Fortran Compiler Research Articles

UnDiFi-2D: An unstructured discontinuity fitting code for 2D grids

UnDiFi-2D, an open source (free software) Unstructured-grid, Discontinuity Fitting code, is presented. The aim of UnDiFi-2D is to model gas-dynamic discontinuities in two-dimensional (2D) flows as if they were true discontinuities of null thickness that bound regions of the flow-field where a smooth solution to the governing PDEs exists. UnDiFi-2D therefore needs to be coupled with an unstructured CFD solver that is used to discretize the governing PDEs within the smooth regions of the flow-field. Two different, in-house developed, CFD solvers are also included in the current distribution.The main features of the UnDiFi-2D software can be summarized as follows:Programming languageUnDiFi-2D is written in standard Fortran 77/95; its design is highly modular in order to enhance simplicity of use, maintenance and allow coupling with virtually any existing CFD solver;Usability, maintenance and enhancement In order to improve the usability, maintenance and enhancement of the code also the documentation has been carefully taken into account. The git distributed versioning system has been adopted to facilitate collaborative maintenance and code development;CopyrightsUnDiFi-2D is a free software that anyone can use, copy, distribute, change and improve under the GNU Public License version 3.The present paper is a manifesto of the first public release of the UnDiFi-2D code. It describes the currently implemented features, which are the result of more than a decade of still ongoing CFD developments. This work is focused on the computational techniques adopted and a detailed description of the main characteristics is reported. UnDiFi-2D capabilities are demonstrated by means of examples test cases. The design of the code allows to easily include existing CFD codes and is aimed at ease code reuse and readability. Program summaryProgram title: UnDiFi-2DCPC Library link to program files:https://doi.org/10.17632/5hwssmc2mx.1Licensing provisions: GNU General Public License, version 3Programming language: Fortran; developed and tested with Intel Fortran Compiler v. 18.0.3 and GNU gfortran.External routines: The code depends on several libraries and third-party packages which are detailed in the corpus of the text.Nature of problem: Numerical computation of flows with discontinuities.Solution method: Shock-fitting technique.Additional comments including restrictions and unusual features:•At present, UnDiFi-2D is validated for inviscid steady and unsteady two-dimensional flows without changes in the number of discontinuity lines and interaction points.•UnDiFi-2D implements a shock-fitting algorithm and can be coupled with unstructured cell-vertex solvers, with an Arbitrary Lagrangian-Eulerian (ALE) formulation.•UnDiFi-2D project adopts git [1], a free and open source distributed version control system. A public repository dedicated to UnDiFi-2D project [2] has been created on github [3], a web-based hosting service for software development projects using git versioning system. Finally, a comprehensive documentation is provided in the form of user manual developed in Pandoc [4].

Using finite element analysis to predict the damage in FGM-3D notched plate under tensile load; Different geometric concept

FGM (functionally graded materials) have experienced rapid expansion in recent years in several industrial fields. The analysis of their mechanical behavior by the finite element method requires the use of subroutines established under a FORTRAN compiler given the difficulty in implementing the type of behavior of the materials constituting the FGM. Our work aims to establish a program in MATLAB (UMM) making possible to introduce the behavior of the FGM by element in the mesh model of the structure, hence the advantage and reliability of graded the material in three dimensions for two or even three constituents of FGM and secondly, for different geometric designs. This technique is more sensitive to the mesh, hence the adaptation strategy of a driven mesh in order to improve the precision and the convergence of results under minimal computation time. The constitutive law of our model follows the von Mises equivalent stress flow theory with a hardening variable in incremental form. Moreover, to describe the elastic–plastic behavior of FGM, the model of TTO (Tamura-Tomota-Ozawa) was used for both methods that of UMAT in the form of a numerical algorithm and for our new method in the form of calculated values by the MATLAB code. The parameters used in the two calculation methods are taken from the results of stress–strain tests of the two materials; ceramic (TiB; Titanium mono biorde) and metal (Ti; Titanium). A comparison between the two methods has taken place in the form of load–displacement curves in order to present the capacities of our technique with respect to the usual UMAT technique. However, for damage, the use of the XFEM technique in our UMM method has shown its advantage in the separation of the structure after crack initiation. The crack path as well as its propagation speed under the effect of the volume fraction exponent of the FGM has been highlighted. The two models used in this study (UMM and UMAT) were validated on the one hand with analytics through the TTO model and on the other hand by the experimentation of a tensile test.

Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods

The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170-175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536; Nguyen & Volkov (2019). Acta Cryst. A75, 448-464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524-536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283-4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10-5 kJ mol-1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28-64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.

ARTEMIS: Ab initio restructuring tool enabling the modelling of interface structures

A program, ARTEMIS, has been developed for the study of interface structures. This software allows for the generation of interfaces by identifying lattice matches between two parent crystal structures. To allow for further exploration of the energetic space of the interface, multiple surface terminations parallel to the Miller plane, interface alignments and intermixings are used to generate sets of potential interfaces for each lattice match. These interface structures can then be used in atomic simulations to determine the most energetically favourable interface. The software reported here can help to both drastically reduce the work of generating and exploring interfaces, and aid in understanding of how the interface structure influences the subsequent properties. Using several test cases, we demonstrate how ARTEMIS can both identify the location of an interface in existing structures, and also predict an optimum interface separation based upon the parents’ atomic structures, which aims to accelerate and inform the study of interface science. Program summaryProgram Title: ARTEMISCPC Library link to program files:http://dx.doi.org/10.17632/5bcrh67xty.1Developer’s repository link:http://www.artemis-materials.co.uk/Licensing provisions: CC BY NC 3.0Programming language: Fortran 2003Nature of problem: Construction and identification of the interface between any two crystals. Complicating factors include the choice of Miller planes, alignment of the two crystals and potential intermixing of them.Solution method: This problem is tackled by generating sets of interface structures that allow the user to explore the energy space using atomic simulations in order to identify the most favourable interface to form between two such crystals.Additional comments: The source code and working examples can be found in the compressed file obtainable from http://www.artemis-materials.co.uk/. The code has been tested and developed using the GNU 7.2.0 and the Intel 17.0.4 Fortran compilers on Unix/Linux operating systems.

Tuning the genomic evaluation system of Holstein-Friesian cattle

The aim of this study was to compare the CPU time of two most widely used Fortran compilers – the Absoft and the Intel, in the context of two programs used in the genomic evaluation system of dairy cattle - a program for re-coding of the raw genotyping data of single nucleotide polymorphisms and a program for the estimation of additive genetic effects of single nucleotide polymorphisms. The data set used for the analysis corresponded to the Polish national routine genomic evaluation for non-return rate of heifers and comprised genotypes of 46,267 single nucleotide polymorphisms for each of 2904 evaluated bulls, which resulted in 130,393,459 non-missing genotype records. Programs were compiled under several different compilation options using the Absoft (release 2015) and the Intel (release 2019) compilers. The CPU times of both programmes significantly differed between compilers. In the program for genotype re-coding the Intel compiler always resulted in shorter running times than the Absoft compiler. More variation was observed in CPU times of the program for effect estimation, for which the Absoft compiler resulted in both, the shortest and the longest computing times. A more detailed run-time memory consumption visualisation of single runs of the fastest Absoft and Intel compiled program executions demonstrated that the former compiler allows for the utilisation of more of the available memory, which in the case of a memory intensive program for effect estimation resulted in a faster execution time. In conclusion, an overall performance of the Intel compiler was better than this of the Absoft compiler. Even though significant differences in CPU time were observed, the Intel compiled execution times were less dependent on the pre-imposed compilation parameters. However, it is important to note that for programs performing a large number of arithmetic evaluations it is possible to tune the Absoft compiler to outperform the Intel compiler. The key compilation parameters are those, which allow for lower floating point accuracy and dedicated optimization of mathematical operations. Although blind use of such options is not recommended, in the case of genomic evaluation the math and floating point based optimisations did not affect the convergence of the solver nor the estimates of single nucleotide polymorphisms’ effects.

Multi-pass laser cutting of carbon/Kevlar hybrid composite: Prediction of thermal stress, heat-affected zone, and kerf width by thermo-mechanical modeling

Numerical modeling offers considerable promise to reduce costs associated with trial-and-error process in the manufacturing industry. In laser cutting of fiber-reinforced composites, the developed thermal stress in the cut region has considerable influence on the application of the machined composite and the end product quality. Nevertheless, measurement of the thermal stress is quite challenging in practice. Here, an uncoupled thermo-mechanical finite element model is developed to accurately predict formation of heat-affected zone, kerf width, thermal field, and thermal residual stress of an anisotropic carbon/Kevlar fiber reinforced composite during multi-pass laser cutting process. A novel approach of element deletion incorporating temperature-dependent Hashin failure criteria and VUMAT subroutine is proposed. The study is carried out using Abaqus interlinked with Fortran compiler to define laser Gaussian beam (DFLUX subroutine) and material removal (VUMAT subroutine) for determining the temperature gradient and cut characteristics, respectively. The numerical results agree well with the experimental scanning electron micrographs of heat-affected zone and kerf width. In addition, residual temperature after subsequent pass results in greater temperature distribution and heat accumulation. It has also been established that the strength of composite gradually decays with the increase of temperature due to stiffness (elastic moduli) degradation in the area of the cutting zone, accelerating damage initiation in both fibers and matrix.

OpenMP 4.5 compiler optimization for GPU offloading

Ability to efficiently offload computational workloads to graphic processing units (GPUs) is critical for the success of hybrid CPU–GPU architectures, such as the Summit and Sierra supercomputing systems. OpenMP 4.5 is a high-level programming model that enables the development of architecture- and accelerator-independent applications. This article describes aspects of the OpenMP implementation in the IBM XL C/C++ and XL Fortran OpenMP compilers that aid programmers to achieve performance objectives. This includes an interprocedural static analysis the XL optimizer uses to specialize code generation of the OpenMP <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">distribute parallel do</i> loop within the dynamic context of a target region, and other compiler optimizations designed to reduce the overhead of data transferred to an offloaded target region. We introduce the heuristic used at runtime to select optimal grid sizes for offloaded target team constructs. These tuned heuristics lead to an average improvement of 2× in the runtime of several target regions in the SPEC ACCEL V1.2 benchmark suite. In addition to performance enhancement, this article also presents an advanced diagnostic feature implemented in the XL Fortran compiler to aid in debugging OpenMP applications offloaded to accelerators.

The diagnostic capability of the Cray, gfortran, Intel, Nag and Oracle Fortran compilers

This version has been updated with details of the Intel 19.1 release and the Nag 7.0 release.

Modification of building energy simulation tool TRNSYS for modelling nonlinear heat and moisture transfer phenomena by TRNSYS/MATLAB integration

Software for numerical simulation of various types of energy used in buildings, i.e. building energy simulation (BES), have become an essential tool for recent research pertaining to building physics. TRNSYS is a well-known BES used in both academia and the construction industry for a wide range of simulations, such as the design and performance evaluation of buildings and related facilities for heating, cooling, and ventilation. TRNSYS has a modular structure comprising various components, and each component is interconnected and compiled through a common interface using a FORTRAN compiler. Its modular structure enables interactions with various external numerical simulation tools, such as MATLAB, Python, and ESP-r. For ordinary simulations of building energy load using TRNSYS, the generic module Type 56 is usually recommended, which provides detailed physics modelling of building thermal behaviours based on unsteady energy conservation equations and Fourier’s law for each building material. However, Type 56 explicitly depends on the transfer function method to discretise the original differential equations; therefore, it cannot model nonlinear phenomena, such as latent heat and moisture transfer between a building surface and ambient air. In other words, the current TRNSYS cannot be used to estimate the effectiveness of evaporation during cooling, which is a typical passive design method. Hence, the authors developed a MATLAB/TRNSYS integration scheme, in which TRNSYS was modified to model simultaneous heat and moisture transfer from the wet roof surface of a building. This scheme enabled TRNSYS to calculate the rate of evaporative heat and moisture transfer dynamically from the roof surface, assuming a control volume approximation of the roof surface. Finally, the effect of evaporative cooling on the thermal performance of an Indian building was estimated using the modified model.

The diagnostic capability of the Cray, gfortran, Intel, Nag and Oracle Fortran compilers

We use several compilers for the development of the examples in our books. The following table summarises the compilers we have used:

GenASiSBasics: Object-oriented utilitarian functionality for large-scale physics simulations (Version 3)

GenASiS Basics provides Fortran 2003 classes furnishing extensible object-oriented utilitarian functionality for large-scale physics simulations on distributed memory supercomputers. This functionality includes physical units and constants; display to the screen or standard output device; message passing; I/O to disk; and runtime parameter management and usage statistics. This revision---Version 3 of Basics---includes a significant name change, some minor additions to functionality, and a major addition to functionality: infrastructure facilitating the offloading of computational kernels to devices such as GPUs.

SPICE, ADVICE, Celerity, and a Case of Beer: Working With a Man of Patience and Understanding

The author s arrived at Bell Labs in 1986 and 1987, about 10 years after Larry Nagel did. During that time, Larry had recreated his Ph.D. thesis-based SPICE circuit simulator at ATaT in a new circuit simulator called ADVICE, fixing many things that he thought were broken or outdated in SPICE and with a much more interactive feel. It is rumored that the high quality of the f77 Fortran compiler written by Stu Feldman owes much to Larry frequently breaking it daily with his ADVICE code. Larry then moved on to another position, and a group was formed to maintain and enhance ADVICE, which by then was the workhorse tool for all circuit design work within ATaT.

Evaluation of mass transfer correlations applying to cryogenic distillation process with non-equilibrium model

Reliable heat and mass transfer model plays a significant role on design and calculation of the distillation process. Since the cryogenic fluids of oxygen, nitrogen and argon have obviously different thermal physical properties compared to the room temperature ones, it is of great necessity to evaluate the feasibility of the existing heat and mass transfer models in the cryogenic distillation calculation. In this study, a non-equilibrium model (NEM) based on the FORTRAN compiler is implemented to investigate the actual cryogenic distillation process in a structured packing column (SPC) of the air separation unit (ASU) with capacity of 17,000 Nm3/h. The complete conservation equations for materials, mass and energy in the phases are numerically solved based on the Thomas algorithm. The commonly used mass transfer coefficient models with different diffusion coefficients, as well as the heat transfer model, are evaluated in the performance prediction of the cryogenic SPC. The multiple imports and exports of the model are validated by the limited available measurements, while the calculated distributions of the component molar fraction, temperature, pressure and flow rates along the column are compared with those from the Rate-based module of Aspen plus simulation. The comparisons verify the solving strategy and help to understand the reliability of the existing basic transfer correlations for future cryogenic distillation calculation.

EKHARA 3.0: An update of the EKHARA Monte Carlo event generator

The Monte Carlo event generator EKHARA was upgraded during last years. The upgrades presented here contain: (a) the inclusion of new final states e+e−→e+e−η, e+e−→e+e−η′, e+e−→e+e−χci and e+e−→e+e−χci(→J∕ψ(→μ+μ−)γ); b) new γ∗−γ∗−P transition form factors and c) the radiative corrections to the reactions e+e−→e+e−P. For the upgrades (a) and (b), we present here only the pieces missing in other publications, mostly algorithms used in the phase space generation. The radiative corrections are presented here for the first time. A new algorithm of the phase space generation for the reaction e+e−→e+e−Pγ being its main part. A comparison with GGRESRC generator is presented. Big differences between the radiative corrections calculated by the EKHARA and the GGRESRC generators are observed. New version program summaryProgram Title: EKHARA 3.0Program Files doi:http://dx.doi.org/10.17632/g5nmv83g5z.1Licensing provisions: GPLv3Programming language: FORTRAN 77Supplementary material: The following publications are relevant for the upgrades presented in Section 2: [3,4,5,6]Journal reference of previous version: H. Czyż, S. Ivashyn, Comput. Phys. Commun. 182 (2011) 1338.Does the new version supersede the previous version?: YesReasons for the new version: Major upgrades.Summary of revisions: The upgrades contain the inclusion of the new final states e+e−→e+e−η, e+e−→e+e−η′, e+e−→e+e−χci and e+e−→e+e−χci(→J∕ψ(→μ+μ−)γ), new γ∗−γ∗−P transition form factors and the radiative corrections to the reactions e+e−→e+e−P.Nature of problem: The program is constructed to help in measurements of transition form factors at meson factories. To do this one needs a good description of the already existing data and calculation of the radiative corrections.Solution method: The models of various form factors were developed in [3,4,5,6] and are implemented in the program. For the radiative corrections a new algorithm of generation of the phase space for the reactions e+e−→e+e−Pγ was developed and is presented here.Additional comments including Restrictions and Unusual features: The program needs a quadruple precision version of a FORTRAN compiler.

Open source Matrix Product States: Opening ways to simulate entangled many-body quantum systems in one dimension

Numerical simulations are a powerful tool to study quantum systems beyond exactly solvable systems lacking an analytic expression. For one-dimensional entangled quantum systems, tensor network methods, amongst them Matrix Product States (MPSs), have attracted interest from different fields of quantum physics ranging from solid state systems to quantum simulators and quantum computing. Our open source MPS code provides the community with a toolset to analyze the statics and dynamics of one-dimensional quantum systems. Here, we present our open source library, Open Source Matrix Product States (OSMPS), of MPS methods implemented in Python and Fortran2003. The library includes tools for ground state calculation and excited states via the variational ansatz. We also support ground states for infinite systems with translational invariance. Dynamics are simulated with different algorithms, including three algorithms with support for long-range interactions. Convenient features include built-in support for fermionic systems and number conservation with rotational U(1) and discrete Z2 symmetries for finite systems, as well as data parallelism with MPI. We explain the principles and techniques used in this library along with examples of how to efficiently use the general interfaces to analyze the Ising and Bose–Hubbard models. This description includes the preparation of simulations as well as dispatching and post-processing of them. Program summaryProgram title: Open Source Matrix Product States (OSMPS), v2.0Program Files doi:http://dx.doi.org/10.17632/vxm2mcmk4v.1Licensing provisions: GNU GPL v3Programming language: Python, Fortran2003, MPI for parallel computingCompilers (Fortran): gfortran, ifort, g95Dependencies: The minimal requirements in addition to the Fortran compiler are BLAS, LAPACK, ARPACK, python, numpy, scipy. Additional packages for plotting include matplotlib, dvipng, and LATEX packages. The Expokit package, available at the homepage http://www.maths.uq.edu.au/expokit/, is required to use the Local Runge–Kutta time evolution.Supplementary material: We provide programs to reproduce selected figures in the Appendices.Nature of problem: Solving the ground state and dynamics of a many-body entangled quantum system is a challenging problem; the Hilbert space grows exponentially with system size. Complete diagonalization of the Hilbert space to floating point precision is limited to less than forty qubits.Solution method: Matrix Product States in one spatial dimension overcome the exponentially growing Hilbert space by truncating the least important parts of it. The error can be well controlled. Local neighboring sites are variationally optimized in order to minimize the energy of the complete system. We can target the ground state and low lying excited states. Moreover, we offer various methods to solve the time evolution following the many-body Schrödinger equation. These methods include e.g. theSuzuki–Trotter decompositions using local propagators or the Krylov method, both approximating the propagator on the complete Hilbert space.

Simulating a Potential Step Using Shareware

Simulation of a potential step experiment of an electrochemical system in an infinite solution using explicit method [1] was done. Listing of program in Fortran was compiled using shareware program FORCE 2.0 FORTRAN compiler and editor [2]. Plot of potential step experiment for Z/Zc vs. X for L/n from above mentioned listing is shown. Simulations done by transliterating Fortran [3] into Turbo Pascal will also be discussed. Symbols are as per [3]. [1] W. Breen and J. Cassidy, Simulation of dynamic electrochemical processes, Curr. Top. Electrochem., 9 (2003) p. 47 [2]www.igpp.ucla.edu/public/rwalker/ess261_2007_spring/Force/Force%20Fortran%20Compiler%20and%20Editor.htm [3]A. J. Bard and L. R. Faulkner, Electrochemical Methods: Fundamentals and Applications, 2nd Edition, Wiley (2001) p. 793 Figure 1

OpenMP GNU and Intel Fortran programs for solving the time-dependent Gross–Pitaevskii equation

We present Open Multi-Processing (OpenMP) version of Fortran 90 programs for solving the Gross-Pitaevskii (GP) equation for a Bose-Einstein condensate in one, two, and three spatial dimensions, optimized for use with GNU and Intel compilers. We use the split-step Crank-Nicolson algorithm for imaginary- and real-time propagation, which enables efficient calculation of stationary and non-stationary solutions, respectively. The present OpenMP programs are designed for computers with multi-core processors and optimized for compiling with both commercially-licensed Intel Fortran and popular free open-source GNU Fortran compiler. The programs are easy to use and are elaborated with helpful comments for the users. All input parameters are listed at the beginning of each program. Different output files provide physical quantities such as energy, chemical potential, root-mean-square sizes, densities, etc. We also present speedup test results for new versions of the programs.

Technical note: PaGELL v.1.5: A flexible parametric program for the Bayesian analysis of longevity data within the context of animal breeding

This technical note presents the program PaGELL v.1.5 (Parametric Genetic Evaluation of Lifespan in Livestock), a flexible software program to analyze (right-censored) longevity data in livestock populations, with a special emphasis on the genetic evaluation of the breeding stock. This software relies on a parametric generalization of the proportional hazard model; more specifically, the baseline hazard function follows a Weibull process and flexibility is gained by including an additional time-dependent effect with the number of change points defined by the user. The program can accommodate 3 different sources of variation (i.e., systematic, permanent environmental, and additive genetic effects) and both fixed and time-dependent patterns (only for systematic and permanent environmental effects). Analyses are performed within a Bayesian context by sampling from the joint posterior distribution of the model, and model fit can be easily determined by the calculation of the deviance information criterion. Although this software has already been used on field data sets, its performance has been double-checked on simulated data set, and results are presented in this technical note. PaGELL v.1.5 was written in Fortran 95 language and, after compiling with the GNU Fortran Compiler v.4.7 and later, it has been tested in Windows, Linux, and MacOS operating systems (both 32- and 64-bit platforms). This program is available at http://www.casellas.info/files/pageII.zip.

CYP2B6 Genotype Guided Dosing of Propofol Anesthesia in the Elderly Based on Nonparametric Population Pharmacokinetic Modeling and Simulations

The primary aim of this article is to test the hypothesis that nonparametric pharmacometric modeling will accurately identify CYP2B6 genotype subgroups based on data from a study that reported results based on parametric pharmacokinetics (PK). Propofol concentration-time data were originally reported in the Kansaku et al. 2011 publication. Nonparametric Nonlinear Mixed Effects Modeling (NLME) was conducted using the PMETRICS R package while population pharmacokinetic model parameters were estimated using a FORTRAN compiler. Finally, model-based dosing simulations were conducted in the MATLAB Simbiology. A total of 51 patients were included in the final PK analysis. A two-compartment gamma multiplicative error model adequately described the propofol concentration-time data. The precision of the goodness-of-fit plots resulted in an R2 of 0.927 and an R2 of 0.992 for the population prediction and individual predictions, respectively. Neither the UGT1A9 nor the CYP2B6 G516T gene variants resulted in statistically significant PK parameter differences while the CYP2B6 A785G gene variants resulted in statistically significant differences for the elimination rate. Model-based dosing-simulations comparing patients with the CYP2B6 AA & AG genotypes to both GG genotypes and patients from a multicenter trial suggest a 50% decrease in propofol infusion dose, to 25mg/kg/min, be made to result in approximately equivalent drug exposures. Based on the pharmacometric modeling and simulation, if no dosage adjustments are made for the elderly CYP2B6 AA and AG genotypes, a 250% higher propofol blood exposure will be evident within 1-hour from the start of the infusion. Thus, based on the pharmacokinetic model, genotyping elderly patients for the CYP2B6 AA and AG gene variants will decrease the total propofol blood exposure during anesthesia and sedation when an infusion dose adjustment is made to 25mg/kg/min.

In Search of the Original Fortran Compiler

In Search of the Original Fortran Compiler Paul McJones (bio) In April 2002, Grady Booch sent out an email with the subject “Preserving classic software products.” His appeal to provide top 10 lists and to suggest where to look for the source code received an enthusiastic response. Grady and the Computer History Museum organized a workshop in October 2003.1 As a result, a month later, a group of Computer History Museum trustees, staff and volunteers (including me) established the Software Collection Committee2 (SCC) to explore the software side of the museum’s mission: “To preserve and present for posterity the artifacts and stories of the information age.” I decided to take on the project of collecting Fortran materials. John Backus’s Fortran project at IBM developed one of the first higher-level programming languages as well as a set of techniques for code optimization that allowed Fortran to compete with hand-tuned assembly language.3 The combination of ease-of-use and efficiency led to Fortran’s rapid adoption and lasting impact on programming language design and implementation. Fortran’s success on the IBM 704/709 led to Fortran compilers for many brands and models of computers, making it possible to port Fortran programs among different computers; Fortran program portability also made Fortran useful for non-numerical projects. While Fortran’s popularity waned as other languages grew up to fill various niches, some high-performance computing users continued to use Fortran, with periodic updates, to the present. The history of the Fortran project is well documented in papers by Backus and others, covering the project, its impact, and technical analysis of the compiler itself.4 However, the artifact itself—the source code for the original Fortran compiler—seemed to me an appropriate starting point to gain experience with collecting, preserving, and presenting historic software. By spring 2006, I had assembled a collection including listings, source and executable code, documentation, and more and had made the collection publicly accessible via a website. Take a look at that website now (http://www.softwarepreservation.org/projects/FORTRAN/)5 to have it mind as you read this article, which describes my collection efforts. I hope my experience will be useful to other computing history researchers from the practitioner world considering similar efforts. Getting Started I started my search for Fortran by calling John Backus, with whom I had worked in the mid-1970s (on functional programming) but had not seen for about 25 years. He did not have a copy of the source code and directed me to Irv Ziller, who had been his first hire on the project. Irv responded to my request, saying that he didn’t have the source code, but he recalled material being sent to the Smithsonian to become part of their collection. I visited the website of the Smithsonian National Museum of American History (NMAH) and located the group that had created the Computer History Collection,6 but my initial attempts to establish communication with the staff were unsuccessful.7 One day I was chatting with a coworker, Jim King, who had worked at IBM Research for many years. Jim had used Fortran II and the Fortran Monitor System on an IBM 709 in college in the early 1960s and had some interesting anecdotes.8 Jim suggested IBM’s SHARE user group library as a potentially interesting source of material, and he also recalled the extensive IBM 7094-related library at Boeing when he worked there in the 1960s. Another member of the SCC, Dick Sites, recalled having seen “handwritten Fortran I documentation in a basement of the Sloan building at MIT in 1965 .… As I remember, it described the overall compiler design and optimizing algorithms. I remember a fairly neat but slightly small handwriting with hand-drawn boxes and arrows for some of the algorithms.” Also, Len Shustek, Computer History Museum founder, pointed out this sentence in Backus’s article9 about Fortran at the first History of Programming Languages conference: “Shortly after the distribution of the system, we distributed—one copy per installation—what was fondly known as the ‘Tome,’ the complete symbolic listing of the entire compiler plus other system and diagnostic information...