Archive for the ‘Month of Math Software’ Category

October 30th, 2011

Welcome to this month’s ‘A month of Math software.’  If you missed the September edition then why not take a look at https://www.walkingrandomly.com/?p=3534. All previous editions can be found at the Month of Math Software Archives.  If you have some mathematical software news for the November 2011 edition then feel free to contact me.

General Mathematics and Statistics

  • After being in beta for a while, version 4 of GeoGebra has been released.  I confess that I’ve never used it but it looks great and it’s free!
  • Wolfram’s Mathematica has seen a minor update with version 8.0.4.  The previous version was 8.0.1 and the list of changes between the two is given here.
  • The free MATLAB clone, Octave, has seen a bug-fix upgrade with version 3.4.3.
  • Version 2.17.12 of the computational algebra package, Magma, has been released.  The change log is at http://magma.maths.usyd.edu.au/magma/releasenotes/2/17/12/
  • Rene Grothmann has updated his Euler Math Toolbox, a numerical package that has some similarities to MATLAB, to version 12.9. This new release includes the LSODA algorithm for stiff equations.  He gives examples of the new functionality at http://euler.rene-grothmann.de/Programs/Examples/Stiff%20Equation.html

Mathematics on GPUs

Scientific Plotting

  • Matplotlib is a very capable plotting library for the Python programming language and it has just been updated.  Version 1.1 has lots of nice new features and you can read about them all at http://matplotlib.sourceforge.net/users/whats_new.html
  • DISLIN is a plotting library that can be called from many languages including C and Fortran.  October saw it updated to version 10.1.5 and you can see what’s new from DISLIN’s news page.

Mobile Mathematics

  • I discovered a couple of free MATLAB clones for Android this month – Addi and Mathmatiz.  My favourite of the two is Addi, partly because Mathmatiz insists on serving me adverts while using it.  I’d happily pay for a version of Mathmatiz that didn’t include adverts though!
  • One mobile application that I’ve been meaning to mention for months is MathScript.  This Android based application allows you to write and run python programs directly on your device.  It also comes with some basic plotting functionality and a full version of SymPy which turns it into a very capable mathematical compute engine.
  • Maplesoft have released The Maple Player for iPad which allows interactive Maple documents to be used on Apple’s tablet devices.  This first release comes with a few pre-installed documents that shows the sort of thing that the software is capable of.  The initial set of topics includes Laplace Transforms, a function plotter, integration tutor and more.  At the moment we can’t publish our own Maple documents to iPad but it looks like this is what Maplesoft are planning for the future.
October 4th, 2011

Welcome to September’s A Month of Math Software.  Last month’s can be found here and the archive is here.  If you’ve got news for next month’s edition then contact me.

General mathematics and statistics

  • The commercial computer algebra package, MAGMA, has been upgraded to version 2.17-11.  The change log is at magma.maths.usyd.edu.au/magma/releasenotes/2/17/11/
  • Version 2011b of MATLAB has been released.  I’m all excited about the improved GPU functionality in the parallel computing toolbox along with the that fact that the MATLAB compiler now supports GPU-enabled code.  This little combination means that we’ll be able to include a small amount of MATLAB/GPU support on Manchester University’s Condor pool.  If GPU support isn’t your thing then maybe you’d like to hear about updates to the MATLAB comparison tool from Mike on the MATLAB Desktop.
  • Version 2.13.2 of the extremely popular free, open source statistics pacakge, R, has been released.  This is intended to be the last of the 2.13 series and you can find out what’s new by going to https://stat.ethz.ch/pipermail/r-announce/2011/000543.html

Freely available linear algebra software

Math software in the blogs

September 2nd, 2011

Welcome to August’s ‘A Month of Math Software’ where I look at everything from blog posts about math libraries through to the latest releases.  Click here for earlier articles in the series.

Mathematical software packages

“Sho is an interactive environment for data analysis and scientific computing that lets you seamlessly connect scripts (in IronPython) with compiled code (in .NET) to enable fast and flexible prototyping.”

Sho console

It certainly looks very interesting with features such as direct integration with Azure (Microsoft’s cloud computing product), Optimization and loads more.  Let me know what you think of it if you try it out.

Mathematical Software Libraries

  • The AMD Core Math Library was upgraded to version 5.0 this month.  I think the following is the complete change-log
    • DGEMM and SGEMM have been tuned for AMD Family 15h processors.  These take advantage of AVX and FMA-4 instructions to achieve high efficiency using either one or both threads of a compute unit.
    • The Fortran code base for the library is compiled with AVX and FMA-4 flags to support the AMD Family 15h processors.  This library will not run on processors that do not support AVX and FMA-4.  The package includes legacy libraries with SSE/SSE2 instructions suitable for use on AMD Family 10h and AMD Family 0fh processors.
    • New 2D and 3D real-to-complex FFT functions have been introduced.  Included are samples demonstrating how to use the new functions.
    • The L’Ecuyer, Whichmann-Hill, and Mersenne Twister random number generator have been updated to improve performance on all processor types.
    • The vector math library dependency has been removed from the library, and libacml_mv has been removed from the build.  These AMD math functions are available as a separate download from the AMD web page.
  • While on the subject of the ACML, check out this interview about the library with Chip Freitag, one of its developers, that was recorded earlier this month.
  • AMD have also released version 1.4 of the AMD Accelerated Parallel Processing Math Libraries (APPML).  This is an OpenCL library aimed at GPUs.  As far as I can tell, this is just a bug fix release and so there are no new routines available.
  • Jack Dongarra et al have moved their linear algebra library for heterogeneous/hybrid architectures, MAGMA, from release candidate 5 to a full version 1.0 release.  Roughly speaking, you can think of this project as LAPACK for CUDA GPUs (although this scope will probably widen in the future).  I believe that it is used in products such as MATLAB’s parallel computing toolbox and Accelereyes’ Jacket (Correction: I’ve since learned that Jacket uses CULA and not MAGMA) among others.
  • Odds and Ends
    • Intel have come up with a new hardware-based random number generator.  Read about it at http://spectrum.ieee.org/computing/hardware/behind-intels-new-randomnumber-generator/ I wonder if hardware based generators will ever replace pseudo random number generators for simulation work?
    • Finally, William Hart released a new version of Coopr back in July but I didn’t learn about it in time to get it into July’s edition of Month of Math Software.  So, I’m telling you about it now (more accurately, I’m quoting William).  ‘Coopr is a collection of Python software packages that supports a diverse set of optimization capabilities for formulating and analyzing optimization models’

    That’s it for this month.  Thanks to everyone who contacted me with news items, this series would be a lot more difficult to compile without you.  If you have found something interesting in the world of mathematical software then feel free to let me know and I’ll include it in a future edition.

    July 31st, 2011

    Welcome to July’s Month of Math Software, my regular summary of news and releases in the world of software for the mathematically inclined.  If you have a news item that you’d like to share in next month’s offering then feel free to contact me to discuss it.  If you like what you see here then take a look at some of the previous editions.

    Commercial Software Releases

    Freeware and Open Source Software Releases

    • If you are working with statistics then R is probably the software package that you need to be using, no matter what operating system you prefer.  Version 2.13.1 was released on July 8th and details of what’s new can be found at http://cran.r-project.org/bin/windows/base/NEWS.R-2.13.1.html
    • Scilab, a high quality free alternative to MATLAB, has seen a minor upgrade.  Version 5.3.3 corrects a couple of bugs.
    • Numpy is a Python add-on that is almost essential if you plan to use Python for numerical computing.  It adds support for vectors and matrices to Python along with facilities such as random number generation and FFTs.  Numpy was upgraded to version 1.6.1, a bugfix release,  on July 20th.
    • PLASMA (The Parallel Linear Algebra for Scalable Multi-core Architectures) has seen a bug-fix release with version 2.4.1

    Blog articles

    July 5th, 2011

    Welcome to the 6th edition of A Month Of Math Software where I take a look at all the shiny new things that are available for a geek like me to play with.  Previous editions are available here.

    Commercial Mathematics Software

    Free Mathematics Software

    • Octave – This open source alternative to MATLAB has seen a very minor update to version 3.4.2 which fixes some minor installation problems.
    • Pari – Version 2.5 of this computer algebra system which specialises in number theory has been released.  Get the changelog here.
    • PLASMA – PLASMA stands for Parallel Linear Algebra for Scalable Multi-core Architectures. The version 2.4 changelog is available at http://icl.cs.utk.edu/plasma/news/news.html?id=270

    Mathematical Software on GPUs

    Unless you’ve been hiding under a scientific computing rock for the last couple of years you’ll know that GPUs (Graphical Processing Units) are how everyone wants to do their computing these days.  For the right kind of problem, GPUs can be faster than standard CPUs by an order of magnitude or more.  Access to such cheap computational power fundamentally changes the type of mathematical and scientific problems that we can realistically tackle– which is nice!  Unfortunately, however, programming GPUs is not particularly easy so it’s a good job that various research groups and software companies have stepped in to do some of heavy lifting for us.  Last month I mentioned a new release of NAG’s GPU offering and April saw a release candidate of v1.0 of MAGMA (open source multicore+GPU linear algebra).  Here’s what happened in June

    Compilers Compilers Compilers

    OK, so this isn’t mathematical software news really but good compilers are essential for fast mathematical code.  There have been a couple of compiler-based news items that have got me excited this month.

    • Pathscale EKOPath 4 compilers go open source – If you have a Linux system and are running some open-source mathematical software then there is a good chance that your software was compiled with the standard open source C-compiler, gcc.  Now, gcc is a fantastic compiler but, according to many benchmarks, Pathscale’s compilers produce faster executables than gcc for many computationally intensive operations.  The practical upshot for most of us is that some of our favourite software packages might be getting a free speed-hit in the near future.  There’s a huge discussion thread about this over at phoronix.com.
    • Intel have released a new open source compiler called ispc.  According to Intel’s site “ispc is a new compiler for “single program, multiple data” (SPMD) programs.” The example program is a simple Mandelbrot renderer.  Make those SIMD lanes in your CPU work harder for you!

    Mathematical software elsewhere on the web

    June 1st, 2011

    Welcome to the 5th installment of A Month of Math software where I take a look at all things math-software related.  If I’ve missed something then let me know in the comments section.

    Open Source releases

    SAGE, possibly the best open-source mathematics package bar-none, has seen an upgrade to version 4.7.  The extensive change-log is here.

    Numpy 1.60 has been released.  Numpy is the fundamental package needed for scientific computing with Python and the list of changes from the previous version can be found in this discussion thread.

    Version 1.15 of the GSL (GNU Scientific Library), a free and open source numerical library for C and C++, has been released.  A copy of the change log is here.

    Scilab, the premier open source alternative to MATLAB, has seen a new minor upgrade with 5.3.2.  Click here to see the differences from version 5.3.1

    The GMP MP Bignum library has been updated to version 5.0.2.  GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.  Check out the release notes for what’s new.

    Commercial releases

    The Numerical Algorithm’s Group (NAG) have released version 0.4 of their CUDA accelerated numerical library.  You can’t actually buy it yet as far as I know but academics can get their hands on it for free by signing a collaborative agreement with NAG.

    Magma seems to have a new release every month.  See what’s new in version 2.17-8 here.

    Math Software in the blogsphere

    Sol Lederman has started a new blog called Playing with Mathematica.  Lots of cool little demonstrations to be found such as the multiple pendulum animation below.
    Animated pendulums

    Gary Ernest Davis discusses Dijkstra’s fusc function – complete with Mathematica code.

    Alasdair looks at the sums of dice throws using Sage.

    May 1st, 2011

    Welcome to the slightly delayed 4th edition of ‘A Month of Math Software’.  If you have some math software news that you’d like including in a future edition then let me know.  Previous articles can be found in the archive.

    News

    Wolfram Research have acquired a company called MathCore Engineering AB – http://www.mathcore.com/.  The practical upshot of this is that we can expect future Mathematica versions to contain Simulink-like functionality.  Wolfram’s press-release is at http://www.wolfram.com/news/mathcoreaquired.html and Stephen Wolfram spoke about this at http://blog.wolfram.com/2011/03/30/launching-a-new-era-in-large-scale-systems-modeling/.

    Commercial releases

    MATLAB 2011a was released by The Mathworks earlier this month.  There have been a lot of changes around various toolboxes along with the usual performance enhancements and so on.  I’ll be doing a write up of it at some point but, for now, here are the release highlights .

    Maplesoft’s Maple has seen a new major version.  Maple 15 has got lots of new goodies.  Check them out at http://www.maplesoft.com/products/maple/new_features/ which includes lots of examples of how Maple 15 is better than previous versions (and, in some cases, the competition).

    The popular data analysis and plotting application, Origin, has seen an upgrade to version 8.5.1.  The what’s new list is at http://www.originlab.com/index.aspx?go=Products/Origin&PID=1750 This package is a firm favourite of users at my workplace, The University of Manchester.  It’s just a shame that it is Windows only.  Ho hum!

    HSL 2011 has been released; the first major release in 4 years.  From the website: “HSL (formerly the Harwell Subroutine Library) is a collection of state-of-the-art packages for large-scale scientific computation written and developed by the Numerical Analysis Group at the STFC Rutherford Appleton Laboratory and other experts.” Although this is a commercial library, it is free for academic use.

    I’ve been writing ‘A month of Math Software’ for four months now and you can always rely on the commercial computational algebra system, Magma, to supply us with some news.  The v2.17-6 release change log is at http://magma.maths.usyd.edu.au/magma/releasenotes/2/17/7/

    Open Source releases

    One of the most powerful statistical programming languages in existence, R, has seen a new major release.  Version 2.13 was released on April 13th.  One of the biggest new developments is a new bytecode compiler for R which has been demonstrated and benchmarked over at Thinking Inside the Box.  The huge list of changes is available in the NEWS file.

    Maxima, the free open source computer algebra system for Windows, Mac and Linux, was upgraded to version 5.24 earlier this month.  The changelog is available at http://maxima.cvs.sourceforge.net/viewvc/maxima/maxima/ChangeLog-5.24

    March 29th, 2011

    Welcome to the March 2011 edition of A Month of Math Software (MMS) where I take you on a brief tour of new things in the world of mathematical software.  If you like what you see then you may also be interested in last month’s edition and possibly January’s too. If I’ve missed anything then contact me and let me know.

    Commercial releases

    A minor update to Mathematica has been released.  Version 8.0.1 contains bug fixes and enhancements and a short list of these is available at http://www.wolfram.com/mathematica/quick-revision-history.html

    Another month, another Magma release.  See what’s new in 2.17-6 here.

    Open source releases

    Version 5.3.1 of Scilab, a superb free MATLAB-like environment, has been released.  Check out http://www.scilab.org/en/products/scilab/download/5.3.1/whatsnew to see what’s new.

    A new minor release (version 4.4.3) of GNUPLOT, a popular open-source plotting package, is now available.  The changelog is available at http://www.gnuplot.info/announce.4.4.3

    SAGE, the open-source mathematics package based on Python, has seen a new minor release.  Version 4.6.2 was released just after I published February’s edition of MMS so I’ve included it here.  For a list of all things new see this thread.

    Version 1.10.14 of Gnumeric, a free alternative to Excel, has been released.  Lots of new goodness listed at http://projects.gnome.org/gnumeric/announcements/1.10/gnumeric-1.10.14.shtml

    Version 12 of EuMaT (Euler Math Toolbox) has been released but I can’t find a changelog (update: changelog is here) .  If you’ve never used this software before then it’s a bit MATLAB-like and uses Maxima for symbolic stuff.

    Euler Math Toolbox

    GP-GPU (General Purpose Graphics Processing Units) related news, tutorials and releases

    NVIDIA have released version 4.0 of their CUDA toolkit.

    Jacket, arguably the most advanced GPU-accelerated toolbox for MATLAB currently available, has been updated to version 1.7  Check out the release notes to see what’s been added.

    PGI insider have an article called Using GPU-enabled Math Libraries with PGI Fortran which covers GPU accelerated libraries such as CUBLAS, CULA and MAGMA.

    Odds and ends

    Version 4.0 of the free MATLAB toolbox, Chebfun, has been released.  Chebfun is a collection of algorithms, and a software system in object-oriented MATLAB, which extends familiar powerful methods of numerical computation involving numbers to continuous or piecewise-continuous functions.  Chebfun is a very interesting project as can be seen from the wide array of examples.

    February 28th, 2011

    Last month I started a new feature called a Month of Math Software and since it turned out to be quite popular I thought I’d do it again. If you have any math software news or reviews that you’d like included in next month’s edition then feel free to contact me.

    Releases – Commercial
    Magma V2.17-5 has been released and the list of changes is here. Magma is a large software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics.

    Releases – Open Source
    A major new version of Octave, a high quality, open-source alternative to MATLAB, has been released. Version 3.4.0 has been available from February 8th and the changelog is available at www.gnu.org/software/octave/NEWS-3.4.html

    A new mathematics package for Mac OS X has been produced – EureKalc 3.  Screenshot below.  Currently at version 3.ß.02

    EureKalc3.png

    Version 11 beta of Euler Math Toolbox has been released with some new symbolic functionality.  There is a blog post on the new functionality at http://sourceforge.net/apps/wordpress/eumat/2011/02/07/version-11/

    A new stable release of Gnumeric (The spreadsheet component of GNOME Office) has been released.  The new version is 1.10.3 and recent changes can be found at http://projects.gnome.org/gnumeric/announcements/1.10/gnumeric-1.10.13.shtml

    Optimization
    Professor Stan Uryasev from the University of Florida has produced a website containing a suite of optimization test problems.

    Version 2 of Sergey Moiseev’s free DirectSearch optimization package for Maple has been released. The DirectSearch package is a collection of commands to numerically compute local and global minimums (maximums) of nonlinear multivariate function with (without) constraints.

    Blog articles about math software
    Mona Zeftel has written an article on PTC’s Mathcad Engineering blog about Mathcad’s new box plots including How-Tos for both Mathcad 15 and Mathcad Prime 1.0.

    The Numerical Algorithms Group (NAG) discusses the double-edged sword of SSE instructions in Wandering Precision.  SSE instructions can make your numerical algorithms significantly faster but this comes at a price.

    Non Deterministic Floating Point conversions in Java.  More SSE weirdness; a very detailed article that explains an odd bug in Java on certain architectures.

    January 27th, 2011

    I tend to keep an eye out for news relating to mathematical software and thought that I’d start sharing my monthly notebook with the world in case it proved to be useful to anyone else.  If you have any math-software news that you’d like to share then feel free to contact me.

    Releases – Commercial

    Mathcad Prime 1.0 has been released by PTC who have almost completely rewrote it from scratch.  Interestingly, you get a version of Mathcad 15.0 thrown in for free when you buy a copy.  See my discussion of this new version here.

    MAGMA v2.17-3 has been released and the changelog is here.  Magma is a large software package designed for computations in algebra, number theory, algebraic geometry and algebraic combinatorics.

    Version 12 of the popular plotting package, Sigmaplot, has been released.  The press release is at www.sigmaplot.com/aboutus/pressroom_details.php?link=jan-2010

    Releases – Open Source

    A bug-fix version of Matplotlib has been released – version 1.0.1 – and the changelog is available on sourceforge.  Matplotlib is a 2D plotting library for Python.

    SAGE 4.6.1 has been released.  The detailed changelog is here.  SAGE’s mission is “Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.”

    deal.II version 7 has been released. deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements.

    JQuantlibLib version 0.2.4 released.  Details here.  JQuantLib is a BSD Licensed, open-source, comprehensive framework for quantitative finance, written in Java.

    Mobile Math Software

    Wolfram Research have released a trio of iPhone apps called Course Assistants.  Essentially these are nice user interfaces to Wolfram Alpha that make it easier to use in specific subject domains.  The initial offering consists of Algebra, Calculus and Music Theory.  Stephen Wolfram has blogged about the new apps.

    MATLAB software community

    The Mathworks have launched a MATLAB-specific question and answer site called MATLAB Answers.  In conjunction with the venerable comp.soft-sys.matlab newsgroup and the more recent Stack Overflow, MATLABers now have more question and answer resources than ever.  The Matworks have a blog article about the new service.

    New Books

    Introduction to Scientific Computing by Victor Eijkhout.  You can download it for free or get a printed copy for under 12 pounds.