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 <t...@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 <andr...@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 <t...@gene.com>, Colin K. Watanabe < >> c...@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 <emoll...@debian.org> >> > : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da >> > `. `' sent from /dev/pts/4, please excuse my verbosity >> > `- >> >> >> >> > _______________________________________________ >> > Debian-med-packaging mailing list >> > debian-med-packag...@alioth-lists.debian.net >> > >> https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-packaging >> >> >> -- >> http://fam-tille.de >> >>
