each bunch center from the initial beam direction is calculated. 2. Code OK3 allows the beamlet number to vary from bunch to bunch. That reduces the calculation error especially in case of very complicated mesh structure with big internal holes. 3. The target temperature rises during the time of energy deposition. 4. Some procedures are improved to perform faster. 5. The energy conservation is checked up on each step of calculation process and corrected if necessary. New procedures included in OK3 1. Procedure BeamCenterRot( ) rotates the beam axis around the impinging direction of each beam. 2. Procedure BeamletRot( ) rotates the beamlet axes that belong to each beam. 3. Procedure Rotation( ) sets the coordinates of rotated beams and beamlets in chamber and pellet systems. 4. Procedure BeamletOut( ) calculates the lost energy of ions that have not impinged on the target. 5. Procedure TargetT( ) sets the temperature of the target layer of energy deposition during the irradiation process. 6. Procedure ECL( ) checks up the energy conservation law at each step of the energy deposition process. 7. Procedure ECLt( ) performs the final check up of the energy conservation law at the end of deposition process. Modified procedures in OK3 1. Procedure InitBeam( ): This procedure initializes the beam radius and coefficients A1, A2, A3, A4 and A5 for Gauss distributed beams [2]. It is enlarged in OK3 and can set beams with radii from 1 to 20 mm. 2. Procedure kBunch( ) is modified to allow beamlet number variation from bunch to bunch during the deposition. 3. Procedure ijkSp( ) and procedure Hole( ) are modified to perform faster. 4. Procedure Espl( ) and procedure ChechE( ) are modified to increase the calculation accuracy. 5. Procedure SD( ) calculates the total relative root-mean-square (RMS) deviation and the total relative peak-to-valley (PTV) deviation in energy deposition non-uniformity. This procedure is not included in code OK2 because of its limited applications (for spherical targets only). It is taken from code OK1 and modified to perform with code OK3. Running time: The execution time depends on the pellet mesh number and the number of beams in the simulated illumination as well as on the beam characteristics (beam radius on the pellet surface, beam subdivision, projectile particle energy and so on). In almost all of the practical running tests performed, the typical running time for one beam deposition is about 30 s on a PC with a CPU of Pentium 4, 2.4 GHz.

Physics Operations With the DIII-D Plasma Control System

The DIII-D device began operation in 1986, and a fully digital plasma control system (PCS [J.L. Luxon, Nucl. Fusion 42, 614 (2002).]) was implemented in 1993. Over time, the success of the PCS to exploit the inherent versatility of the DIII-D device led to a philosophy of using the PCS to control all available plasma system actuators. This made the PCS a very powerful physics tool that is at the core of Physics Operations at DIII-D. The complexity of the DIII-D device and all the systems the PCS must control makes proper setup of the PCS for new experiments a daunting task. A cadre of physicists specially trained in PCS operation forms the Physics Operations staff at DIII-D. They are the interface between experimental plans and successful execution and, as such, are a critical component of each experiment. Physics Operations is also a set of tools and procedures. We will briefly examine some of those tools, such as the TokSys control design and modeling environment, and the ‘smart’ PCS setup checklist, that greatly reduces human error in reconfiguring the PCS for a new experiment. We will examine the procedures that allow efficient use of those tools and some of the human factors that can affect productivity.

MCNP Output Data Analysis with ROOT (MODAR)

MCNP Output Data Analysis with ROOT (MODAR) is a tool based on CERN's ROOT software. MODAR has been designed to handle time–energy data issued by MCNP simulations of neutron inspection devices using the associated particle technique. MODAR exploits ROOT's Graphical User Interface and functionalities to visualize and process MCNP simulation results in a fast and user-friendly way. MODAR allows to take into account the detection system time resolution (which is not possible with MCNP) as well as detectors energy response function and counting statistics in a straightforward way. Program summary Program title: MODAR Catalogue identifier: AEGA_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEGA_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 155 373 No. of bytes in distributed program, including test data, etc.: 14 815 461 Distribution format: tar.gz Programming language: C++ Computer: Most Unix workstations and PC Operating system: Most Unix systems, Linux and windows, provided the ROOT package has been installed. Examples where tested under Suse Linux and Windows XP. RAM: Depends on the size of the MCNP output file. The example presented in the article, which involves three two-dimensional 139 × 740 bins histograms, allocates about 60 MB. These data are running under ROOT and include consumption by ROOT itself. Classification: 17.6 External routines: ROOT version 5.24.00 ( http://root.cern.ch/drupal/) Nature of problem: The output of an MCNP simulation is an ASCII file. The data processing is usually performed by copying and pasting the relevant parts of the ASCII file into Microsoft Excel. Such an approach is satisfactory when the quantity of data is small but is not efficient when the size of the simulated data is large, for example when time–energy correlations are studied in detail such as in problems involving the associated particle technique. In addition, since the finite time resolution of the simulated detector cannot be modeled with MCNP, systems in which time–energy correlation is crucial cannot be described in a satisfactory way. Finally, realistic particle energy deposit in detectors is calculated with MCNP in a two-step process involving type-5 then type-8 tallies. In the first step, the photon flux energy spectrum associated to a time region is selected and serves as a source energy distribution for the second step. Thus, several files must be manipulated before getting the result, which can be time consuming if one needs to study several time regions or different detectors performances. In the same way, modeling counting statistics obtained in a limited acquisition time requires several steps and can also be time consuming. Solution method: In order to overcome the previous limitations, the MODAR C++ code has been written to make use of CERN's ROOT data analysis software. MCNP output data are read from the MCNP output file with dedicated routines. Two-dimensional histograms are filled and can be handled efficiently within the ROOT framework. To keep a user friendly analysis tool, all processing and data display can be done by means of ROOT Graphical User Interface. Specific routines have been written to include detectors finite time resolution and energy response function as well as counting statistics in a straightforward way. Additional comments: The possibility of adding tallies has also been incorporated in MODAR in order to describe systems in which the signal from several detectors can be summed. Moreover, MODAR can be adapted to handle other problems involving two-dimensional data. Running time: The CPU time needed to smear a two-dimensional histogram depends on the size of the histogram. In the presented example, the time–energy smearing of one of the 139 × 740 two-dimensional histograms takes 3 minutes with a DELL computer equipped with INTEL Core 2.

Multi-functional vehicle mount antenna system using magnetic coupling for FM/TDMB/PCS applications

A new multi-functional vehicle antenna, consisting of LNA-integrated non-uniform helical antenna for both FM and terrestrial digital multimedia broadcasting (TDMB) operation, and a monopole antenna for the PCS operation is proposed. The proposed architecture combines the three antennas in such a way as to maximum the reuse of the antenna structure and, thereby, reduces the overall antenna size. To realize a single-port excitation of three different band antennas, the PCS antenna and FM antenna is simultaneously excited with the help of steel stud while the TDMB antenna is magnetically coupled from a portion of the FM antenna body.

Study of User Uninterruptibility Estimation based on focused Application-Switching

In this paper, we proposed the user uninterruptibility estimation method based on focused Application-Switching (AS) during PC work for establishing information display timing control scheme with less intelligent activity disturbance for users. At first, we collected and analyzed the PC operation records and the subjective uninterruptibility of users. From the analysis, we selected features in AS timing that affect user uninterruptibility. Then, we provided the estimation method based on co-occurring features that are observed in AS timing, and confirmed the availability of our method.

A new version of Visual tool for estimating the fractal dimension of images

Abstract This work presents a new version of a Visual Basic 6.0 application for estimating the fractal dimension of images (Grossu et al., 2009 [1]). The earlier version was limited to bi-dimensional sets of points, stored in bitmap files. The application was extended for working also with comma separated values files and three-dimensional images. New version program summary Program title: Fractal Analysis v02 Catalogue identifier: AEEG_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEG_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 9999 No. of bytes in distributed program, including test data, etc.: 4 366 783 Distribution format: tar.gz Programming language: MS Visual Basic 6.0 Computer: PC Operating system: MS Windows 98 or later RAM: 30 M Classification: 14 Catalogue identifier of previous version: AEEG_v1_0 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1999 Does the new version supersede the previous version?: Yes Nature of problem: Estimating the fractal dimension of 2D and 3D images. Solution method: Optimized implementation of the box-counting algorithm. Reasons for new version: 1. The previous version was limited to bitmap image files. The new application was extended in order to work with objects stored in comma separated values (csv) files. The main advantages are: a) Easier integration with other applications (csv is a widely used, simple text file format); b) Less resources consumed and improved performance (only the information of interest, the “black points”, are stored); c) Higher resolution (the points coordinates are loaded into Visual Basic double variables [2]); d) Possibility of storing three-dimensional objects (e.g. the 3D Sierpinski gasket). 2. In this version the optimized box-counting algorithm [1] was extended to the three-dimensional case. Summary of revisions: 1. The application interface was changed from SDI (single document interface) to MDI (multi-document interface). 2. One form was added in order to provide a graphical user interface for the new functionalities (fractal analysis of 2D and 3D images stored in csv files). Additional comments: User friendly graphical interface; Easy deployment mechanism. Running time: In the first approximation, the algorithm is linear.

Model-Driven Development for scientific computing. Computations of RHEED intensities for a disordered surface. Part II

Modelling, simulation, and visualisation together create the third branch of human knowledge on equal footing with theory and experiment. Model-Driven Development (MDD) has been proposed as a means to support the software development process through the use of a model-centric approach. The objective of this paper is to address the design of an architecture for scientific application that may execute as multithreaded computations, as well as implementations of the related shared data structures. New version program summary Program title: Growth09 Catalogue identifier: ADVL_v3_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADVL_v3_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 30 940 No. of bytes in distributed program, including test data, etc.: 3 119 488 Distribution format: tar.gz Programming language: Embarcadero Delphi Computer: Intel Core Duo-based PC Operating system: Windows XP, Vista, 7 RAM: more than 1 GB Classification: 4.3, 7.2, 6.2, 8, 14 Catalogue identifier of previous version: ADVL_v2_1 Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1219 Subprograms used: Cat Id Title Reference ADUY_v4_0 RHEED1DProcess CPC 999 (9999) 9999 Does the new version supersede the previous version?: No Nature of problem: Molecular beam epitaxy (MBE) is a technique for epitaxial growth via the interaction of one or several molecular or atomic beams that occurs on a surface of a heated crystalline substrate. Reflection high-energy electron diffraction (RHEED) is an important in situ analysis technique, which is capable of giving quantitative information about the growth process of thin films and its control. The analysis of RHEED intensity oscillations has two purposes. One is to control the film growth, and the other is to understand the mechanism of the film growth using the MBE through the analysis of surface morphology as a function of time. Such control allows the development of structures where the electrons can be confined in space, giving quantum wells or even quantum dots. Such layers are now a critical part of 3 many modern semiconductor devices, semiconductor lasers, light-emitting diodes and new devices for the magnetic storage industry. Solution method: The present paper reports a practical and pragmatic approach for MDD technology [1] that has been used during design of the Growth09 program. Growth09 is a numerical model that uses multithreaded and partially nested transactions for simulation of epitaxial growth of thin films. Reasons for new version: Responding to user feedback the program has been upgraded to a standard that allows a slave process, carrying out computations of the RHEED intensities for a disordered surface, to be run. Also, functionality and documentation of the program have been improved. Summary of revisions: 1. The MDD technology has been used to design a computer model that allows the user to carry out numerical calculations layers coverage during the growth of thin epitaxial films, surface roughness, and the RHEED intensities for a disordered surface. This computer model can be applied to interpret the experimental data in real time [2]. 2. The logical structure of the Platform-Specific Model of the Growth06_v2 program has been modified according to the scheme shown in Fig. 1*. The class diagram in Fig. 1* is a static view of the main platform-specific elements of the Growth09 application architecture. Fig. 2* provides a dynamic view by showing the creation and destruction simplistic sequence diagram. Fig. 3* presents the Growth09 use case model. 3. As can be seen in Figs. 1–3* the Growth09 has been designed as a master program for the slave RHEED1DProcess (see A. Daniluk, Model-Driven Development for scientific computing. Computations of RHEED intensities for a disordered surface. Part I). 4. The slave RHEED1DProcess can be run as separate thread of the Growth09. Fig. 4* depicts the Platform-Specific Model for the development elements of the new distribution. *The figures mentioned can be downloaded, see “Supplementary material” below. Unusual features: The program is distributed in the form of main project Growth09.dproj, with associated files, and should be compiled using Embarcadero RAD Studio 2010 along with Together visual modelling platform. The program should be compiled with English/USA regional and language options. Additional comments: This version of the GROWTH program is designed to run in conjunction with the RHEED1DProcess (ADUY_v4_0) program. It does not replace the previous, stand alone, GROWTH06-v2 (ADVL_v2_1) version. Running time: The typical running time is machine and user-parameters dependent.

Model-Driven Development for scientific computing. Computations of RHEED intensities for a disordered surface. Part I

Scientific computing is the field of study concerned with constructing mathematical models, numerical solution techniques and with using computers to analyse and solve scientific and engineering problems. Model-Driven Development (MDD) has been proposed as a means to support the software development process through the use of a model-centric approach. This paper surveys the core MDD technology that was used to develop an application that allows computation of the RHEED intensities dynamically for a disordered surface.

An electron tomography algorithm for reconstructing 3D morphology using surface tangents of projected scattering interfaces

Upon discerning the mere shape of an imaged object, as portrayed by projected perimeters, the full three-dimensional scattering density may not be of particular interest. In this situation considerable simplifications to the reconstruction problem are possible, allowing calculations based upon geometric principles. Here we describe and provide an algorithm which reconstructs the three-dimensional morphology of specimens from tilt series of images for application to electron tomography. Our algorithm uses a differential approach to infer the intersection of projected tangent lines with surfaces which define boundaries between regions of different scattering densities within and around the perimeters of specimens. Details of the algorithm implementation are given and explained using reconstruction calculations from simulations, which are built into the code. An experimental application of the algorithm to a nano-sized Aluminium tip is also presented to demonstrate practical analysis for a real specimen. Program summary Program title: STOMO version 1.0 Catalogue identifier: AEFS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2988 No. of bytes in distributed program, including test data, etc.: 191 605 Distribution format: tar.gz Programming language: C/C++ Computer: PC Operating system: Windows XP RAM: Depends upon the size of experimental data as input, ranging from 200 Mb to 1.5 Gb Supplementary material: Sample output files, for the test run provided, are available. Classification: 7.4, 14 External routines: Dev-C++ ( http://www.bloodshed.net/devcpp.html) Nature of problem: Electron tomography of specimens for which conventional back projection may fail and/or data for which there is a limited angular range. The algorithm does not solve the tomographic back-projection problem but rather reconstructs the local 3D morphology of surfaces defined by varied scattering densities. Solution method: Reconstruction using differential geometry applied to image analysis computations. Restrictions: The code has only been tested with square images and has been developed for only single-axis tilting. Running time: For high quality reconstruction, 5–15 min

TIERRAS: A package to simulate high energy cosmic ray showers underground, underwater and under-ice

Abstract In this paper we present TIERRAS, a Monte Carlo simulation program based on the well-known AIRES air shower simulations system that enables the propagation of particle cascades underground, providing a tool to study particles arriving underground from a primary cosmic ray on the atmosphere or to initiate cascades directly underground and propagate them, exiting into the atmosphere if necessary. We show several cross-checks of its results against CORSIKA, FLUKA, GEANT and ZHS simulations and we make some considerations regarding its possible use and limitations. The first results of full underground shower simulations are presented, as an example of the package capabilities. Program summary Program title: TIERRAS for AIRES Catalogue identifier: AEFO_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFO_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 36 489 No. of bytes in distributed program, including test data, etc.: 3 261 669 Distribution format: tar.gz Programming language: Fortran 77 and C Computer: PC, Alpha, IBM, HP, Silicon Graphics and Sun workstations Operating system: Linux, DEC Unix, AIX, SunOS, Unix System V RAM: 22 Mb bytes Classification: 1.1 External routines: TIERRAS requires AIRES 2.8.4 to be installed on the system. AIRES 2.8.4 can be downloaded from http://www.fisica.unlp.edu.ar/auger/aires/eg_AiresDownload.html . Nature of problem: Simulation of high and ultra high energy underground particle showers. Solution method: Modification of the AIRES 2.8.4 code to accommodate underground conditions. Restrictions: In AIRES some processes that are not statistically significant on the atmosphere are not simulated. In particular, it does not include muon photonuclear processes. This imposes a limitation on the application of this package to a depth of 1 km of standard rock (or 2.5 km of water equivalent). Neutrinos are not tracked on the simulation, but their energy is taken into account in decays. Running time: A TIERRAS for AIRES run of a 10 20 eV shower with statistical sampling (thinning) below 10 12 eV and 0.2 weight factor (see [1]) uses approximately 1 h of CPU time on an Intel Core 2 Quad Q6600 at 2.4 GHz. It uses only one core, so 4 simultaneous simulations can be run on this computer. Aires includes a spooling system to run several simultaneous jobs of any type.

The two-electron atomic systems. S-states

Abstract A simple Mathematica program for computing the S -state energies and wave functions of two-electron (helium-like) atoms (ions) is presented. The well-known method of projecting the Schrodinger equation onto the finite subspace of basis functions was applied. The basis functions are composed of the exponentials combined with integer powers of the simplest perimetric coordinates. No special subroutines were used, only built-in objects supported by Mathematica. The accuracy of results and computation time depend on the basis size. The precise energy values of 7–8 significant figures along with the corresponding wave functions can be computed on a single processor within a few minutes. The resultant wave functions have a simple analytical form consisting of elementary functions, that enables one to calculate the expectation values of arbitrary physical operators without any difficulties. Program summary Program title: TwoElAtom-S Catalogue identifier: AEFK_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 10 185 No. of bytes in distributed program, including test data, etc.: 495 164 Distribution format: tar.gz Programming language: Mathematica 6.0; 7.0 Computer: Any PC Operating system: Any which supports Mathematica; tested under Microsoft Windows XP and Linux SUSE 11.0 RAM: ⩾ 10 9 bytes Classification: 2.1, 2.2, 2.7, 2.9 Nature of problem: The Schrodinger equation for atoms (ions) with more than one electron has not been solved analytically. Approximate methods must be applied in order to obtain the wave functions or other physical attributes from quantum mechanical calculations. Solution method: The S-wave function is expanded into a triple basis set in three perimetric coordinates. Method of projecting the two-electron Schrodinger equation (for atoms/ions) onto a subspace of the basis functions enables one to obtain the set of homogeneous linear equations F . C = 0 for the coefficients C of the above expansion. The roots of equation det ( F ) = 0 yield the bound energies. Restrictions: First, the too large length of expansion (basis size) takes the too large computation time giving no perceptible improvement in accuracy. Second, the order of polynomial Ω (input parameter) in the wave function expansion enables one to calculate the excited nS -states up to n = Ω + 1 inclusive. Additional comments: The CPC Program Library includes “A program to calculate the eigenfunctions of the random phase approximation for two electron systems” (AAJD). It should be emphasized that this fortran code realizes a very rough approximation describing only the averaged electron density of the two electron systems. It does not characterize the properties of the individual electrons and has a number of input parameters including the Roothaan orbitals. Running time: ∼10 minutes (depends on basis size and computer speed)

A C-code for the double folding interaction potential of two spherical nuclei

We present a C-code designed to obtain the nucleus–nucleus potential by using the double folding model (DFM) and in particular to find the Coulomb barrier. The program calculates the nucleus–nucleus potential as a function of the distance between the centers of mass of colliding nuclei. The most important output parameters are the Coulomb barrier energy and the radius. Since many researchers use a Woods–Saxon profile for the nuclear term of the potential we provide an option in our code for fitting the DFM potential by such a profile. Program summary Program title: DFMSPH Catalogue identifier: AEFH_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEFH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 5929 No. of bytes in distributed program, including test data, etc.: 115 740 Distribution format: tar.gz Programming language: C Computer: PC Operating system: Windows XP (with the GCC-compiler version 2) RAM: Below 10 Mbyte Classification: 17.9 Nature of problem: The code calculates in a semimicroscopic way the bare interaction potential between two colliding spherical nuclei as a function of the center of mass distance. The height and the position of the Coulomb barrier are found. The calculated potential is approximated by a conventional Woods–Saxon profile near the barrier. Dependence of the barrier parameters upon the characteristics of the effective NN forces (like, e.g. the range of the exchange part of the nuclear term) can be investigated. Solution method: The nucleus–nucleus potential is calculated using the double folding model with the Coulomb and the effective M3Y NN interactions. For the direct parts of the Coulomb and the nuclear terms, the Fourier transform method is used. In order to calculate the exchange parts the density matrix expansion method is applied. Running time: Less than 1 minute using a PC with a 1.60 GHz processor.

Digital Games Distribution: The Presence of the Past and the Future of Obsolescence

Digital Games Distribution: The Presence of the Past and the Future of Obsolescence

Numerical investigation on the heat transfer and flow in the mini-fin heat sink for CPU

Fluid flow and heat transfer in the mini-rectangular fin heat sink for CPU of PC using de-ionized water as working fluid are numerically investigated. Based on the real PC operating conditions, the three-dimensional governing equations for fluid flow and heat transfer characteristics are solved using finite volume scheme. The standard k– ε turbulent model is employed to describe the flow structure and behavior. The predicted results obtained from the model are verified by the measured data. There is a reasonable agreement between the predicted results and experiments. The results of this study are expected to lead to guidelines that will allow the design of the cooling system with improved cooling performance of the electronic equipments increasing reliable operation of these devices.

Simulation of electron spin resonance spectroscopy in diverse environments: An integrated approach

We discuss in this work a new software tool, named E-SpiReS (Electron Spin Resonance Simulations), aimed at the interpretation of dynamical properties of molecules in fluids from electron spin resonance (ESR) measurements. The code implements an integrated computational approach (ICA) for the calculation of relevant molecular properties that are needed in order to obtain spectral lines. The protocol encompasses information from atomistic level (quantum mechanical) to coarse grained level (hydrodynamical), and evaluates ESR spectra for rigid or flexible single or multi-labeled paramagnetic molecules in isotropic and ordered phases, based on a numerical solution of a stochastic Liouville equation. E-SpiReS automatically interfaces all the computational methodologies scheduled in the ICA in a way completely transparent for the user, who controls the whole calculation flow via a graphical interface. Parallelized algorithms are employed in order to allow running on calculation clusters, and a web applet Java has been developed with which it is possible to work from any operating system, avoiding the problems of recompilation. E-SpiReS has been used in the study of a number of different systems and two relevant cases are reported to underline the promising applicability of the ICA to complex systems and the importance of similar software tools in handling a laborious protocol. Program summary Program title: E-SpiReS Catalogue identifier: AEEM_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEEM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.0 No. of lines in distributed program, including test data, etc.: 311 761 No. of bytes in distributed program, including test data, etc.: 10 039 531 Distribution format: tar.gz Programming language: C (core programs) and Java (graphical interface) Computer: PC and Macintosh Operating system: Unix and Windows Has the code been vectorized or parallelized?: Yes RAM: 2 048 000 000 Classification: 7.2 External routines: Babel-1.1, CLAPACK, BLAS, CBLAS, SPARSEBLAS, CQUADPACK, LEVMAR Nature of problem: Ab initio simulation of cw-ESR spectra of radicals in solution Solution method: E-SpiReS uses an hydrodynamic approach to calculate the diffusion tensor of the molecule, DFT methodologies to evaluate magnetic tensors and linear algebra techniques to solve numerically the stochastic Liouville equation to obtain an ESR spectrum. Running time: Variable depending on the task. It takes seconds for small molecules in the fast motional regime to hours for big molecules in viscous and/or ordered media.

Wintel Under the Antitrust Microscope: A Comparison of the European Intel Case with the U.S. Microsoft Cases, Updated as of May 12, 2009

European Union has issued a statement of objections, and a supplemental statement of objections, to Intel regarding the company’s conduct aimed at suppressing competition from Intel’s chief rival, AMD. Although the statements of objections remain confidential, the allegations in AMD’s private litigation are public and provide a useful basis for analysis. Intel dominates the PC chip market almost to the same degree that Microsoft dominates the PC operating system market. As in the Microsoft case, Intel’s aggressive marketing tactics prevented OEMs from offering rival products to consumers. And like Microsoft, Intel has engaged in this conduct to maintain its existing monopoly. These parallels between the Microsoft and Intel suggest that Intel’s anticompetitive practices harm consumers, including American consumers, by denying them the access to innovative products at lower prices from rivals. The United States established that Microsoft repeatedly and willfully violated the antitrust laws, but failed to achieve an effective remedy. The EU, however, should have an easier time achieving an effective remedy. First, unlike the OS market, a viable competitor still exists in the chip market, i.e., AMD. Second, Intel has relied primarily on exclusionary rebates, not commingling of intellectual property, to maintain its monopoly. Consequently, the EU should be able to fashion a remedy that does not require Intel to redesign its product.