Bug#1041451: [Sender Not Verified] Re: Bug#1041451: gmap: FTBFS on all !amd64 archs
Hi Andreas, I have restored the non-SIMD binaries in the latest version 2023-10-01 of GMAP, which includes various other improvements and bug fixes. This version can be downloaded from our Web server at http://research-pub.gene.com/gmap. Please let me know if you find any problems with this release. Thanks, Tom On Tue, Sep 19, 2023 at 11:50 AM Thomas Wu wrote: > > 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 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 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 , 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: /<>/build/src/gmap.avx2 does not exist. For >>> faster speed, may want to compile package on an AVX2 machine >>> > Note: /<>/build/src/gmap.sse42 does not exist. For >>> faster speed, may want to compile package on an SSE4.2 machine >>> > Note: /<>/build/src/gmap.sse41 does not exist. For >>> faster speed, may want to compile package on an SSE4.1 machine >>> > Note: /<>/build/src/gmap.ssse3 does not exist. For >>> faster speed, may want to compile package on an SSSE3 machine >>> > Note: /<>/build/src/gmap.sse2 does not exist. For >>> faster speed, may want to compile package on an SSE2 machine >>> > Note: /<>/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 >>> > : :' : 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 >>> >>>
Bug#1041451: [Sender Not Verified] Re: Bug#1041451: gmap: FTBFS on all !amd64 archs
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 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 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 , 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: /<>/build/src/gmap.avx2 does not exist. For >> faster speed, may want to compile package on an AVX2 machine >> > Note: /<>/build/src/gmap.sse42 does not exist. For >> faster speed, may want to compile package on an SSE4.2 machine >> > Note: /<>/build/src/gmap.sse41 does not exist. For >> faster speed, may want to compile package on an SSE4.1 machine >> > Note: /<>/build/src/gmap.ssse3 does not exist. For >> faster speed, may want to compile package on an SSSE3 machine >> > Note: /<>/build/src/gmap.sse2 does not exist. For >> faster speed, may want to compile package on an SSE2 machine >> > Note: /<>/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 >> > : :' : 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 >> >>
Bug#1041451: [Sender Not Verified] Re: Bug#1041451: gmap: FTBFS on all !amd64 archs
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 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 , 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: /<>/build/src/gmap.avx2 does not exist. For > faster speed, may want to compile package on an AVX2 machine > > Note: /<>/build/src/gmap.sse42 does not exist. For > faster speed, may want to compile package on an SSE4.2 machine > > Note: /<>/build/src/gmap.sse41 does not exist. For > faster speed, may want to compile package on an SSE4.1 machine > > Note: /<>/build/src/gmap.ssse3 does not exist. For > faster speed, may want to compile package on an SSSE3 machine > > Note: /<>/build/src/gmap.sse2 does not exist. For > faster speed, may want to compile package on an SSE2 machine > > Note: /<>/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 > > : :' : 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 > >
