Your message dated Sun, 02 Oct 2022 16:55:08 +0000
with message-id <e1of2fa-00g7x1...@fasolo.debian.org>
and subject line Bug#1020793: fixed in gmap 2021-12-17+ds-2
has caused the Debian Bug report #1020793,
regarding gmap: FTBFS on avx512 host in buster
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1020793: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1020793
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: gmap
Version: 2019-01-24-1
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the past)
Control: fixed -1 2021-02-22+ds-1
Hi,
during a local rebuild of all contrib and non-free packages I noticed
that gmap/buster did FTBFS while it succeeded two years ago.
Comparing the build logs I noticed that the new build targted avx512
while the old build targeted sse42. (The old machine has been
decommissioned inbetween ...)
I cannot reproduce this with the versions found in stretch or bullseye.
gcc -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -pthread
-DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\"
-DMAX_STACK_READLENGTH=300 -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1
-DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1
-msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -mavx512f -mavx512cd -g -O2
-fdebug-prefix-map=/build/gmap-2019-01-24=. -fstack-protector-strong -Wformat
-Werror=format-security -c -o gsnapl_avx512-merge-uint8.o `test -f
'merge-uint8.c' || echo './'`merge-uint8.c
merge-uint8.c: In function 'merge_4x4':
merge-uint8.c:72:29: error: incompatible type for argument 1 of '_mm_max_epu64'
*vMergedB = _mm_max_epu64(vTmp, vMax);
^~~~
In file included from /usr/lib/gcc/x86_64-linux-gnu/8/include/immintrin.h:53,
from merge-uint8.c:15:
/usr/lib/gcc/x86_64-linux-gnu/8/include/avx512vlintrin.h:8037:24: note:
expected '__m128i' {aka '__vector(2) long long int'} but argument is of type
'__m256i' {aka '__vector(4) long long int'}
_mm_max_epu64 (__m128i __A, __m128i __B)
~~~~~~~~^~~
merge-uint8.c:72:35: error: incompatible type for argument 2 of '_mm_max_epu64'
*vMergedB = _mm_max_epu64(vTmp, vMax);
^~~~
In file included from /usr/lib/gcc/x86_64-linux-gnu/8/include/immintrin.h:53,
from merge-uint8.c:15:
/usr/lib/gcc/x86_64-linux-gnu/8/include/avx512vlintrin.h:8037:37: note:
expected '__m128i' {aka '__vector(2) long long int'} but argument is of type
'__m256i' {aka '__vector(4) long long int'}
_mm_max_epu64 (__m128i __A, __m128i __B)
~~~~~~~~^~~
make[3]: *** [Makefile:35387: gsnapl_avx512-merge-uint8.o] Error 1
BTW, the package content should not depend on the build host cpu.
The sid package currently has avx2 binaries, if I rebuild it it gets
avx512 binaries, who knows what happens after a binNMU? This can easily
lead to significant performance regressions for some users.
As there seems to be some kind of runtime cpu detection, perhaps a
bigger list of cpu targets could be built and shipped (even targets
not supported by the buildd cpu). For correctness validation,
a separate package containing the tests (if any) could be provided...
Andreas
PS: I have no clue what this package is good for :-)
--- End Message ---
--- Begin Message ---
Source: gmap
Source-Version: 2021-12-17+ds-2
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
gmap, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1020...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated gmap package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 02 Oct 2022 18:00:07 +0200
Source: gmap
Architecture: source
Version: 2021-12-17+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1020793
Changes:
gmap (2021-12-17+ds-2) unstable; urgency=medium
.
[ Nilesh Patra ]
* [skip ci] Remove myself from uploaders
.
[ Étienne Mollier ]
* d/rules: enforce a given simd level for build reproducibility.
* d/control: add myself to uploaders.
* d/rules: disable simd on non-amd64 and limit to sse2 on amd64.
(Closes: #1020793)
* d/gmap.lintian-overrides: update mismatched override.
* d/control: declare compliance to standards version 4.6.1.
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