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PAUP on Power Macintosh

Jeroen Coppieters jecop at gengenp.rug.ac.be
Wed Mar 16 04:07:10 EST 1994

On 15 Mar 1994 j0m1742 at venus.tamu.edu wrote:

> I just ran a comparative test on several types of Macs using
> PAUP 3.1.1 with a data set that contained 34 rbcL sequences
> (1407 bp in length) to see how the new Power Macs performed
> relative to 030 and 040 Macs and I thought that some of the
> readers of this group would be interested in the results.  
> This was a heuristic search using "General" settings.  
> You should remember that the
> Power Macs are running in 040 emulation mode and that in
> "native" mode they will be much faster if a native version
> of PAUP is produced.
> Machine          Runtime
> IIfx             1:08
> Quadra 840AV     0:27
> 6100/60          1:28
> 8100/80          1:01
> These results indicate that even the fastest Power Mac
> (8100/80) is barely faster in emulation mode than a
> 40 MHz 030 chip (IIfx) while the 6100/60 is significantly slower
> than the IIfx.  The Quadra 840AV is the real peformer in
> this group, over two times faster than any of the other
> machines.
> It is obvious that the Power Mac is not a good platform for
> running PAUP unless you are using it mainly for other things
> and are satisfied with IIfx-like performance.  I understand that
> David Swofford is working on a Unix version of PAUP and if that
> is the case, PAUP users who will be analyzing large data sets
> should probably save their money and wait for that option.
> *********************************************************************
> Jim Manhart, Dept. of Biology, Texas A&M University, College Station, 
> TX 77843-3258, (409) 845-3356, email:  J-Manhart at TAMU.EDU (Internet) 
> *********************************************************************
This gives a completely wrong impression. I do not have PAUP here so I'm 
not sure about it. But I had a similar experience with ClustalV
The reason of the slow performing PowerMac was that 
1)ClustalV is written in Think C (Is PAUP in Think C?)
2) Think C has an it's own set of routines for emulating the 
coprocessor. If this is turned of, the code is not portable to Macs 
without co-processor.
So, If you run Think C code that needs a coprocessor, it will be slow 
because you run an emulation of a 68040 with a disabled coprocessor.
Recompile the program with switched coprocessor option and you will 
already see a big increase in performance, even though you still run the 
68040 emulation, and not a native compiled program.


		jecop at gengenp.rug.ac.be
                    /     Jeroen Coppieters
     \ \   /\/\  /\/      Lab of Genetics
      \ \ / /\ \/ /\      University of Gent.
       \ /\/  \/\/  \    /\   AG    GC    C       Ledeganckstraat 35
                     \  /  \ T  A  G  A  A        B-9000 Gent (Belgium)
                      \/    A    AA    GA         32-9-2645189

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