<div dir="ltr"><br><div>Hi Andreas,</div><div><br></div><div>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.</div><div><br></div><div>Thanks,</div><div><br></div><div>Thomas Wu</div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 19, 2023 at 8:48 AM Thomas Wu <<a href="mailto:twu@gene.com">twu@gene.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><br><div>Hi Andreas,</div><div><br></div><div>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.</div><div><br></div><div>Thanks,</div><div><br></div><div>Thomas Wu</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Sep 19, 2023 at 7:44 AM Andreas Tille <<a href="mailto:andreas@an3as.eu" target="_blank">andreas@an3as.eu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">**Warning** The sender address (Andreas Tille ) can not be verified, sender email address could be spoofed. Please take care to proceed.<br>
Control: tags -1 upstream<br>
Control: forwarded -1 Thomas Wu <<a href="mailto:twu@gene.com" target="_blank">twu@gene.com</a>>, Colin K. Watanabe <<a href="mailto:ckw@gene.com" target="_blank">ckw@gene.com</a>><br>
<br>
<br>
Hi Thomas and Colin,<br>
<br>
the Debian packaged gmap fails to build since version 2023-06-01 for all<br>
release architectures besides amd64. You can read about this bug on our<br>
bug tracker[1]. I think the analysis from Étienne below is a sensible<br>
explanation for the issue.<br>
<br>
It would be really helpful if you could clarify why you disabled SIMD?<br>
Does this mean you suggest we should provide gmap for amd64 only?<br>
<br>
Kind regards<br>
Andreas.<br>
<br>
<br>
[1] <a href="https://bugs.debian.org/1041451" rel="noreferrer" target="_blank">https://bugs.debian.org/1041451</a><br>
<br>
Am Tue, Aug 15, 2023 at 12:42:09PM +0200 schrieb Étienne Mollier:<br>
> Hi,<br>
> <br>
> The relevant part of the error message shows that the generic<br>
> fully scalar gmap.nosimd executable is never built for any cpu<br>
> architecture:<br>
> <br>
> Note: /<<PKGBUILDDIR>>/build/src/gmap.avx2 does not exist. For faster speed, may want to compile package on an AVX2 machine<br>
> Note: /<<PKGBUILDDIR>>/build/src/gmap.sse42 does not exist. For faster speed, may want to compile package on an SSE4.2 machine<br>
> Note: /<<PKGBUILDDIR>>/build/src/gmap.sse41 does not exist. For faster speed, may want to compile package on an SSE4.1 machine<br>
> Note: /<<PKGBUILDDIR>>/build/src/gmap.ssse3 does not exist. For faster speed, may want to compile package on an SSSE3 machine<br>
> Note: /<<PKGBUILDDIR>>/build/src/gmap.sse2 does not exist. For faster speed, may want to compile package on an SSE2 machine<br>
> Note: /<<PKGBUILDDIR>>/build/src/gmap.nosimd does not exist. For faster speed, may want to compile package on an non-SIMD machine<br>
> Error: appropriate GMAP version not found<br>
> <br>
> Looking into src/Makefile.am, indeed they seem disabled upstream<br>
> for the current gmap versions:<br>
> <br>
> # intersect-uint2.c requires SIMD<br>
> #bin_PROGRAMS += gmap.nosimd<br>
> #bin_PROGRAMS += gmapl.nosimd<br>
> #bin_PROGRAMS += gsnap.nosimd<br>
> #bin_PROGRAMS += gsnapl.nosimd<br>
> <br>
> My quick attempts to bring the necessary support in the<br>
> aforementioned intersect-uint2.c file were not very fruitful so<br>
> far. Something in there looks to prevent use of simde.<br>
> <br>
> Anyways, in hope this helps further investigations,<br>
> -- <br>
> .''`. Étienne Mollier <<a href="mailto:emollier@debian.org" target="_blank">emollier@debian.org</a>><br>
> : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da<br>
> `. `' sent from /dev/pts/4, please excuse my verbosity<br>
> `-<br>
<br>
<br>
<br>
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<br>
<br>
-- <br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
<br>
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