Re: LEG: Optimisation and porting - assembly

[Andreas Tille <andreas@an3as.eu>]

Hi Patrick,

On Wed, Apr 03, 2013 at 06:04:59AM -0400, Patrick Schloss wrote:
> We shouldn't have any assembly code

Ahhh, sorry, read again that it is a false positive.  Comment says:

    x86 asm for timer access, actually unused

Sorry for the noise and thanks for providing mothur as Free Software

     Andreas.

> Pat Schloss (mothur)
> 
> 
> Sent frim my iPhone, expext more typos then nirmal
> 
> On Apr 3, 2013, at 3:49, Andreas Tille <andreas@an3as.eu> wrote:
> 
> > Hi,
> >
> > you might have read about the initiative from Linaro to detect assembly
> > code in Free Software to increase portablility.  I checked their list
> > for packages inside Debian Med (which became fairly easy by using the
> > recent not yet published stuff to solve #703402) and here is the list of
> > packages with some relevance for Debian Med that might deserve some
> > checking whether it might be possible to dissable / remove assembly
> > code.  I also add relevant contact (upstream or Debian maintainer in
> > case of generic packages like octave) in CC.
> >
> >  abyss       <sjackman@bcgsc.ca>
> >  bowtie      <blangmea@jhsph.edu>
> >  emboss      <emboss-bug@emboss.open-bio.org>
> >  genometools <steinbiss@zbh.uni-hamburg.de>
> >  ginkgocadx  <carlos.barrales@metaemotion.com>
> >  gmap        <twu@gene.com>
> >  gromacs     <nbreen@ofb.net>
> >  jellyfish   <gmarcais@umd.edu>
> >  maude       <eker@csl.sri.com>
> >  mothur      <pschloss@umich.edu>
> >  octave      <pkg-octave-devel@lists.alioth.debian.org>
> >  paraview    <mathieu.malaterre@gmail.com>
> >  praat       <rafael@laboissiere.net>
> >  r-base      <edd@debian.org>
> >  ugene       <ugene@unipro.ru>
> >
> > For more information about the ASM issue I attached an extract from the
> > result of the study concerning the packages listed above.  It would be
> > nice if you could check the possibility to remove / replace / deactivate
> > assembly code to make the software easily portable (for instance to cool
> > architectures like ARM64).
> >
> > BTW, I also think that
> >
> >  fis-gtm     <luis.ibanez@kitware.com>, <Amul.Shah@fisglobal.com>
> >
> > (which is not yet released as Debian package and thus not part of the
> > study) is affected.
> >
> > Kind regards
> >
> >      Andreas.
> >
> > [1] https://wiki.linaro.org/LEG/Engineering/OPTIM/Assembly
> > --
> > http://fam-tille.de
> > <debian-med_asm_packages.html>
> 

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