[Debian-med-packaging] Bug#1041451: [Sender Not Verified] Re: Bug#1041451: gmap: FTBFS on all !amd64 archs

[Thomas Wu]

Hi Andreas,

The GMAP package should compile on both Intel and Apple architectures.  I
think we are now requiring SIMD or its equivalent Neon, though, which is
why we are no longer building the *.nosimd binaries.  I don't think that's
a problem since every modern computer supports SIMD or Neon.  Does Debian
require a non-SIMD target machine?  I will try to look at your bug report
to understand what is going on.

Thanks,

Thomas Wu


On Tue, Sep 19, 2023 at 7:44 AM Andreas Tille <andreas at an3as.eu> wrote:

> **Warning** The sender address (Andreas Tille ) can not be verified,
> sender email address could be spoofed. Please take care to proceed.
> Control: tags -1 upstream
> Control: forwarded -1 Thomas Wu <twu at gene.com>, Colin K. Watanabe <
> ckw at gene.com>
>
>
> Hi Thomas and Colin,
>
> the Debian packaged gmap fails to build since version 2023-06-01 for all
> release architectures besides amd64.  You can read about this bug on our
> bug tracker[1].  I think the analysis from Étienne below is a sensible
> explanation for the issue.
>
> It would be really helpful if you could clarify why you disabled SIMD?
> Does this mean you suggest we should provide gmap for amd64 only?
>
> Kind regards
>     Andreas.
>
>
> [1] https://bugs.debian.org/1041451
>
> Am Tue, Aug 15, 2023 at 12:42:09PM +0200 schrieb Étienne Mollier:
> > Hi,
> >
> > The relevant part of the error message shows that the generic
> > fully scalar gmap.nosimd executable is never built for any cpu
> > architecture:
> >
> >       Note: /<<PKGBUILDDIR>>/build/src/gmap.avx2 does not exist.  For
> faster speed, may want to compile package on an AVX2 machine
> >       Note: /<<PKGBUILDDIR>>/build/src/gmap.sse42 does not exist.  For
> faster speed, may want to compile package on an SSE4.2 machine
> >       Note: /<<PKGBUILDDIR>>/build/src/gmap.sse41 does not exist.  For
> faster speed, may want to compile package on an SSE4.1 machine
> >       Note: /<<PKGBUILDDIR>>/build/src/gmap.ssse3 does not exist.  For
> faster speed, may want to compile package on an SSSE3 machine
> >       Note: /<<PKGBUILDDIR>>/build/src/gmap.sse2 does not exist.  For
> faster speed, may want to compile package on an SSE2 machine
> >       Note: /<<PKGBUILDDIR>>/build/src/gmap.nosimd does not exist.  For
> faster speed, may want to compile package on an non-SIMD machine
> >       Error: appropriate GMAP version not found
> >
> > Looking into src/Makefile.am, indeed they seem disabled upstream
> > for the current gmap versions:
> >
> >       # intersect-uint2.c requires SIMD
> >       #bin_PROGRAMS += gmap.nosimd
> >       #bin_PROGRAMS += gmapl.nosimd
> >       #bin_PROGRAMS += gsnap.nosimd
> >       #bin_PROGRAMS += gsnapl.nosimd
> >
> > My quick attempts to bring the necessary support in the
> > aforementioned intersect-uint2.c file were not very fruitful so
> > far.  Something in there looks to prevent use of simde.
> >
> > Anyways, in hope this helps further investigations,
> > --
> >   .''`.  Étienne Mollier <emollier at debian.org>
> >  : :' :  gpg: 8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
> >  `. `'   sent from /dev/pts/4, please excuse my verbosity
> >    `-
>
>
>
> > _______________________________________________
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> > Debian-med-packaging at alioth-lists.debian.net
> >
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>
>
> --
> http://fam-tille.de
>
>
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