NA Digest Sunday, March 30, 2014 Volume 14 : Issue 08

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

Submissions for NA Digest:


From: Bruce Bailey
Date: March 26, 2014
Subject: New Spotlights series will illuminate timely topics

SIAM will publish a new book series, SIAM Spotlights
(, comprising brief and
enlightening books on timely topics in applied and computational
mathematics and scientific computing. The books, spanning 125 pages
or less, will be produced on an accelerated schedule and priced

Potential authors should contact Elizabeth Greenspan
( or Sara Murphy (


From: Randy LeVeque
Date: March 27, 2014
Subject: Coursera Class, High Performance Scientific Computing

I've been teaching a class for the past several years that has been
video taped for our online Masters degree program, and last year the
videos were cleaned up a bit for a Coursera version. This class will
run again this year starting on Monday, March 31, 2014:

Like most of us probably, I find it painful to watch myself lecture so
I recommend this with some trepidation, but last year several
colleagues at other universities told me they found it useful for
their students. The course is very much an *introduction* to high
performance computing, with the goal of taking students who have some
experience programming (e.g. in Matlab) and teaching them about
compiled languages (Fortran 90 in particular), Makefiles, OpenMP, MPI,
IPython notebooks, and version control using Git.

A bit about my philosophy on MOOCs: My primary reason for agreeing to
do this was similar to why I've written a couple of textbooks. After
putting so much effort into developing material for a class it's nice
if it can be useful beyond the handful of students I teach at UW. But
like a textbook, a MOOC doesn't eliminate the need for courses with
live instructors, it only gives a another tool to help educate. All
of the lecture notes and slides to accompany the videos are also
openly available on my webpage from last year,
and the notes will be updated this Spring Quarter,
(I'm flipping the class and using last year's lectures.) Many things
I borrowed from generous colleagues, so I hope some of these materials
are also useful to others.


From: Tim Davis
Date: March 28, 2014
Subject: Algorithmic artwork and the London electronic music scene

In a new artistic sideline, I've been creating algorithmic artwork
via sparse matrices, graph algorithms, FFTs, MATLAB, and
force-directed graph visualization. I did the theme artwork for
the London Electronic Music Festival last November.

Cleve Moler wrote a blog on it a few weeks ago:

And SIAM asked me to write a blog as well:

You can see my full gallery at .

Tim Davis


From: Victorita Dolean
Date: March 24, 2014
Subject: Challenges in Medical Imaging, UK, May 2014

Challenges in medical imaging: numerics, high performance computing,
inverse problems ( )

May 21, 2014 - May 23, 2014, University of Strathclyde, Glasgow.

The aim of this workshop is to gather specialists on Numerical
Methods, High Performance Computing, Inverse Problems, Microwave

Microwave Tomography is a novel, early stage development way of
imaging with a number of potentially attractive medical applications.

The three challenges addressed by this applications are:
(i) Methodological and numerical development robust inversion tools,
associated with the numerical solution of the electromagnetic
forward problem.
(ii) Development of general parallel open source simulation codes,
based on the high- level integrated development environments,
using the state-of-art high order methods and solution techniques
forward modelling the scattering of arbitrary electromagnetic
waves in highly heterogeneous media, over a wide frequency range
in the microwave domain.
(iii) Design of antenna elements and arrays and simulations using
anatomical phantoms.

There is no registration fee. The invited speakers are Simon Arridge;
Ian Craddock; Simon Chandler-Wilde; Ivan Graham; Martin J. Gander;
Christophe Geuzaine; Markus Grote; Frederic Hecht; Marie Kray; Rolf
Krause; Frederic Nataf; Christian Pichot; Francesca Rapetti; Richard
Pasquetti; Serguei Semenov


From: Martina Bukac
Date: March 25, 2014
Subject: Computational Geomechanics, USA, May 2014

Workshop on Computational Geomechanics
May 22-23, 2014,
Pittsburgh PA, USA.

The workshop will focus on recent advances in modeling, design,
analysis, and implementation of numerical methods for problems in
geomechanics. Relevant applications include, but are not limited
to, hydraulic fracturing, groundwater flow, reservoir engineering,
and poroelastic filters. There will be a poster session for
graduate students and recent PhDs.

Keynote Speakers: Andrew Bunger, Armando Duarte, Luca Formaggia,
Marcio Murad, Jan Nordbotten, Guglielmo Scovazzi, Hamdi Tchelepi,
Mary Wheeler, Paolo Zunino

For further information about the workshop please visit

The registration for the workshop via the webpage is open.


For any questions please contact Martina Bukac at


From: Kengo Nakajima
Date: March 25, 2014
Subject: Call for Posters, VECPAR 2014, USA, Jun-Jul 2014

You are invited to make submissions for POSTER presentation at:

11th International Meeting on High-Performance Computing
or Computational Science (VECPAR 2014)
U. Oregon & Hilton Conf. Ctr., Eugene, OR, USA
June 30 - July 3, 2014,

Interested authors should log in
and go to the 'new submission' page.

The deadline for submission is April 15, 2014.

The submission should be limited to 2-pages,
and formatted according to the Rules of the Springer LNCS,
Accepted submissions will be included in the material to be
distributed to the participants of the meeting

If you have any questions, please consult the conference website:, or
contact the organizing committee (


From: Gilles Fourestey
Date: March 24, 2014
Subject: European Trilinos User Group, Switzerland, Jun 2014

On behalf of the organizers and the Swiss National Computing Center, I
would like to invite you to the 3nd European Trilinos User Group
meeting, which will be held in Lugano, on June 30th to July 1st. This
year, the EuroTUG will be co-organized with the PMAA14 conference

Details and registration are available at the following link:

The EuroTUG is a satellite to the TUG meeting held annually at Sandia
National Labs, which brings together communication between Trilinos
users, clients and developers from all over Europe and provides an
outlook in current trends in development of Trilinos as well as to
current trends in HPC in general.

We encourage participants to indicate their specific interests during
the registration process to allow the organizers to define focus
points. Also, participants are encouraged to present their individual
research/work that involves utilisation or development of packages
from Trilinos.

Peter Arbenz, ETHZ
Simone Deparis, EPFL
Gilles Fourestey, CSCS
Michael Gee, TUM
Mike Heroux, Sandia National Labs


From: Ridgway Scott
Date: March 29, 2014
Subject: FEniCS'14 Registration Now Open, France, Jun 2014

The FEniCS14 Workshop will be held in Paris 16-17 June 2014 at the
University of Chicago Center in Paris.

Registration and abstract submission is now open.

See for


From: A. Ismael F. Vaz
Date: March 24, 2014
Subject: Optimization 2014, Portugal, Jul 2014

Optimization 2014
uimarães, Portugal
July 28-30, 2014

Optimization 2014 is the eighth edition of a series of Optimization
international conferences held every three or four years, in Portugal.
This meeting aims to bring together researchers and practitioners from
different areas and with distinct backgrounds, but with common
interests in optimization.

Confirmed plenary speakers:
Masao Fukushima | Nanzan Univ.
Serge Gratton | ENSEEIHT and CERFACS, Toulouse
C. Tim Kelley | NC State Univ.
Nenad Mladenovic | Brunel Univ.
Maarten H. Van der Vlerk | Univ. Groningen
François Vanderbeck | Univ. Bordeaux

Deadline for abstract submission - March 31, 2014
Notification of acceptance - May 1, 2014
Early Registration - Before May 15, 2014

Additional information regarding registration, contributed talks,
deadlines, and accommodation will be available from the conference web

For any questions regarding Optimization 2014, please contact:


From: Bora Ucar
Date: March 24, 2014
Subject: SIAM CSC14, France, Jul 2014

The Sixth SIAM Workshop on Combinatorial Scientific Computing will
take place July 21-23, 2014 at Ecole Normale Superieure de Lyon,
Lyons, France.

We are now accepting submissions for posters.

The CSC14 Workshop's focus is on combinatorial mathematics and
algorithms in high performance computing, broadly interpreted. Posters
in this broadly defined area as well as those on traditional CSC
topics, including but not limited to parallel computing, sparse matrix
computations, combinatorial problems in optimization, automatic
differentiation, mesh generation, computational biology, and
combinatorial matrix theory are welcome.

May 2, 2014: Deadline for poster submissions
May 19, 2014: Notification of acceptance (of posters)
July 21-23, 2014: Workshop

We invite 1-page abstracts for poster presentations. Submissions are
through EasyChair:

Invited Speakers:
Petros Drineas, Rensselaer Polytechnic Institute
Tamara G. Kolda, Sandia National Laboratories
Sivan Toledo, Tel-Aviv University

Registration: No registration fee.


From: Chee Yap
Date: March 25, 2014
Subject: ICMS, Korea, Aug 2014

Please consider submitting an abstract to:

The 4th International Congress on Mathematical Software (ICMS)
August 5 - 9 2014, Seoul Korea

Invited Plenary Speakers:
Jonathan Borwein (Australia)
Bruno Buchberger (Austria)
Wolfram Decker (Germany)
Andrew Sommese (USA)
Lloyd N. Trefethen (UK)

Official satellite conference of International Congress of
Mathematicians (ICM):

This is a forum for researchers to share challenges, achievements and
progress in mathematical software research, their design, development
and use.

- Short abstract March 31 2014
- Extended abstract April 30 2014

Feel free to contact for more information.


From: Siddhartha Mishra
Date: March 28, 2014
Subject: ANAPDE 14 (honoring E. Tadmor), Switzerland, Sep 2014

We are pleased to announce the conference "ANAPDE 14" -- Analysis and
Numerical approximation of PDES, organized at ETH Zurich from the 8th
to 10th September, 2014.

This conference will cover latest developments in the analysis and
numerical approximation of nonlinear PDEs. The conference will honor
Prof. Eitan Tadmor on his 60th birthday. All talks will be given by
invited plenary speakers. There will be a poster session for
interested participants.

Invited Speakers: R. Caflisch (UCLA); W. Dahmen (RWTH, Aachen); C. De
Lellis (Zurich); U. S. Fjordholm (Trondheim); H. Holden (Trondheim);
A. Kiselev (Rice); D. Kroener (Freiburg); A. Kurganov (Tulane);
P. LeFloch (Paris VI); Y. Maday (Paris VI); S. Mallat (Ecole
Polytechnique); P. Marcati (L' Aquila); P. Markowich (KAUST); B. Popov
(Texas A&M); G. Russo (Catania); J. Tanner (Oxford); M. Vogelius

More details on the conference can be found at


From: Pamela Bye
Date: March 25, 2014
Subject: IMA Numerical Linear Algebra and Optimisation, UK, Sep 2014

University of Birmingham, UK
3 – 5 September 2014

The IMA and the University of Birmingham are pleased to announce the
Fourth Biennial IMA Conference on Numerical Linear Algebra and
Optimisation. The meeting is co-sponsored by SIAM, whose members will
receive the IMA members’ registration rate.

Conference topics include any subject that could be of interest to
both communities, such as: Direct and iterative methods for large
sparse linear systems; Eigenvalue computation and optimisation;
Large-scale nonlinear and semidefinite programming; Effect of
round-off errors, stopping criteria, embedded iterative procedures;
Optimisation issues for matrix polynomials; Fast matrix computations;
Compressed/sparse sensing; PDE-constrained optimisation; Applications
and real time optimisation

Invited speakers: Michele Benzi (Emory Univ); Iain Duff (Rutherford
Appleton Laboratory and CERFACS Toulouse) - SIAM UKIE Speaker; Michael
Friedlander (Univ of British Columbia); Andreas Grothey (Univ of
Edinburgh); Joerg Liesen (TU Berlin); Yuri Nesterov (Univ Catholique
de Louvain); Nancy Nichols (Univ of Reading)

Mini-symposia proposals: 31 March 2014
Notification of acceptance of mini-symposia: 10 April 2014
Abstract submission: 30 April 2014
Notification of acceptance of abstracts: 30 May 2014


From: Marius Lysaker
Date: March 24, 2014
Subject: Energy Min Methods in Computer Vision, Hong Kong, Jan 2015

Energy Minimization Methods have become an established computational
paradigm in Computer Vision and Pattern Recognition. EMMCVPR is a
regular bi-annual international conference dedicated to advancing the
state-of-the-art regarding development and applications of energy
minimization methods. The upcoming conference will take place in
January 13-16, 2015 in Institute of Advanced Studies at Hong Kong
University of Science and Technology. As with the previous editions,
the proceedings will be published by Springer in the Lecture Notes on
Computer Science (LNCS) series. The size of each paper will be limited
to 14 pages. The scientific program of EMMCVPR 2015 will include the
presentation of invited plenary talks and contributed research papers.

Important Dates:
Conference Dates: Jan 13, 2015 - Jan 16, 2015
Conference location: Hong Kong
Submission Deadline Jul 15, 2014
Notification Due Sep 14, 2014
Final Version Due Sep 24, 2014

Refer to the conference webpage for more details:


From: Chen Greif
Date: March 29, 2014
Subject: SIAM Applied Linear Algebra, USA, Oct 2015

The next SIAM Conference on Applied Linear Algebra will take place on
October 26–30, 2015, at the Hyatt Regency in Atlanta, Georgia,
USA. Please save the dates! The conference webpage is

Chen Greif and Jim Nagy
Conference Co-Chairs


From: Alexis Michael Rizon
Date: March 28, 2014
Subject: Postdoc Position, George Mason Univ

George Mason University
Postdoctoral Research Fellow, Molecular Neuroscience/Computational

The George Mason University, Krasnow Institute seeks a Postdoctoral
Research Fellow to develop and use multiscale spatiotemporal models of
cardiac mitochondria to understand how mitochondrial structure and
function are related.

Qualifications: The ideal candidate is expected to have expertise in
biological modeling, computer programming, and related numerical
methods. Programming on parallel architectures is also desirable, as
is knowledge of mitochondrial modeling.

This project involves close collaboration with experimental
collaborators. The duration of the position is subject to available
research funding.

For full consideration, applicants must apply for position number
F9804z at; complete and submit the online
application; and upload a CV, a list of three references with contact
information, and a description of research accomplishments. These
three required documents will need to be uploaded to the Other Doc
category as a single (multipaged) document. Questions may be addressed

Apply Here:


From: Karl Meerbergen
Date: March 28, 2014
Subject: Postdoc Position, KU Leuven, Belgium

KU Leuven (Karl Meerbergen, Dirk Roose) has a postdoctoral research
position for a research project on high performance computing for Life
Sciences. The researcher will work on one of the two following topics:
1) parametric model order reduction of nonlinear dynamical systems for
parameter estimation in biostatistics or 2) non-negative and binary
matrix factorizations for machine learning in chemogenomics.

The successful candidate should be interested in high performance
computing, parameter estimation, high dimensional numerical
integration and parametric model order reduction or non-negative and
binary matrix factorizations and is expected to have expertise in at
least one of these themes. In addition, the interested candidate
should be willing to develop HPC codes in C++. The researcher will
work in close collaboration with the University of Antwerp (Wim
Vanroose) and scientists from Jansen Pharma and Intel. Part of the
time will be spent in the ExaScience lab in Leuven, an
interdisciplinary lab on bio-statistics, chemogenomics,
bio-informatics, and programming models for HPC. The starting data of
the position is any time between May 1st and September 1st, 2014. The
position ends on June 30th, 2015.

Candidates should send their CV with full list of publications to


From: Luc Giraud
Date: March 26, 2014
Subject: Postdoc Position, Linear solver for hypersonic simulations, Inria

A 18 month postdoc position is available in the HiePACS project at
Inria Bordeaux-Sud Ouest in collaboration with CEA_CESTA for the
design of high performance solvers for simulations of 3D hypersonic
flows on petascale supercomputers.

PhD degree in computer science, computational science, applied
mathematics or a related scientific application domain area such as
fluid mechanics is required. Excellent written and oral communication
skills and a good experience with code development are required too.

Interested candidates should submit a vita, as well as the name of
three persons who could provide us with a letter of recommendation.

The position can be starting any time from now, once the selection and
hiring process is completed.

For further information go to


From: Stéphane Lanteri
Date: March 25, 2014
Subject: Postdoc and PhD Positions, High perf computing, Inria

C2S@Exa is a multi-disciplinary, multi-team, Inria initiative
gathering numerical mathematicians and computer scientists sharing
their expertise in view of the the development of numerical modeling
methodologies that fully exploit the processing capabilities of modern
massively parallel architectures.

Several postdoctoral and PhD positions are opened in the context of
this initiative. Subjects and application details are available at the
URL of the C2S@exa IPL,


From: Bernhard Müller
Date: March 28, 2014
Subject: PhD Position, Fluid-Structure Interaction, NTNU, Norway

At the Norwegian University of Science and Technology (NTNU), a PhD
scholarship on Mathematical Modeling of Fluid-Structure Interaction is
available at the Division of Fluids Engineering, Department of Energy
and Process Engineering, Faculty of Engineering Science and
Technology. The PhD project is a part of an interdisciplinary research
project entitled Modeling of Obstructive Sleep Apnea by
Fluid-Structure Interaction in the Upper Airways, which is mainly
funded by the Research Council of Norway. The objective of that
research project is to develop a clinical tool to predict the response
of surgeries for Obstructive Sleep Apnea Syndrome (OSAS) patients and
to identify the decisive pathophysiological mechanisms for the
development of OSAS.

The main tasks of the PhD project are:
- to extend a high order finite difference method based on the
arbitrary Lagrangian– Eulerian (ALE) approach to fluid-structure
interaction (FSI) of the soft palate in the pharynx,
- to develop an immersed boundary method for FSI with large
deformations of the soft palate in the pharynx,
- to study basic biomechanical mechanisms of OSAS using a simplified
model in collaboration with two other PhD candidates in the
interdisciplinary research project, and
- to provide very accurate results of FSI with a simplified OSAS model
for the verification of commercial software employed by our research

The candidate should hold a master's degree in mechanical engineering,
applied mathematics, physics or similar. Very good proficiency in
fluid mechanics, structural mechanics, and numerical methods for
partial differential equations as well as very good programming skills
are required. Proficiency in the GNU/Linux environment is an
advantage. Excellent communication skills in scientific writing and
oral presentation are needed. The PhD position is limited to 3 years.

Application deadline: May 15, 2014.

Further information about the PhD position and the online application
procedure can be found at
within-mathematical-modeling-of-fluid-structure-interaction .


From: Ned Nedialkov
Date: March 27, 2014
Subject: PhD Positions, McMaster Univ

PhD Positions Available in the Computing and Software Department at
McMaster University

For excellent candidates, two PhD positions are available in the
Computing and Software Department at McMaster University, in Hamilton,
Ontario, Canada. The positions will focus on developing certifiable
scientific and engineering software using a Literate Process that
eliminates duplication between software artifacts and explicitly
incorporates traceability between these artifacts. The motivating
case study for the research will be nuclear safety analysis software.

Applicants should have a strong background in software engineering or
computer science, mathematical maturity and experience with technology
and software development. Knowledge of computational mathematics and
physics will be considered an asset. Due to the funding model,
preference will be given to domestic students or landed immigrants in

Interested candidates should apply for graduate studies with the
Computing and Software Department
( and they should
send an e-mail expressing interest to one of the project supervisors:
Dr. Spencer Smith (, Dr. Jacques Carette
( or Dr. Ned Nedialkov (

Applicants will be accepted until the two positions are filled. The
projected start date is September 2014, but this is negotiable.

Please feel free to forward this advertisement to any potentially
interested candidates.


From: Mike Heroux
Date: March 24, 2014
Subject: Contents, ACM Transactions on Mathematical Software, 40 (2)

Volume 40, Issue 2, February 2014

This issue is available at:

Unified form language: A domain-specific language for weak
formulations of partial differential equations, Martin S. Alnæs,
Anders Logg, Kristian B. Ølgaard, Marie E. Rognes, Garth N. Wells

Computing the sparsity pattern of Hessians using automatic
differentiation, Robert Mansel Gower, Margarida Pinheiro Mello

How do you compute the midpoint of an interval? Frédéric Goualard

Optimally packed chains of bulges in multishift QR algorithms, Lars
Karlsson, Daniel Kressner, Bruno Lang

A parallel implementation of Davidson methods for large-scale
eigenvalue problems in SLEPc, Eloy Romero, Jose E. Roman

Algorithm 935: IIPBF, a MATLAB toolbox for infinite integral of
products of two Bessel functions, J. Tilak Ratnanather, Jung H. Kim,
Sirong Zhang, Anthony M. J. Davis, Stephen K. Lucas

Algorithm 936: A Fortran message processor, Fred T. Krogh

Algorithm 937: MINRES-QLP for symmetric and Hermitian linear equations
and least-squares problems, Sou-Cheng T. Choi, Michael A. Saunders

Algorithm 938: Compressing circular buffers, John C. Gunther

End of Digest