Subject: NA Digest, V. 14, # 24 NA Digest Monday, July 21, 2014 Volume 14 : Issue 24 Today's Editor: Daniel M. Dunlavy Sandia National Labs [log in to unmask] Today's Topics: ulmBLAS: A Tutorial for High-Performance GEMM New Book, A Math Primer for Engineers New Book, Lectures on Stochastic Programming, 2nd Edition IMA Struct Preserving Discret of PDE & FEM Circus, USA, Oct 2014 Numerical Analysis of PDEs, Chile, Jan 2015 eXtended Discretization MethodS X-DMS, Italy, Sep 2015 Call for preliminary bids for ISMP, August 2018 Canada Research Chair Position, Sci Comp & NA Research Fellow Position, Mathematics, Univ of Sussex Postdoc Position, Numerics of PDEs, Univ of Vienna: new deadline PhD Fellowship Position: Pharmacometrics & Comp Disease Modeling PhD Position, Comp Model of Polycrystalline Fracture, UK Contents, ACM Transactions on Math Software (TOMS), 40 (4) Subscribe, unsubscribe, change address, or for na-digest archives: http://www.netlib.org/na-digest-html/faq.html Submissions for NA Digest: http://icl.cs.utk.edu/na-digest/ ------------------------------------------------------- From: Michael Lehn [log in to unmask] Date: July 14, 2014 Subject: ulmBLAS: A Tutorial for High-Performance GEMM This semester I gave an undergraduate lecture "Software Basics on High Performance Computing". Crucial for the performance of numerical libraries like LAPACK is the efficient implementation of the Matrix-Matrix Produkt (GEMM). The GEMM function is part of the BLAS layer and efficient implementations are provided through libraries like OpenBLAS, BLIS, ATLAS or Intel's MKL. For understanding how these libraries can achieve such an extreme performance we closely followed the paper "BLIS: A Framework for Rapidly Instantiating BLAS Functionality" by Field G. van Zee and Robert A. van deE Geijn (University of Texas at Austin). For getting a hands-on experience the students were guided through a sequence of assignments that led to their own GEMM implementation. The assignments where supplemented by a small framework (ulmBLAS) that e.g. contains the Netlib BLAS test suite and ATLAS benchmark suite. I compiled the GEMM part of the lecture in a 13 step tutorial on https://apfel.mathematik.uni-ulm.de/~lehn/sghpc/gemm/index.html The tutorial starts with a plain ANSI C implementation of GEMM. This variant implements in less than 450 lines of code the matrix-matrix product as described in the above paper. Unlike in a naive implementation the performance does not drop when matrix sizes exceed cache sizes. On the subsequent pages the tutorial shows step by step how optimizing only 10 lines in the micro-kernel finally leads to a GEMM implementation that is on par with the Intel MKL. Note that the micro kernel we end up is basically the BLIS micro kernel for the x86-64 SSE architecture. I hope others can benefit from the material. ------------------------------------------------------- From: Colin W Cryer [log in to unmask] Date: July 15, 2014 Subject: New Book, A Math Primer for Engineers The purpose of this Math Primer is to provide a brief introduction to those parts of mathematics which are, or could be, useful in engineering, especially bioengineering. The aim is to summarize the ideas covered in each subject area without going into exhaustive detail. Formulas and equations have not been avoided, but every effort has been made to keep them simple in the hope of persuading readers that they are not only useful but also accessible. The wide range of topics covered includes introductory material such as numbers and sequences, geometry in two and three dimensions, linear algebra, and the calculus. Building on these foundations, linear spaces, Sobolev spaces,tensor analysis and Fourier analysis are introduced. All these concepts are used to first formulate problems for ordinary and partial differential equations and then solve such problems, either analytically or numerically. Illustrative applications are taken from a variety of engineering disciplines. and the choice of a suitable model is considered from the point of view of both the mathematician and the engineer. After a brief introduction to Optimization the book concludes with short chapters on Modelling, Computer Software, and Mathematical Proofs. Throughout the book, examples and remarks are used to illustrate the theory and provide background historical information, in the hope that this will improve the mutual understanding between mathematicians and engineers. Publisher: IOS Press, Amsterdam 2014 495+xv pages ISBN 978-1-61499-298-1(print) ISBN 978-1-61499-299-8(online) ------------------------------------------------------- From: Bruce Bailey [log in to unmask] Date: July 16, 2014 Subject: New Book, Lectures on Stochastic Programming, 2nd Edition Announcing the July 8, 2014, publication by SIAM of: Lectures on Stochastic Programming: Modeling and Theory, Second Edition, by Alexander Shapiro, Darinka Dentcheva, and Andrzej Ruszczyński 2014 / xviii + 494 pages / Hardcover / 978-1-611973-42-6 / List Price $125.00 / SIAM/MOS Member Price $87.50 / Order Code MO16 In this second edition, the authors introduce new material to reflect recent developments in stochastic programming, including: an analytical description of the tangent and normal cones of chance constrained sets; analysis of optimality conditions applied to nonconvex problems; a discussion of the stochastic dual dynamic programming method; an extended discussion of law invariant coherent risk measures and their Kusuoka representations; and in-depth analysis of dynamic risk measures and concepts of time consistency, including several new results. It is intended for researchers working on theory and applications of optimization. It also is suitable as a text for advanced graduate courses in optimization. To order or for more about this book, including links to its table of contents, preface, and index, please visit http://bookstore.siam.org/mo16/. ------------------------------------------------------- From: Fadil Santosa [log in to unmask] Date: July 14, 2014 Subject: IMA Struct Preserving Discret of PDE & FEM Circus, USA, Oct 2014 IMA Workshop on Structure Preserving Discretizations of PDEs, Oct 22-24, 2014 The Institute for Mathematics and its Applications (IMA) is holding a workshop focusing on numerical methods for partial differential equations that are based on the approach of structure preserving discretizations. These approaches include finite element exterior calculus and mimetic finite differences. The goal of this workshop is to communicate recent developments in the area and the important role topology and geometry play in numerical analysis. This workshop will also be an occasion to celebrate the 60th birthday of Douglas N. Arnold, whose work has made profound contributions to the field of numerical analysis of PDEs. More details about the workshop, including a list of speakers and application form is available at http://www.ima.umn.edu/2014-2015/SW10.22-24.14 A meeting of the Finite Element Circus, devoted to the theory and applications of the finite element method and related areas of numerical analysis and PDEs, will immediately follow the IMA Special Workshop, taking place on October 24-25, 2014, at the same location. Registration taken at http://www.ima.umn.edu/2014-2015/SW10.24-25.14 ------------------------------------------------------- From: Gabriel Gatica [log in to unmask] Date: July 15, 2014 Subject: Numerical Analysis of PDEs, Chile, Jan 2015 It is our pleasure to announce the Workshop LA SERENA NUMERICA II (the Eighth Meeting on Numerical Analysis of Partial Differential Equations) which will take place at the Universidad de La Serena, La Serena, Chile, during the days January 14 - 16, 2015. Invited speakers are: Johnny Guzman, Norbert Heuer, Pep Mulet, Ricardo Ruiz-Baier, Kai Schneider, and Martin Vohralik. Detailed information can be found on the website http://www.ci2ma.udec.cl/lsn2/ Deadline for studentships application, registration and submission of abstracts is September 30, October 31 and November 14, respectively. We are happy to invite you to participate in the workshop. Please note that there is a limit on the number of presentations. ------------------------------------------------------- From: Alessio Fumagalli [log in to unmask] Date: July 14, 2014 Subject: eXtended Discretization MethodS X-DMS, Italy, Sep 2015 The conference X-DMS continues and replaces the successful X-FEM conference cycle and aims at including a wider variety of methodologies coming from different areas of computational mechanics and numerical analysis. This new conference cycle intends to gather all scientists working on these techniques so to foster the exchange of ideas among different approaches and discuss about open issues and their possible solution. The conference topics include: - Partition of Unity methods (Meshfree, XFEM/GFEM); - Patch Methods; - Fictitious Domain Methods; - Strong Discontinuity Approaches (SDA); - Local/Global Non-Intrusive Coupling; - Finite Cell Methods; - Multiscale Discretization; - Special techniques for static and evolving interfaces; - Crossover approaches, such as integration of PUFEM with isogeometric method. Conference website: http://x-dms2015.sciencesconf.org/ ------------------------------------------------------- From: Jan Karel Lenstra [log in to unmask] Date: July 17, 2014 Subject: Call for preliminary bids for ISMP, August 2018 The Symposium Advisory Committee (SAC) of the Mathematical Optimization Society issues a call for pre-proposals to organize and host ISMP 2018, the triennial International Symposium on Mathematical Programming. ISMP is the flagship event of our society, regularly gathering over 1,000 scientists from around the world. The conference is usually held in or around the month of August. Hosting ISMP provides a vital service to the mathematical optimization community and often has a lasting effect on the visibility of the hosting institution. This call for pre-proposals is addressed at local groups willing to take up that challenge. The tradition would be that only sites outside of USA and Canada are eligible to host ISMP 2018. Preliminary bids will be examined by the SAC, which will then issue invitations for detailed bids. The final decision will be made and announced during ISMP 2015 in Pittsburgh. Members of the SAC are Michael Juenger (Germany), Jan Karel Lenstra (chair, the Netherlands), Jeff Linderoth (USA), Andy Philpott (New Zealand), Kim- Chuan Toh (Singapore) and Luis Nunes Vicente (Portugal). Preliminary bids should be brief and contain information pertaining to the location, facilities, logistics (accommodation and transportation) and likely local organizers. Further information can be obtained from any member of the SAC. Please address your preliminary bids until October 15, 2014 to Jan Karel Lenstra . ------------------------------------------------------- From: Mary Wall [log in to unmask] Date: July 16, 2014 Subject: Canada Research Chair Position, Sci Comp & NA Tier II Canada Research Chair in Numerical Analysis and Scientific Computing, MEMORIAL UNIVERSITY OF NEWFOUNDLAND DEPARTMENT OF MATHEMATICS AND STATISTICS, Position VPA-MAST-2014-002 The Department of Mathematics and Statistics at Memorial University of Newfoundland (MUN) invites applications for a Canada Research Chair (CRC) - Tier II, in the area of Numerical Analysis and Scientific Computing. This will be a tenure track appointment at the rank of Assistant Professor. The successful candidate will be expected to develop a vibrant independent research program in the core disciplines of numerical analysis and scientific computing while engaging in interdisciplinary research which builds upon existing collaborations between the Department of Mathematics and Statistics, the Department of Earth Sciences, and the Faculty of Engineering at MUN. The successful candidate will also be expected to participate in the undergraduate, graduate, and postgraduate teaching activities in the Department of Mathematics and Statistics as well as make academic service contributions. Candidates must have a Ph.D. in Mathematics, Applied Mathematics or related field awarded within the past 10 years. Details of the Canada Research Chairs program can be found at www.chairs.gc.ca. Application information can be found at http://www.mun.ca/math/employment/Advertisement-CRChair2014.pdf. The closing date for applications will be August 15, 2014. ------------------------------------------------------- From: Dr Anotida Madzvamuse [log in to unmask] Date: July 20, 2014 Subject: Research Fellow Position, Mathematics, Univ of Sussex School of Mathematical and Physical Sciences Department of Mathematics Fixed term for 3 years, full time Salary range: starting at £30,728 and rising to £36,661 per annum. It is normal to appoint at the first point of the salary scale. Closing date for applications: 21 August 2014 Expected start: 1 September 2014 or as soon as possible thereafter We seek to hire a highly motivated and talented Postdoctoral Fellow within our research group on a fixed term 3 years full time position starting September 2014. This is a highly desirable position supported by the Leverhulme Trust research project grant (RPG-2014-149: Unravelling new mathematics for 3D cell migration) to undertake cutting-edge research on the development, analysis and simulations of bulk-surface partial differential equations for cell motility. Modelling 3D cell motility is an emerging open-frontier research problem spanning several disciplines such as mathematics, numerical analysis, scientific computing, image analysis, cell biology, plant biology, developmental biology and biophysics. Hence the aim of this fellowship is to unravel new 3D whole-cell mathematical and computational models for cell migration through coupling of internal cell dynamics (in the bulk) to cell-surface dynamics as well as modelling how cells interact with their environment. Key to this development is the understanding of the geometric quantities describing 3D cell shape and movement as well as the molecular biology underpinning cell movement and deformation. Prospective candidates should hold a PhD in Numerical Analysis, Applied Mathematics, Computational Biology and/or other related disciplines. Candidates should include with their application the following: 1) Academic CV; 2) Official academic transcripts; 3) Contact details for two suitable referees; 4) A personal statement (500 words maximum) outlining their suitability for the position and research experience to date relevant to the project; 5) Application form Enquiries: All enquiries should be directed to Dr Anotida Madzvamuse ([log in to unmask]), Dr Vanessa Styles ([log in to unmask]) Further details can be found at the website: http://www.sussex.ac.uk/aboutus/jobs/737 ------------------------------------------------------- From: Ilaria Perugia [log in to unmask] Date: July 18, 2014 Subject: Postdoc Position, Numerics of PDEs, Univ of Vienna: new deadline At the University of Vienna one position of University Assistant (post doc) at the Faculty of Mathematics (40 hours/week; duration of employment 4 years; starting September 1, 2014) is open. The application deadline has been extended to August 6, 2014. Information for application: http://jobcenter.univie.ac.at/ Identification number: 4919 (Finite Element approximation of PDE's) E-Mail: [log in to unmask] Areas of work: The advertised post doc positions are associated with the chair for Numerics of PDE's of Prof. Ilaria Perugia ([log in to unmask]). Topics of current interest to the group include non standard finite element methods, such as Discontinuous Galerkin methods, finite elements with operator-based (Trefftz) approximating spaces, and mimetic/virtual element methods, for problems arising in acoustics, electromagnetics, elasticity, and reaction- diffusion. The job holder's responsibilities include independent research and holding classes due to extent regulations of wage agreement and the usual administrative duties. The University of Vienna intends to increase the number of women on its faculty, particularly in high level positions, and therefore specifically invites applications by women. ------------------------------------------------------- From: Cornelia Böhnstedt [log in to unmask] Date: July 16, 2014 Subject: PhD Fellowship Position: Pharmacometrics & Comp Disease Modeling The Graduate Research Training Program PharMetrX: Pharmacometrics & Computational Disease Modelling is an interdisciplinary PhD program bridging pharmacy and mathematics. PharMetrX offers its graduate students a unique opportunity to experience research in drug development and optimising drug therapy jointly within academia and industry. The PhD program is designed as a 3-year research program including a structured research training curriculum of advanced academic and industrial modules and a competitive research fellowship. We are currently inviting applications to start the PharMetrX PhD program in March 2015. Deadline for applications: September 15th, 2014. For details see https://www.PharMetrX.de. PharMetrX is a joint program of the Freie Universität Berlin and the Universität Potsdam, supported by several research-driven pharmaceutical companies. Charlotte Kloft & Wilhelm Huisinga Program Chairs ------------------------------------------------------- From: Anton Shterenlikht [log in to unmask] Date: July 14, 2014 Subject: PhD Position, Comp Model of Polycrystalline Fracture, UK Faculty of Engineering, The University of Bristol, UK has several fully funded PhD studentships, for UK/EU students only. The project is on developing a library for multi-scale multi-physics polycrystalline fracture library [1,2]. A good 2.1 or 1st class degree is required. Good math and computer skills are required. Familiarity with Unix development environment is desirable. Backgrounds in physics, engineering, computer science, maths are desirable. For more details contact Anton Shterenlikht ([log in to unmask]). [1] http://eis.bris.ac.uk/~mexas/cgpack/ [2] http://eis.bris.ac.uk/~mexas/abumpack/ [3] http://www.bristol.ac.uk/prospectus/postgraduate/2014/apply/ ------------------------------------------------------- From: Michael Heroux [log in to unmask] Date: July 14, 2014 Subject: Contents, ACM Transactions on Math Software (TOMS), 40 (4) ACM Transactions on Mathematical Software (TOMS), Volume 40, Issue 4 HSL_MI28: An Efficient and Robust Limited-Memory Incomplete Cholesky Factorization Code, Jennifer Scott, Miroslav Tůma High-Performance Evaluation of Finite Element Variational Forms via Commuting Diagrams and Duality, Robert C. Kirby Fast Reverse-Mode Automatic Differentiation using Expression Templates in C++, Robin J. Hogan Computing Petaflops over Terabytes of Data: The Case of Genome-Wide Association Studies, Diego Fabregat-Traver, Paolo Bientinesi Algorithm 943: MSS: MATLAB Software for L-BFGS Trust-Region Subproblems for Large- Scale Optimization, Jennifer B. Erway, Roummel F. Marcia Algorithm 944: Talbot Suite: Parallel Implementations of Talbot's Method for the Numerical Inversion of Laplace Transforms, Laura Antonelli, Stefania Corsaro, Zelda Marino, Mariarosaria Rizzardi Algorithm 945: modred - A Parallelized Model Reduction Library, Brandt A. Belson, Jonathan H. Tu, Clarence W. Rowley Algorithm 946: ReLIADiff - A C++ Software Package for Real Laplace Transform Inversion based on Algorithmic Differentiation, Luisa D'amore, Rosanna Campagna, Valeria Mele, Almerico Murli ------------------------------------------------------- End of Digest **************************