Fortran Compiler Research Articles

A C++11 implementation of arbitrary-rank tensors for high-performance computing

This article discusses an efficient implementation of tensors of arbitrary rank by using some of the idioms introduced by the recently published C++ ISO Standard (C++11). With the aims at providing a basic building block for high-performance computing, a single Array class template is carefully crafted, from which vectors, matrices, and even higher-order tensors can be created. An expression template facility is also built around the array class template to provide convenient mathematical syntax. As a result, by using templates, an extra high-level layer is added to the C++ language when dealing with algebraic objects and their operations, without compromising performance. The implementation is tested running on both CPU and GPU. New version program summaryProgram title: cpp-arrayCatalogue identifier: AESA_v1_1Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESA_v1_1.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU Lesser General Public License, version 3No. of lines in distributed program, including test data, etc.: 12376No. of bytes in distributed program, including test data, etc.: 81669Distribution format: tar.gzProgramming language: C++.Computer: All modern architectures.Operating system: Linux/Unix/Mac OS.RAM: Problem dependentClassification: 5.External routines: GNU CMake build system and BLAS implementation. NVIDIA CUBLAS for GPU computing.Does the new version supersede the previous version?: YesCatalogue identifier of previous version: AESA_v1_0Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 1681Nature of problem:Tensors are a basic building block for any program in scientific computing. Yet, tensors are not a built-in component of the C++ programming language.Solution method:An arbitrary-rank tensor class template is crafted by using the new features introduced by the C++11 set of requirements. In addition, an entire expression template facility is built on top, to provide mathematical straightforward notation without damaging performance.Reasons for new version:The reason for this version is to make the library more portable.Summary of revisions:The first version of the library relied on the presence of a C interface to the BLAS library (CBLAS). This new version gives priority to a Fortran BLAS implementation when a Fortran compiler is provided during the configuration process. Some minor changes have also been made, including an improved Doxygen documentation, fixed installation when using CUDA, and fixed other minor bugs.Running time:Problem dependent. The tests provided take only seconds. The examples take approximately 15 min.

FDCHQHP: A Fortran package for heavy quarkonium hadroproduction

FDCHQHP is a Fortran package to calculate the transverse momentum (pt) distribution of yield and polarization for heavy quarkonium hadroproduction at next-to-leading-order (NLO) based on non-relativistic QCD(NRQCD) framework. It contains the complete color-singlet and color-octet intermediate states in present theoretical level, and is available to calculate different polarization parameters in different frames. As the LHC running now and in the future, it supplies a very useful tool to obtain theoretical prediction on the heavy quarkonium hadroproduction. Program summaryProgram title: FDCHQHP v1.0Catalogue identifier: AETT_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AETT_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 12020165No. of bytes in distributed program, including test data, etc.: 103178384Distribution format: tar.gzProgramming language: Fortran 77.Computer: Any computer with Linux operating system, Intel Fortran Compiler and MPI library.Operating system: Linux.Has the code been vectorized or parallelized?: Parallelized with MPI.Classification: 11.1.External routines: MPI LibraryNature of problem:This package is for the calculation of the heavy quarkonium hadroproduction at NRQCD NLO.Solution method:The Fortran codes of this package are generated by the FDC system [1] automatically.Additional comments:It is better to run the package on supercomputers or multi-core computers.!!!!! The distribution file for this program is over 100 MB and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. !!!!!Running time:For an independent sub-process, it may take several seconds to several hours depending on the number of sample points if one CPU core is used. For a complete prompt production of heavy quarkonium hadroproduction (ψ(Ns) or Y(Ns)) at one pt point, it may take an hour to thousands of hours depending on the number of sample points if one CPU core is used. In our test with less sample points, it takes 16 min to compile and 25 min to run the whole program with 4 processes with the CPU Intel®Core. I7-3770k @ 3.5 GHz × 8.

The TDHF code Sky3D

The nuclear mean-field model based on Skyrme forces or related density functionals has found widespread application to the description of nuclear ground states, collective vibrational excitations, and heavy-ion collisions. The code Sky3D solves the static or dynamic equations on a three-dimensional Cartesian mesh with isolated or periodic boundary conditions and no further symmetry assumptions. Pairing can be included in the BCS approximation for the static case. The code is implemented with a view to allow easy modifications for including additional physics or special analysis of the results. Program summaryProgram title: Sky3DCatalogue identifier: AESW_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESW_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 43187No. of bytes in distributed program, including test data, etc.: 1423973Distribution format: tar.gzProgramming language: Fortran 90. The OpenMP version requires a relatively recent compiler; it was found to work using gfortran 4.6.2 or later and the Intel compiler version 12 or later.Computer: All computers with a Fortran compiler supporting at least Fortran 90.Operating system: All operating systems with such a compiler. Some of the Makefiles and scripts depend on a Unix-like system and need modification under Windows.Has the code been vectorized or parallelized?: Yes, Runs under OpenMP and MPI, unlimited number of processors can be used.RAM: 1 GBClassification: 17.16, 17.22, 17.23.External routines: LAPACK, FFTW3Nature of problem:The time-dependent Hartree–Fock equations can be used to simulate nuclear vibrations and collisions between nuclei for low energies. This code implements the equations based on a Skyrme energy functional and also allows the determination of the ground-state structure of nuclei through the static version of the equations. For the case of vibrations the principal aim is to calculate the excitation spectra by Fourier-analyzing the time dependence of suitable observables. In collisions, the formation of a neck between nuclei, the dissipation of energy from collective motion, processes like charge transfer and the approach to fusion are of principal interest.Solution method:The nucleonic wave function spinors are represented on a three-dimensional Cartesian mesh with no further symmetry restrictions. The boundary conditions are always periodic for the wave functions, while the Coulomb potential can also be calculated for an isolated charge distribution. All spatial derivatives are evaluated using the finite Fourier transform method. The code solves the static Hartree–Fock equations with a damped gradient iteration method and the time-dependent Hartree–Fock equations with an expansion of the time-development operator. Any number of initial nuclei can be placed into the mesh in with arbitrary positions and initial velocities.Restrictions:The reliability of the mean-field approximation is limited by the absence of hard nucleon–nucleon collisions. This limits the scope of applications to collision energies about a few MeV per nucleon above the Coulomb barrier and to relatively short interaction times. Similarly, some of the missing time-odd terms in the implementation of the Skyrme interaction may restrict the applications to even–even nuclei.Unusual features:The possibility of periodic boundary conditions and the highly flexible initialization make the code also suitable for astrophysical nuclear-matter applications.Running time:The running time depends strongly on the size of the grid, the number of nucleons, and the duration of the collision. For a single-processor PC-type computer it can vary between a few minutes and weeks.

OFF, Open source Finite volume Fluid dynamics code: A free, high-order solver based on parallel, modular, object-oriented Fortran API

OFF, an open source (free software) code for performing fluid dynamics simulations, is presented. The aim of OFF is to solve, numerically, the unsteady (and steady) compressible Navier–Stokes equations of fluid dynamics by means of finite volume techniques: the research background is mainly focused on high-order (WENO) schemes for multi-fluids, multi-phase flows over complex geometries. To this purpose a highly modular, object-oriented application program interface (API) has been developed. In particular, the concepts of data encapsulation and inheritance available within Fortran language (from standard 2003) have been stressed in order to represent each fluid dynamics “entity” (e.g. the conservative variables of a finite volume, its geometry, etc…) by a single object so that a large variety of computational libraries can be easily (and efficiently) developed upon these objects. The main features of OFF can be summarized as follows:Programming LanguageOFF is written in standard (compliant) Fortran 2003; its design is highly modular in order to enhance simplicity of use and maintenance without compromising the efficiency;Parallel Frameworks Supported the development of OFF has been also targeted to maximize the computational efficiency: the code is designed to run on shared-memory multi-cores workstations and distributed-memory clusters of shared-memory nodes (supercomputers); the code’s parallelization is based on Open Multiprocessing (OpenMP) and Message Passing Interface (MPI) paradigms;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 documentation is built upon comprehensive comments placed directly into the source files (no external documentation files needed): these comments are parsed by means of doxygen free software producing high quality html and latex documentation pages; the distributed versioning system referred as git has been adopted in order to facilitate the collaborative maintenance and improvement of the code;CopyrightsOFF is a free software that anyone can use, copy, distribute, study, change and improve under the GNU Public License version 3.The present paper is a manifesto of OFF code and presents the currently implemented features and ongoing developments. This work is focused on the computational techniques adopted and a detailed description of the main API characteristics is reported. OFF capabilities are demonstrated by means of one and two dimensional examples and a three dimensional real application. Program summaryProgram title:OFFCatalogue identifier: AESV_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AESV_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public Licence, version 3No. of lines in distributed program, including test data, etc.: 60466No. of bytes in distributed program, including test data, etc.: 595575Distribution format: tar.gzProgramming language: Fortran (standard 2003 or newer); developed and tested with Intel Fortran Compiler v. 12.x or newer.Computer: Designed for shared-memory multi-cores workstations and for hybrid distributed/shared-memory supercomputers, but any computer system with a Fortran (2003+) compiler is suited.Operating system: Designed for POSIX architecture and tested on GNU/Linux one.Has the code been vectorized or parallelized?: Hybrid parallelization by means of MPI library and OpenMP paradigm, tested on up to 256 processors.RAM: [1 MB; 1 GB] x core, simulation-dependentClassification: 4.3, 4.10, 12.External routines: The proprietary library [1] must be linked for producing binary outputs in Tecplot Inc. format; the MPI library [2] must be linked for running on distribute-memory parallel systemsNature of problem:Numerical solution of the Compressible Navier–Stokes equations for multi-fluids multi-phase flows in complex geometriesSolution method:Fully-conservative Finite Volume scheme based on very high-order WENO Positivity-Preserving reconstruction technique and Strong Stability Preserving high-order Runge–Kutta time integration. Structured multi-block general curvilinear and body-fitted grids constitute the underlining numerical grids. MPI and OpenMP paradigms are used for parallel computations. Pre-processing tool to deal with commercial meshing softwares is provided as well as post-processing one for numerical results visualizationRestrictions:At present, OFF is validated for simulating inviscid and single-phase flows (viscous fluxes computation and fully coupled Eulerian /Lagrangian schemes have still to be validated, but they are already implemented); modern Fortran compiler is mandatoryUnusual features:OFF is a complex CFD software strongly based on Object-Oriented Programming paradigm by means of modern Fortran standard (2003 or higher)Additional comments:OFF project adopts Git [3], a free and open source distributed version control system. A public repository dedicated to OFF project [4] has been created on github, a web-based hosting service for software development projects using git versioning system. Finally, a comprehensive documentation [5] is provided parsing source code comments by means of doxygen software [6]Running time:The running time depends on the available computation resources, the complexity of the problem and the selected accuracy of the numerical scheme. Simple one dimensional problems require few minutes on personal workstation-like systems whereas complex three dimensional problems needing high accuracy (e.g. DNS) could require weeks on supercomputers. OFF has proven to have a good scalability on small clusters (e.g. CASPUR facilities, namely on Matrix, a GNU/Linux cluster composed by 320 nodes each one constituted by a dual Opteron quadcore at 2.1GHz with 16/32 GB of RAM)

Carlomat, version 2 of the program for automatic computation of lowest order cross sections

Version 2 of carlomat, a program for automatic computation of the lowest order cross sections of multiparticle reactions, is described. The substantial modifications with respect to version 1 of the program include: generation of a single phase space parameterization for the Feynman diagrams of the same topology, an interface to parton density functions, improvement of the color matrix computation, the Cabibbo–Kobayashi–Maskawa mixing in the quark sector, the effective models including scalar electrodynamics, the Wtb interaction with operators of dimension up to 5 and a general top–Higgs coupling. Moreover, some minor modifications have been made and several bugs in the program have been corrected. Program summaryProgram title: carlomat, version 2.0Catalogue identifier: AEDQ_v2_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDQ_v2_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 49058No. of bytes in distributed program, including test data, etc.: 25748755Distribution format: tar.gzProgramming language: Fortran 90/95Computer: AllOperating system: LinuxClassification: 4.4, 11.2Catalogue identifier of previous version: AEDQ_v1_0Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 1671Does the new version supersede the previous version?: YesNature of problem:Leading order predictions for reactions of two particle scattering into a final state with up to 10 particles within the Standard Model and some effective models.Solution method:As in version 1 of the program, the matrix element in the helicity basis and multichannel Monte Carlo phase space integration routine are generated automatically for a user specified process. The color matrix is divided into smaller routines and written down as a stand alone program that is calculated prior to compilation and execution of the Monte Carlo program for computation of the cross section. The phase space integration routine is substantially shortened in order to speed up its compilation. The code generation part of the program is modified to incorporate the scalar electrodynamics and effective Lagrangians of the top quark interactions with the W and Higgs bosons. Routines necessary for computing the helicity amplitudes of new couplings are added.Reasons for new version:The main reasons for the revision are: 1.To adjust the program for the description of hadron collisions.2.To facilitate computation of the color matrix that is usually much more involved for processes of the hadron–hadron collision than for processes of electron–positron annihilation.3.To shorten compilation time of the generated kinematical routines.4.To implement some extensions of the standard model in the program.Summary of revisions:A few substantial modifications are introduced with respect to version 1.0 of the program. First, a single phase space parameterization is generated for the Feynman diagrams of the same topology taking into account possible differences in mappings of peaks in the individual diagrams, which speeds up a compilation time of the Monte Carlo program for multiparticle reactions by a factor 4–5 with respect to the previous version. Second, an interface to parton density functions is added that allows predictions to be made for hadron collisions. Third, calculation of the color matrix is facilitated. Fourth, the Cabibbo–Kobayashi–Maskawa mixing in the quark sector is implemented. Fifth, the effective models including scalar electrodynamics, the Wtb interaction with operators of dimension up to 5 and a general top–Higgs coupling are implemented. Moreover, some minor modifications have been made and several bugs in the program have been corrected.Restrictions:Although the compilation time has been shortened in the current version, it still may be quite long for processes with 8 or more final state particles. Another limitation is the size of the color matrix that, if too big, may prevent compilation or result in a very long execution time of the color compilation program. This actually may happen already for some QCD processes with 7 partons such as gg→5g, the commutation time of the color matrix of which, is about 200 h.Running time:Depends strongly on the selected process and, to a lesser extent, on the Fortran compiler used. The following amounts of time are needed at different computation stages of the top quark pair production parton level process gg→bud̄b̄μ−ν̄μ, to produce the appended test output files on a PC with the Pentium 4 3.0 GHz processor with Absoft (GNU, Intel) Fortran compilers: code generation takes 3.7 s (3.7 s, 2.4 s), compilation, computation and simplification of the color matrix takes about 1 s (1 s, 1 s), compilation of all the generated routines takes just a few seconds and execution of the Monte Carlo program takes about 44 s (41 s, 23 s).

BEEC: An event generator for simulating the [formula omitted] meson production at an [formula omitted] collider

The Bc meson is a doubly heavy quark–antiquark bound state and carries flavors explicitly, which provides a fruitful laboratory for testing potential models and understanding the weak decay mechanisms for heavy flavors. In view of the prospects in Bc physics at the hadronic colliders such as Tevatron and LHC, Bc physics is attracting more and more attention. It has been shown that a high luminosity e+e− collider running around the Z0-peak is also helpful for studying the properties of Bc meson and has its own advantages. For this purpose, we write down an event generator for simulating Bc meson production through e+e− annihilation according to relevant publications. We name it BEEC, in which the color-singlet S-wave and P-wave (cb̄)-quarkonium states together with the color-octet S-wave (cb̄)-quarkonium states can be generated. BEEC can also be adopted to generate the similar charmonium and bottomonium states via the semi-exclusive channels e++e−→|(QQ̄)[n]〉+Q+Q̄ with Q=b and c respectively. To increase the simulation efficiency, we simplify the amplitude as compact as possible by using the improved trace technology. BEEC is a Fortran program written in a PYTHIA-compatible format and is written in a modular structure, one may apply it to various situations or experimental environments conveniently by using the GNU C compiler make. A method to improve the efficiency of generating unweighted events within PYTHIA environment is proposed. Moreover, BEEC will generate a standard Les Houches Event data file that contains useful information of the meson and its accompanying partons, which can be conveniently imported into PYTHIA to do further hadronization and decay simulation. Program summaryProgram title: BEECCatalogue identifier: AEQC_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQC_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 114868No. of bytes in distributed program, including test data, etc.: 963939Distribution format: tar.gzProgramming language: FORTRAN 77/90.Computer: Any computer with Fortran compiler, the program is tested with GNU Fortran compiler and Intel Fortran compiler.Operating system: UNIX, Linux and Windows.RAM: About 2.0 MB.Classification: 11.2.Nature of problem:Production of charmonium, (cb̄)-quarkonium and bottomonium via e+e− annihilation channel around the Z0 peak.Solution method:The production of heavy (QQ̄′)-quarkonium (Q,Q′=b,c) via e+e− annihilation are estimated by using the improved trace technology. The (QQ̄′)-quarkonium in color-singlet 1S-wave state, 1P-wave state, and the color-octet 1S-wave states have been studied within the framework of non-relativistic QCD. The code with option can generate weighted and unweighted events conveniently, in particular, the unweighted events are generated by using an improved hit-and-miss approach so as to improve the generating efficiency.Restrictions:The generator is aimed at the production of double heavy quarkonium through e+e− annihilation at the Z0 peak. The considered processes are those that are associated with two heavy quark jets, which could provide sizable quarkonium events around the Z0 peak.Running time:It depends on which option one chooses to match PYTHIA when generating the heavy quarkonium events. Typically, for the production of the S-wave quarkonium states, if setting IDPP=2 (unweighted events), then it takes about 2 h on a 2.9 GHz AMD Athlon (tm) II×4 635 Processor machine to generate 105 events; if setting IDPP=3 (weighted events), it takes only ∼16 min to generate 105 events. For the production of the P-wave quarkonium states, the time will be almost one hundred times longer than the case of the S-wave quarkonium.

Population pharmacokinetics of valnemulin in swine

This study was carried out in 121 pigs to develop a population pharmacokinetic (PPK) model by oral (p.o.) administration of valnemulin at a single dose of 10 mg/kg. Serum biochemistry parameters of each pig were determined prior to drug administration. Three to five blood samples were collected at random time points, but uniformly distributed in the absorption, distribution, and elimination phases of drug disposition. Plasma concentrations of valnemulin were determined by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The concentration-time data were fitted to PPK models using nonlinear mixed effect modeling (NONMEM) with G77 FORTRAN compiler. NONMEM runs were executed using Wings for NONMEM. Fixed effects of weight, age, sex as well as biochemistry parameters, which may influence the PK of valnemulin, were investigated. The drug concentration-time data were adequately described by a one-compartmental model with first-order absorption. A random effect model of valnemulin revealed a pattern of log-normal distribution, and it satisfactorily characterized the observed interindividual variability. The distribution of random residual errors, however, suggested an additive model for the initial phase (<12 h) followed by a combined model that consists of both proportional and additive features (≥ 12 h), so that the intra-individual variability could be sufficiently characterized. Covariate analysis indicated that body weight had a conspicuous effect on valnemulin clearance (CL/F). The featured population PK values of Ka , V/F and CL/F were 0.292/h, 63.0 L and 41.3 L/h, respectively.

Porting marine ecosystem model spin-up using transport matrices to GPUs

Abstract. We have ported an implementation of the spin-up for marine ecosystem models based on transport matrices to graphics processing units (GPUs). The original implementation was designed for distributed-memory architectures and uses the Portable, Extensible Toolkit for Scientific Computation (PETSc) library that is based on the Message Passing Interface (MPI) standard. The spin-up computes a steady seasonal cycle of ecosystem tracers with climatological ocean circulation data as forcing. Since the transport is linear with respect to the tracers, the resulting operator is represented by matrices. Each iteration of the spin-up involves two matrix-vector multiplications and the evaluation of the used biogeochemical model. The original code was written in C and Fortran. On the GPU, we use the Compute Unified Device Architecture (CUDA) standard, a customized version of PETSc and a commercial CUDA Fortran compiler. We describe the extensions to PETSc and the modifications of the original C and Fortran codes that had to be done. Here we make use of freely available libraries for the GPU. We analyze the computational effort of the main parts of the spin-up for two exemplar ecosystem models and compare the overall computational time to those necessary on different CPUs. The results show that a consumer GPU can compete with a significant number of cluster CPUs without further code optimization.

"Wat For Ever:" Student-Oriented Computing at the University of Waterloo

In 1965, four undergraduates at the University of Waterloo wrote Watfor, a fast student-oriented Fortran compiler for the school's IBM 7040, largely because the available Fortran compiler was slow and offered weak diagnostic and debugging tools. This article describes the birth and evolution of the Watfor family and explores how it fits into the University of Waterloo's unique-within-Canada cooperative education program and pedagogical philosophy.

From the Editor's Desk

This issue features two important aspects of history of computing: computers in education and microcircuitry. Specifically, the issue includes features on the development of Watfor, a fast student-oriented Fortran compiler, at the University of Waterloo; a history of time-shared microcomputers in the early 1980s; a history of educational computers in Australia; Geoffrey W.A. Dummer's semiconductor innovation at the British Royal Radar Establishment in the 1950s; and Jay W. Lathrop's description of developing the photolithographic approach to microcircuits at the US Army Diamond Ordnance Fuze Laboratory.

Logical inference techniques for loop parallelization

This paper presents a fully automatic approach to loop parallelization that integrates the use of static and run-time analysis and thus overcomes many known difficulties such as nonlinear and indirect array indexing and complex control flow. Our hybrid analysis framework validates the parallelization transformation by verifying the independence of the loop's memory references. To this end it represents array references using the USR (uniform set representation) language and expresses the independence condition as an equation, S =0, where S is a set expression representing array indexes. Using a language instead of an array-abstraction representation for S results in a smaller number of conservative approximations but exhibits a potentially-high runtime cost. To alleviate this cost we introduce a language translation F from the USR set-expression language to an equally rich language of predicates ( F ( S ) ==&gt; S = 0). Loop parallelization is then validated using a novel logic inference algorithm that factorizes the obtained complex predicates (F( S )) into a sequence of sufficient independence conditions that are evaluated first statically and, when needed, dynamically, in increasing order of their estimated complexities. We evaluate our automated solution on 26 benchmarks from PERFECT-Club and SPEC suites and show that our approach is effective in parallelizing large, complex loops and obtains much better full program speedups than the Intel and IBM Fortran compilers.

Fortran code for SU(3) lattice gauge theory with and without MPI checkerboard parallelization

We document plain Fortran and Fortran MPI checkerboard code for Markov chain Monte Carlo simulations of pure SU(3) lattice gauge theory with the Wilson action in D dimensions. The Fortran code uses periodic boundary conditions and is suitable for pedagogical purposes and small scale simulations. For the Fortran MPI code two geometries are covered: the usual torus with periodic boundary conditions and the double-layered torus as defined in the paper. Parallel computing is performed on checkerboards of sublattices, which partition the full lattice in one, two, and so on, up to D directions (depending on the parameters set). For updating, the Cabibbo–Marinari heatbath algorithm is used. We present validations and test runs of the code. Performance is reported for a number of currently used Fortran compilers and, when applicable, MPI versions. For the parallelized code, performance is studied as a function of the number of processors.Program summaryProgram title: STMC2LSU3MPICatalogue identifier: AEMJ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMJ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 26666No. of bytes in distributed program, including test data, etc.: 233126Distribution format: tar.gzProgramming language: Fortran 77 compatible with the use of Fortran 90/95 compilers, in part with MPI extensions.Computer: Any capable of compiling and executing Fortran 77 or Fortran 90/95, when needed with MPI extensions.Operating system:1.Red Hat Enterprise Linux Server 6.1 with OpenMPI + pgf77 11.8-0,2.Centos 5.3 with OpenMPI + gfortran 4.1.2,3.Cray XT4 with MPICH2 + pgf90 11.2-0.Has the code been vectorised or parallelized?: Yes, parallelized using MPI extensions. Number of processors used: 2 to 11664RAM: 200 Mega bytes per process.Classification: 11.5.Nature of problem:Physics of pure SU(3) Quantum Field Theory (QFT). This is relevant for our understanding of Quantum Chromodynamics (QCD). It includes the glueball spectrum, topological properties and the deconfining phase transition of pure SU(3) QFT. For instance, Relativistic Heavy Ion Collision (RHIC) experiments at the Brookhaven National Laboratory provide evidence that quarks confined in hadrons undergo at high enough temperature and pressure a transition into a Quark-Gluon Plasma (QGP). Investigations of its thermodynamics in pure SU(3) QFT are of interest.Solution method:Markov Chain Monte Carlo (MCMC) simulations of SU(3) Lattice Gauge Theory (LGT) with the Wilson action. This is a regularization of pure SU(3) QFT on a hypercubic lattice, which allows approaching the continuum SU(3) QFT by means of Finite Size Scaling (FSS) studies. Specifically, we provide updating routines for the Cabibbo-Marinari heatbath with and without checkerboard parallelization. While the first is suitable for pedagogical purposes and small scale projects, the latter allows for efficient parallel processing. Targetting the geometry of RHIC experiments, we have implemented a Double-Layered Torus (DLT) lattice geometry, which has previously not been used in LGT MCMC simulations and enables inside and outside layers at distinct temperatures, the lower-temperature layer acting as the outside boundary for the higher-temperature layer, where the deconfinement transition goes on.Restrictions: The checkerboard partition of the lattice makes the development of measurement programs more tedious than is the case for an unpartitioned lattice. Presently, only one measurement routine for Polyakov loops is provided.Unusual features:We provide three different versions for the send/receive function of the MPI library, which work for different operating system +compiler +MPI combinations. This involves activating the correct row in the last three rows of our latmpi.par parameter file. The underlying reason is distinct buffer conventions.Running time:For a typical run using an Intel i7 processor, it takes (1.8-6) E-06 seconds to update one link of the lattice, depending on the compiler used. For example, if we do a simulation on a small (4 * 83) DLT lattice with a statistics of 221 sweeps (i.e., update the two lattice layers of 4 * (4 * 83) links each 221 times), the total CPU time needed can be2 * 4 * (4 * 83) * 221 * 3 E-06 seconds = 1.7 minutes,where2— two layers of lattice4— four dimensions83 * 4— lattice size221— sweeps of updating6 E-06 s— average time to update one link variable. If we divide the job into 8 parallel processes, then the real time is (for negligible communication overhead) 1.7 mins / 8 = 0.2 mins.

Methodology to evaluate the performance of simulation models for alternative compiler and operating system configurations

Simulation modelers increasingly require greater flexibility for model implementation on diverse operating systems, and they demand high computational speed for efficient iterative simulations. Additionally, model users may differ in preference for proprietary versus open-source software environments. These issues necessitate the development of strategies to maximize model compatibility across operating systems, to ensure numerically accurate simulations for alternative compiler selections, and to understand how these choices affect computational speed. We developed an approach to evaluate model performance using diverse Fortran compilers on multiple computer operating systems. A single desktop computer with five identical hard drives was designed to permit meaningful comparisons between five operating systems while minimizing differences in hardware configuration. Three Fortran compilers and relevant software development tools were installed on each operating system. Both proprietary and open-source versions of compilers and operating systems were used. Compatibility and performance issues among compiler and operating system combinations were assessed for an example case: the Cropping System Model (CSM) as implemented in version 4.5 of the Decision Support System for Agrotechnology Transfer (DSSAT). A simulation study that included 773 simulations and assessed the full suite of crop growth modules within DSSAT-CSM was conducted for each compiler and operating system configuration. For a given simulation, results were identical for anthesis date (ADAT), maturity date (MDAT), and maximum leaf area index (LAIX) regardless of the compiler or operating system used. Over 94% of the simulations were identical for canopy weight at maturity (CWAM) and cumulative evapotranspiration at maturity (ETCM). Differences in CWAM were predominantly less than 2 kg ha −1 and were likely the result of differences in floating point handling among compilers. Larger CWAM discrepancies highlighted areas for improvement of the model code. Model implementations with the Intel Fortran compiler on the Linux Ubuntu operating system provided the fastest simulations, which averaged 9.0 simulations s −1. Evaluating simulation models for alternative compiler and operating system configurations is invaluable for understanding model performance constraints and for improving model robustness, portability, usefulness, and flexibility.

An improved algorithm and a Fortran 90 module for computing the conical function [formula omitted

In this paper we describe an algorithm and a Fortran 90 module ( Conical) for the computation of the conical function P − 1 2 + i τ m ( x ) for x > − 1 , m ⩾ 0 , τ > 0 . These functions appear in the solution of Dirichlet problems for domains bounded by cones; because of this, they are involved in a large number of applications in engineering and physics. In the Fortran 90 module, the admissible parameter ranges for computing the conical functions in standard IEEE double precision arithmetic are restricted to ( x , m , τ ) ∈ ( − 1 , 1 ) × [ 0 , 40 ] × [ 0 , 100 ] and ( x , m , τ ) ∈ ( 1 , 100 ) × [ 0 , 100 ] × [ 0 , 100 ] . Based on tests of the three-term recurrence relation satisfied by these functions and direct comparison with Maple, we claim a relative accuracy close to 10 − 12 in the full parameter range, although a mild loss of accuracy can be found at some points of the oscillatory region of the conical functions. The relative accuracy increases to 10 − 13 – 10 − 14 in the region of the monotonic regime of the functions where integral representations are computed ( − 1 < x < 0 ). Program summary Program title: Conical Catalogue identifier: AELD_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AELD_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.: 5387 No. of bytes in distributed program, including test data, etc.: 49 615 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any supporting a FORTRAN compiler Operating system: Any supporting a FORTRAN compiler RAM: A few MB Classification: 4.7 Nature of problem: Conical functions appear in a large number of applications because these functions are the natural function basis for solving Dirichlet problems bounded by conical domains. Also, they are the Kernel of the Mehler–Fock transform. Solution method: The algorithm uses different methods of computation depending on the range of parameters: asymptotic expansions, quadrature methods and recurrence relations. Restrictions: In order to avoid underflow/overflow problems, the admissible parameter ranges for computing the conical functions in standard IEEE double precision arithmetic are restricted to ( x , m , τ ) ∈ ( − 1 , 1 ) × [ 0 , 40 ] × [ 0 , 100 ] and ( x , m , τ ) ∈ ( 1 , 100 ) × [ 0 , 100 ] × [ 0 , 100 ] . Additional comments: The module Conical uses a Fortran 90 version of the routine dkia (developed by the authors) for computing the modified Bessel functions K i a ( x ) and its derivative. This routine is included in the distribution file and is also available at http://toms.calgo.org. Running time: Depending on the parameter range: when numerical quadrature is used (for x < 0 ), the algorithm is 10–20 times slower than the computations made using asymptotic expansions + recurrence relations.

Flat-Dosing Versus BSA-Based Dosing for MLN9708, An Investigational Proteasome Inhibitor: Population Pharmacokinetic (PK) Analysis of Pooled Data From 4 Phase-1 Studies

Abstract 1433 Background:Investigational agent MLN9708 is a potent, reversible and specific 20S proteasome inhibitor. Both intravenous (IV) and oral administration are being studied on a twice-weekly (Days 1, 4, 8, and 11; 21-day cycles) and weekly (Days 1, 8, and 15; 28-day cycles) schedule. The twice-weekly doses studied are 0.125–2.34 mg/m2 for IV and 0.24–2.23 mg/m2 for oral dosing. Weekly doses tested are 0.125–1.4 mg/m2 for IV and 0.24–3.95 mg/m2 for oral dosing. MLN9708 completely hydrolyzes to the pharmacologically active MLN2238 in aqueous solutions. Here we report a population PK analysis of pts with solid tumors, lymphoma or multiple myeloma (MM) enrolled in 4 ongoing phase 1 studies of IV and oral dosing on a twice-weekly (Days 1, 4, 8, 11; 21-day cycle) and weekly (Days 1, 8, 15; 28-day cycle) schedule. Methods:MLN9708 dose was based on body surface area (BSA) for both twice-weekly and weekly dosing schedules in solid tumor, lymphoma and MM patients (N=85). MLN2238 concentration-time data were analyzed using a non-linear mixed effects modeling approach (NONMEM® VII), with Intel® Visual Fortran Compiler, and the output was processed with SPLUS v8.1. Compartmental PK models were coded using the ADVAN 12 subroutine of NONMEM. A log-transform both sides approach was used. Estimation was by the First Order Conditional Estimation (FOCE) method with eta-epsilon interaction. Covariates tested included body weight, BSA, age, sex, dose and albumin on both clearance (CL) and volume, while creatinine clearance (CrCl), bilirubin, AST and ALT were only tested on CL parameters. Model validation and robustness were assessed using bootstrap simulations (N=1000) and visual predictive checks (N=100). Results:Mean age of 85 pts was 60.7 years, mean body weight was 80.0 kg, 87% of pts were Caucasian, and 58% were male. MLN9708 population PK was described by a three-compartment model with first order elimination. All model parameters were estimated with adequate precision when IV and oral data were fitted together. Of all the covariates tested, only body size descriptors (body weight and BSA) were found to be a significant covariate only on peripheral volume of distribution, V3 (p<0.01). Since BSA was more significant than body weight it was kept in the final model. Mean [%CV] CL (1.86 [7.0] L/h) and central volume of distribution (V2, 11.7 [13.1] L) were not affected by body weight or BSA. Inter-individual variability (IIV) was approximately 45% for CL, 82% for V2 and 30% for peripheral volume of distribution, with 17% of IIV in V3 explained by BSA. Absolute bioavailability (F) was estimated to be 62% based on this analysis. Based on simulations using the final population PK model, there was no difference in concentration-time profile or exposures (AUC or Cmax) between the BSA-based and the flat doses. Conclusions:Population PK analysis showed that the plasma concentration-time profile of MLN2238 can be well described by a three-compartment model with first order elimination process. Body size did not significantly impact AUC or Cmax, supporting a switch from BSA-based dosing to flat dosing in all ongoing and planned clinical studies. Ability to use a flat dosing paradigm may be a benefit for oral administration of MLN9708 due to its potential to simplify clinical management. Disclosures:Gupta:Millennium Pharmaceuticals, Inc.: Employment. Off Label Use: Investigational agent in clinical development for the treatment of solid tumors, lymphoma and MM. Saleh:Millennium Pharmaceuticals, Inc.: Student internship. Venkatakrishnan:Millennium Pharmaceuticals, Inc.: Employment.

A Fortran 90 Hartree–Fock program for one-dimensional periodic π-conjugated systems using Pariser–Parr–Pople model

Pariser–Parr–Pople (P-P-P) model Hamiltonian is employed frequently to study the electronic structure and optical properties of π-conjugated systems. In this paper we describe a Fortran 90 computer program which uses the P-P-P model Hamiltonian to solve the Hartree–Fock (HF) equation for infinitely long, one-dimensional, periodic, π-electron systems. The code is capable of computing the band structure, as also the linear optical absorption spectrum, by using the tight-binding and the HF methods. Furthermore, using our program the user can solve the HF equation in the presence of a finite external electric field, thereby, allowing the simulation of gated systems. We apply our code to compute various properties of polymers such as trans-polyacetylene, poly- para-phenylene, and armchair and zigzag graphene nanoribbons, in the infinite length limit. Program summary Program title: ppp_bulk.x Catalogue identifier: AEKW_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKW_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.: 87 464 No. of bytes in distributed program, including test data, etc.: 2 046 933 Distribution format: tar.gz Programming language: Fortran 90 Computer: PCs and workstations Operating system: Linux, Code was developed and tested on various recent versions of 64-bit Fedora including Fedora 14 (kernel version 2.6.35.12-90). Classification: 7.3 External routines: This program needs to link with LAPACK/BLAS libraries compiled with the same compiler as the program. For the Intel Fortran Compiler we used the ACML library version 4.4.0, while for the gfortran compiler we used the libraries supplied with the Fedora distribution. Nature of problem: The electronic structure of one-dimensional periodic π-conjugated systems is an intense area of research at present because of the tremendous interest in the physics of conjugated polymers and graphene nanoribbons. The computer program described in this paper provides an efficient way of solving the Hartree–Fock equations for such systems within the P-P-P model. In addition to the Bloch orbitals, band structure, and the density of states, the program can also compute quantities such as the linear absorption spectrum, and the electro-absorption spectrum of these systems. Solution method: For a one-dimensional periodic π-conjugated system lying in the xy-plane, the single-particle Bloch orbitals are expressed as linear combinations of p z -orbitals of individual atoms. Then using various parameters defining the P-P-P Hamiltonian, the Hartree–Fock equations are set up as a matrix eigenvalue problem in the k-space. Thereby, its solutions are obtained in a self-consistent manner, using the iterative diagonalizing technique at several k points. The band structure and the corresponding Bloch orbitals thus obtained are used to perform a variety of calculations such as the density of states, linear optical absorption spectrum, electro-absorption spectrum, etc. Running time: Most of the examples provided take only a few seconds to run. For a large system, however, depending on the system size, the run time may be a few minutes to a few hours.

Process simulation of formation and emission of NO and N2O during coal decoupling combustion in a circulating fluidized bed combustor using Aspen Plus

A process simulation model of coal decoupling combustion in a 30kW circulating fluidized bed (CFB) combustor has been developed for predicting NO and N2O emissions based on the built-in modules/blocks provided by Aspen Plus software as well as the external subroutines from FORTRAN compiler. The gas–solid hydrodynamics in the decoupling CFB combustor and macro-chemical reaction kinetics of coal combustion have been included in the process simulation model of CFB coal decoupling combustion. The profiles of average bed temperature and concentrations of gas components along the CFB riser height can be successfully predicted by the developed process simulation model. The effects of excess air percentage, first stage stoichiometry, and the introduction position of secondary air on concentrations of the emitted gaseous components, especially concentrations of NO and N2O can be simulated by the developed process simulation model. The contribution ratios of all relevant combustion reactions to emissions of NO and N2O can be quantitatively predicted. A good agreement between the simulated and measured results can be obtained during CFB coal decoupling combustion process under a large variation range of the CFB operation conditions.

Recent Advances and Future Prospects for Monte Carlo

The history of Monte Carlo methods is closely linked to that of computers: The first known Monte Carlo program was written in 1947 for the ENIAC; a pre-release of the first Fortran compiler was used for Monte Carlo In 1957; Monte Carlo codes were adapted to vector computers in the 1980s, clusters and parallel computers in the 1990s, and teraflop systems in the 2000s. Recent advances include hierarchical parallelism, combining threaded calculations on multicore processors with message-passing among different nodes. With the advances In computmg, Monte Carlo codes have evolved with new capabilities and new ways of use. Production codes such as MCNP, MVP, MONK, TRIPOLI and SCALE are now 20-30 years old (or more) and are very rich in advanced featUres. The former 'method of last resort' has now become the first choice for many applications. Calculations are now routinely performed on office computers, not just on supercomputers. Current research and development efforts are investigating the use of Monte Carlo methods on FPGAs. GPUs, and many-core processors. Other far-reaching research is exploring ways to adapt Monte Carlo methods to future exaflop systems that may have 1M or more concurrent computational processes.

An algebraic formulation and implementation of the tetrahedron linear method for the Brillouin zone integration of spectral functions

A package of FORTRAN subroutines is provided for the Brillouin zone (BZ) integration of the Greenʼs functions (GF) and spectral functions. The relevant weighting factors at sampling points in the BZ are evaluated to high precision with the help of the formulas for both the real and imaginary parts. The analytical properties of implemented expressions are discussed, and their range of validity is determined. The limiting cases when values at the tetrahedron corners coincide are worked out in terms of the finite difference quotients and replaced by the derivatives. The present numerical algorithms are developed for one-, two- and three-dimensional simplexes, with the potential ability of handling simplexes with higher dimensions as well. As an example, the results of computation the simple cubic lattice GFʼs are presented. Program summary Program title: SimTet Catalogue identifier: AEKF_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKF_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.: 3176 No. of bytes in distributed program, including test data, etc.: 19 416 Distribution format: tar.gz Programming language: Fortran Computer: Any computer with a Fortran compiler Operating system: Unix, Linux, Windows RAM: 512 Mbytes Classification: 4.11, 7.3 Nature of problem: The integration of the Greenʼs function over the Brillouin zone appears in the computations of many physical quantities in solid-state physics. Solution method: The integral over the Brillouin zone is computed with the tetrahedron linear method. The complex weights are generated with the novel algebraic formulas free of apparent singularities and well suited for automatic computations. Running time: A few μsec per integral.

New Climate Diagnostic Method of Activity of Typhoons over the Northwestern Pacific Ocean

A new conception, called the Most Direct Impact Area (MDIA) of typhoons, is put forward in this paper. After the computational method is explained in detail, the databank of 1955 typhoons of China Meteorological Administration (CMA) have been calculated on the Linux operational platform with a Fortran compiler in a computer. The results via calculating the geographic distribution of the MDIA of typhoons show that the characteristic of typhoon activity in a year can be easily identified in quantity. A most interesting feature has been found that typhoon activity is abnormally active over the ocean to the south of Japan in three typical El Niño years.