The Need for Speed

Julian julian.robinson at plant-sciences.oxford.ac.uk
Thu Sep 16 11:19:28 EST 1999

In response to these questions of speed etc, I think it would be useful
(or even just intrinsically interesting) to compile a list of computer
on a single data set. PAUP outputs time and rearrangements so it should
be a simple matter of deciding on a data set or sets and then distributing
Any  suggestions? I have several data sets of varying sizes etc.

Bernard de la Cruz <delacruz at biomail.ucsd.edu> wrote in message
news:7rp8vv$t38 at net.bio.net...
> This is in response to the thread on AltiVec and the Apple PowerMac G4s.
> I don't claim to be an expert but I asked some folks involved with
> development of AltiVec/Velocity Engine support about the issue.
> To summarize:  First, you'll have to use a non-gcc compiler. Apparently
> the
> gcc group does not intend to support AltiVec; however Apple has
> resources
> for capable compilers at their web site.  Second, given the right
> compiler,
> you don't even need to rewrite the code--it will automatically take
> appropriate
> functions and chunk them for passing to AltiVec.  Third, , as a parallel
> vector
> processor, AltiVec can handle FP of at least 32-bit precision.  Given
> 128-bit wide
> paths, you should be able to pass 4 calculations to AltiVec at the same
> time.
> I've included some of the response below with permission from its
> author.
> I hope it is helpful.
> Bernard de la Cruz
> Bernard J. de la Cruz                      <delacruz at biomail.ucsd.edu>
> Biology Ph.D. Candidate                    LAB: 858/534-3107
> UC San Diego                               FAX: 858/534-0053
> Bonner 3205, 9500 Gilman Drive, MC 0322 La Jolla, California 92093-0322
> ---begin excerpted file---
> > but i'm confused about the meaning of the "vector" calculations.
>   Vector operations group similar data and perform the same operation
> on all of them in parallel.  For instance, if you had byte arrays, A
> and B, and you wanted to add each byte in A to its corresponding byte
> in B and store them in C, then you would traditionally do this:
> byte A[512];
> byte B[512];
> byte C[512];
> int  i;
> for ( i = 0; i < 512; i++ ) C[i] = A[i] + B[i];
> This code fragment would load a byte value into a register from the
> memory allocated to A, load a byte value into another register from
> the memory allocated to B, add them together, and store the result
> into the memory allocated to C, 512 times.  That's 1536 accesses to
> memory and 512 adds, total.
> If you have 128-bit vector registers, then you can use one load
> operation to read 16 bytes at a time into a register, one addition
> operation to add two vector registers' worth of bytes together,
> and one store operation to write them all back into memory as one
> contiguous 16-byte chunk.  Hence:
> vector byte A[32]; /* 32 vectors x 16 bytes/vector = 512 bytes */
> vector byte B[32];
> vector byte C[32];
> int i;
> for ( i = 0; i < 32; i++ ) C[i] = A[i] + B[i];
> This code does the exact same amount of useful work as the previous
> code fragment, except that it only had to use 96 memory accesses and
> 32 additions to do it.
> (Note it's not quite as cut-n-dried as this .. more of the first code
> fragment's memory access will actually be cache accesses, and since the
> early G4's are on motherboards with 64-bit main memory busses "one"
> vector
> load will actually take two bus cycles, etc, but you still see lots of
> gain from using vectors.)
> <stuff deleted>
> There are two ways a compiler can support vector architectures --
> implicitly and explicitly.  Implicit support involves analyzing
> non-vector
> code and trying to automatically convert it into vector code (eg, from
> the
> first code fragment in this post into the other).  This has the
> advantage
> of making the reams and reams of old code we have lying around suddenly
> altivec-enabled with a simple recompile.
> <stuff deleted>
> Explicit support is easier for the compiler, but harder for the
> programmer.
> It involves adding keywords to the compiled language so that programmers
> can write their code to use vector data types, as described in the
> AltiVec
> Technology Programming Interface Manual and illustrated in my second
> code
> fragment.  This can give much better performing-code than implicit
> vector
> code, since the human coder has a better idea of what's "safe" and what
> isn't than does the compiler, but it involves more work (training and
> ap-
> plication of intelligence) on the programmer's part, makes the
> conversion
> of old code to altivec-utilizing code arduous, limits your ability to
> support the code (ie, a programmer who is not trained in using the
> vector
> language extensions cannot maintain source code that uses it, and
> automated
> quality assurance tools which need to parse the sources will choke and
> die
> on the extensions, making them unusable until the company selling the
> tool
> can be coaxed into rewriting the tool to support the extension), and
> opens
> the possibility of having multiple, mutually-incompatible
> implementations
> of compilers which extend the language, damaging portability of code and
> limiting one's options for migrating between development environments.
> There's another way an application can support altivec, and that's by
> using altivec-enabled libraries.  Libraries are collections of functions
> which are used in a variety of tasks.  For instance, there is a library
> function for calculating the length of a string, or for converting a
> tiff-formatted image into a jpeg-formatted image.  The programmers just
> call functions from these libraries so they do not have to write them
> themselves.  The libraries are then "linked" into their code either when
> the application is compiled from source code into an executable binary
> (static linking) or when the application is loaded from disk on the end-
> user's computer and executed (dynamic linking).  In either case, if a
> library gets replaced with another library that "looks" the same (ie,
> same
> function names, same arguments, etc) but uses completely different code
> to
> get its task done, then the application will happily use the new library
> without any changes having to be made to the non-library part of the
> code.
> ---end excerpted file---

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