[Beowulf] Teaching Scientific Computation (looking for the perfect text)

Nathan Moore ntmoore at gmail.com
Tue Nov 20 13:43:37 PST 2007

RGB, Thanks for the references.  Oh btw, the link to the C projects seems


On Nov 20, 2007 2:23 PM, Robert G. Brown <rgb at phy.duke.edu> wrote:

> On Tue, 20 Nov 2007, Nathan Moore wrote:
> > After reflection though, I've started to wonder about the wisdom of my
> > choice.  Specifically (like RGB), I love the GSL library, and extending
> > to fortran in an intro class is non-trivial.  Additionally, most vendors
> > supply "fast" hardware libraries in C (I may be ignorant, but if a
> student
> > wants to call an AMD ACML fast-math function(
> > http://developer.amd.com/acml.jsp), or write a linear algebra function
> to
> > run on a graphics card(http://developer.nvidia.com/object/cuda.html),
> the
> > vendors seem to assume that you'll write the code in C).
> >
> > Also, and more relevant, I assume that most employers word-associate
> > "Fortran is to backwards as C is to competence".
> >
> > So, I'm thinking about reworking the class to favor C, and fearing 3
> weeks
> > of pointer and addressing hell.  For those of you who teach scientific
> > computation (and also those of you who hire undergrads), I'd be grateful
> for
> > your thoughts.  One specific question I have is what text covers
> scientific
> > programming and touches on MPI using the C language.
> Ah, grasshopper, you have finally managed to snatch the stone.  (Or is it
> drink the kool-ade, I never can remember...;-)
> Let's see.  There are some truly excellent books that have helped my
> independent study students on programming (most of whom are trained in
> Java only these days, God help us all:-( learn C.  There are also two
> free online C reference manuals, three if you count Gnu's (which
> unfortunately is by far the worst of them).  I will endeavor to provide
> you with a short shopping list, as I keep pretty much a complete C
> programmer's reference toolkit on my laptop at all times including the
> two aforementioned C textbook/manuals, various other free/online
> manuals, and of course the man pages.  Even though I write a LOT of C I
> still have to look things up -- what programmer doesn't?  When I'm
> online I have even more access to free resources as GIYF.
> To my mind, the most difficult aspect of programming in linux for a
> newbie isn't the compiler, it is the programming environment and
> learning how to create a project directory, put it under subversion (or
> possibly CVS) control, pick a text editor (not a WYSIWYG WP, an editor,
> ideally one that groks compilation and make), and write that first hello
> world program.  The second longest thing is teaching them a sane way of
> getting variables off of the command line and into a program, especially
> when some of the kids have never really used a command line at all in
> the past.  Drop the mice, guys -- fingers on those home keys!  That's
> where you type, after all...
> This process is greatly sped up if you provide them with a "standard
> program template" like the one here:
>   http://www.phy.duke.edu/~rgb/General/project.php<http://www.phy.duke.edu/%7Ergb/General/project.php>
> which can create a work directory for you by running a little script and
> prepopulate it with a functional Makefile and a set of hello-world
> sources complete with a routine that parses the command line and can
> fairly easily be hacked to add new CL arguments.  Note that this
> template is always changing and you'll like have to modify it and test
> it to meet the needs of your students, but it will TREMENDOUSLY improve
> your ability to grade projects as they can "make tgz" and ship you a
> project tarball, ready to unpack, build, test.
> I personally like the jove (Jonathan's Own Version of Emacs) for all
> text editing because emacs is maddeningly complex, crufted, overladen
> with features, and hence all but unlearnable.  jove installs easy, there
> is a teachjove tutorial that will walk students through all they need to
> know to use jove as a semi-IDE, and you're done.  I've got jove
> tarball/rpm's, or it is in debian ready to roll from what I've heard
> (what isn't?:-).
> One of the two C books I'd recommend is here:
>   http://www.phy.duke.edu/~rgb/General/c_book.php<http://www.phy.duke.edu/%7Ergb/General/c_book.php>
> which is a legal mirror of the original book.  Note well the license is
> a "beer" license.  You have to buy the authors beer if the opportunity
> to do so presents itself.  This may present problems for your students
> if they are underage, but I imagine the authors of the book will be down
> with that.  So each student can mirror my mirror, or they can find the
> original online with google or otherwise and mirror that.  That way they
> can have an entire, quite readable book on C, replete with cut-n-paste
> examples, free, installed on their personal computers where it is always
> handy and useful.
> This is a "beginner" level book -- complete enough for simple code, but
> not really up to snuff on things like threads or advanced data
> structures.  For the SERIOUS student, or the student working on an
> advanced project where forking, threads, and so on are necessary, I'd
> recommend that they use Dave Marshall's book:
>   http://www.cs.cf.ac.uk/Dave/C/CE.html
> This is a GREAT book.  A full out, pro-grade book on C including some
> very advanced stuff.  Parts are a tiny bit dated -- the first chapter of
> the book deals with CDE on Solaris -- but it is a killer reference.
> Online access is free, and if you contact Dave regarding redistribution
> of the book to a class full of students in PDF format (which he has, and
> for that matter so do I) he might be open to it.  He sent one to me
> willingly enough when I asked him about it, so I've got it on my laptop
> for eternity, network or not.  He was going to look into a Gnu OPL for
> it when last we communicated.  At this point I'd suggest (to him)
> throwing it up onto Lulu for cheap download in PDF or paper print with a
> reasonable markup -- he'd make money and students would get a generally
> lovely book in whatever form(s) they prefer.
> Then there are a variety of algorithm books or programming environment
> books I like to recommend to students I'm teaching:
>  * King Abel and Graham Glass's book.
> http://www.amazon.com/Linux-Programmers-Users-Graham-Glass/dp/0131857487
> I've used this book since it was just glass and Unix instead of Linux.
> A classic.  Way too EXPENSIVE a classic at $84, but a classic.
>  * Mastering Algorithms in C (O'Reilly Seahorse IIRC).  Excellent
> reference for stock-in-trade stuff like data structures, linked lists,
> sorting, numerical methods (to a point).
>  * Kernighan and Pike's The Practice of Programming.  I'd actually make
> this a requirement for any new C programmer.  It covers things like
> BESIDES "BARF"?  so that you don't have to yell QUITE so much at your
> students and has lots of other wisdom as well.
>  * Optionally Kernighan and Pike's The Unix Programming Environment
> isn't quite as good as Abel and Glass, but it is still damn good and and
> excellent reference.
> For numerical methods per se, well, there is STILL Numerical Recipes in
> C, but I no longer use it in any code because it sucks in so many ways.
> It is encumbered, with a code-reuse license out of the dark ages, I mean
> a really, really, really bad one (in spite of the fact that some of the
> code they are trying to encumber comes right out of the literature).  I
> personally think that all they need is the GSL itself and the GSL's
> manual, online or otherwise.  At this point anything you're at all
> likely to have beginners doing is well-supported there, with
> documentation and code examples, with a list to ask difficult questions
> on.  And yes, they can buy a paper copy of this from Amazon (and help
> support the project at the same time).  And it is even cheap.
> My actual favorite numerical methods book is alas in fortran --
> Forsythe, Malcom and Moler -- but all that they really need from any
> such textbook is a two lecture discussion on discretization error and
> bad ways of doing what appear to be straightforward tasks because
> computers do discrete arithmetic.  If the course were going to FOCUS on
> numerical methods, e.g. derive a 4th-5th order RK ODE solver and code
> it, you'd likely need t textbook to help, but to USE an RK ODE solver --
> just the GSL, just the GSL.
> The last reference I like to recommend is (of course) Knuth's TAOP.
> 'Nuff said.  Expensive as hell for the full set, but it IS the only
> reference you'll ever need, unless you plan to do network programming in
> which case you'll likely need one or more of Stevens' excellent books,
> or plan to do systems programming at the kernel level, in which case
> you'll need several books I'm not going to list here, or MPI or PVM, in
> which case you'll need -- what?  Well there are a few excellent books
> from IIRC MIT press on them, but they may be dated at this point.  There
> are the many superb articles on www.clustermonkey.new and in the Linux
> Magazine archives.  Again, having a good template goes a long way --
> there is a PVM template on my website but I don't use MPI (or PVM, much,
> anymore) so you'll have to get them from other folks.
> I've found that some subset of the *'d references and free references
> above can take a student that can program in ANY language already and
> make a credible C programmer out of them in a semester.
> And jeeze, man.  Pointers rock.  If you want students to actually learn
> how computers work so that they can UNDERSTAND what they are doing they
> are peerless (if painful) instruments of learning.  Want a block of
> memory?  Go get it, lay it out, access it, all with fairly high level
> commands.  Want to overlay a secondary addressing scheme on top of it?
> Sure, why not.  Allocate a vector, pack its addressing into a ***pointer
> to make a matrix[][][] that you can still pass to an ODE solver that
> wants vectors only, while addressing it in a completely natural way in
> the deriv evaluator.  You can do things in C easily that you can't do AT
> ALL in other languages, all because of pointers and the ability to
> recast variables.  Sure, you can break a program more horribly than you
> ever could in Fortran (although I've managed to break fortran pretty
> horribly).  That's why you get them K&P and make them read it FIRST, and
> why you teach them about adding
> #define MYDEBUG(b)  if ( (verbose == b) || (verbose == D_ALL) )
>  typedef enum {
>    D_QUIET,
>    D_ALL,
>    D_V_2,
>    D_V_3,
>    D_V_3,
>    N_DEBUG };
> into their primary program header and sticking:
> x = 1.0;
>  fprintf(stderr,"# This is my subroutine 1, and variable x = %f\n",x);
> }
> chunklets all over their damn code as they write it.  Run the program as
>   $myprog -v 2
> and out spews:
> # This is my subroutine 1, and variable x = 1.000000
> Run it as
>   $myprog
> and it doesn't.  I instrument my code so that at any instant I can get a
> completely verbose picture of everything it is doing as it goes along,
> or "zoom in" on just one subroutine.  It is tricks like this that make C
> programming robust and doable.  One should do it in any language, of
> course, but in C it is ESSENTIAL to make sure that the program is doing
> what it is supposed to be doing, not overwriting array boundaries, and
> so on.  In fortran you are lulled into a false sense of security because
> you THINK the compiler or runtime engine will catch errors for you when
> in fact there are lots of errors they will miss, and then you are REALLY
> dead.
> HTH,
>    rgb
> > regards,
> >
> > Nathan Moore
> >
> >
> >
> --
> Robert G. Brown
> Duke University Dept. of Physics, Box 90305
> Durham, N.C. 27708-0305
> Phone(cell): 1-919-280-8443
> Web: http://www.phy.duke.edu/~rgb <http://www.phy.duke.edu/%7Ergb>
> Lulu Bookstore: http://stores.lulu.com/store.php?fAcctID=877977

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Nathan Moore
Assistant Professor, Physics
Winona State University
AIM: nmoorewsu
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