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

[Thomas Wu]

Hi Andreas,

I have decided to restore the non-SIMD binaries.  I have just written code
to do that, and will release a new version once some large-scale test runs
complete successfully.

Thanks,

Thomas Wu



On Tue, Sep 19, 2023 at 8:48 AM Thomas Wu <twu at gene.com> wrote:

>
> 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
>> >
>> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging
>>
>>
>> --
>> http://fam-tille.de
>>
>>
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