NA Digest Monday, July 21, 2014 Volume 14 : Issue 24

Today's Editor:
Daniel M. Dunlavy
Sandia National Labs

Submissions for NA Digest:


From: Michael Lehn
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

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
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

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

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
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

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


From: Fadil Santosa
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

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


From: Gabriel Gatica
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

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
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:


From: Jan Karel Lenstra
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

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
Date: July 16, 2014
Subject: Canada Research Chair Position, Sci Comp & NA

Tier II Canada Research Chair in Numerical Analysis and Scientific
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

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 Application
information can be found at The
closing date for applications will be August 15, 2014.


From: Dr Anotida Madzvamuse
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
(, Dr Vanessa Styles (

Further details can be found at the website:


From: Ilaria Perugia
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:
Identification number: 4919 (Finite Element approximation of PDE's)

Areas of work:
The advertised post doc positions are associated with the chair for
Numerics of PDE's of Prof. Ilaria Perugia

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
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

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

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
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 (



From: Michael Heroux
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