forked from pool/htscodecs
Accepting request 1086716 from science
OBS-URL: https://build.opensuse.org/request/show/1086716 OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/htscodecs?expand=0&rev=3
This commit is contained in:
Dominique Leuenberger
Git OBS Bridge
commit
de8df63b04
@ -1,99 +0,0 @@
|
||||
From 843d4f63b1c64905881b4648916a4d027baa1a1c Mon Sep 17 00:00:00 2001
|
||||
From: James Bonfield <jkb@sanger.ac.uk>
|
||||
Date: Wed, 17 Aug 2022 15:27:04 +0100
|
||||
Subject: [PATCH] Improvements for intel -m32 builds.
|
||||
|
||||
On this platform _mm256_extract_epi64 isn't defined, but the rest of
|
||||
AVX2 is. It needs to fail auto-detection.
|
||||
|
||||
Also we get unaligned accesses in the SSE4 code with tbuf due to
|
||||
differing data alignment caused by 32-bit pointers instead of 64-bit.
|
||||
This exposes an underlying problem of using aligned SIMD writes on
|
||||
tbuf without explicitly asking for alignment. (The new code is also
|
||||
sometimes a little faster.)
|
||||
|
||||
See also samtools/htslib#1500
|
||||
---
|
||||
configure.ac | 3 ++-
|
||||
htscodecs/rANS_static32x16pr_avx2.c | 2 +-
|
||||
htscodecs/rANS_static32x16pr_avx512.c | 2 +-
|
||||
htscodecs/rANS_static32x16pr_sse4.c | 2 +-
|
||||
m4/ax_check_compile_flag.m4 | 6 +++++-
|
||||
5 files changed, 10 insertions(+), 5 deletions(-)
|
||||
|
||||
diff --git a/configure.ac b/configure.ac
|
||||
index 4c8ad54..eb2f44e 100644
|
||||
--- a/configure.ac
|
||||
+++ b/configure.ac
|
||||
@@ -165,7 +165,8 @@ AX_CHECK_COMPILE_FLAG([-mavx2], [
|
||||
]],[[
|
||||
__m256i a = _mm256_set_epi32(1, 2, 3, 4, 5, 6, 7, 8);
|
||||
__m256i b = _mm256_add_epi32(a, a);
|
||||
- return *((char *) &b);
|
||||
+ long long c = _mm256_extract_epi64(b, 0);
|
||||
+ return (int) c;
|
||||
]])
|
||||
])
|
||||
AM_CONDITIONAL([RANS_32x16_AVX2],[test "x$MAVX2" != "x"])
|
||||
diff --git a/htscodecs/rANS_static32x16pr_avx2.c b/htscodecs/rANS_static32x16pr_avx2.c
|
||||
index 2dd14f1..c36f23c 100644
|
||||
--- a/htscodecs/rANS_static32x16pr_avx2.c
|
||||
+++ b/htscodecs/rANS_static32x16pr_avx2.c
|
||||
@@ -1123,7 +1123,7 @@ unsigned char *rans_uncompress_O1_32x16_avx2(unsigned char *in,
|
||||
union {
|
||||
unsigned char tbuf[32][32];
|
||||
uint64_t tbuf64[32][4];
|
||||
- } u;
|
||||
+ } u __attribute__((aligned(32)));
|
||||
unsigned int tidx = 0;
|
||||
|
||||
if (0) {
|
||||
diff --git a/htscodecs/rANS_static32x16pr_avx512.c b/htscodecs/rANS_static32x16pr_avx512.c
|
||||
index 0d1456f..e9cce46 100644
|
||||
--- a/htscodecs/rANS_static32x16pr_avx512.c
|
||||
+++ b/htscodecs/rANS_static32x16pr_avx512.c
|
||||
@@ -735,7 +735,7 @@ unsigned char *rans_uncompress_O1_32x16_avx512(unsigned char *in,
|
||||
union {
|
||||
unsigned char tbuf[32][32];
|
||||
uint64_t tbuf64[32][4];
|
||||
- } u;
|
||||
+ } u __attribute__((aligned(32)));
|
||||
#else
|
||||
uint32_t tbuf[32][32];
|
||||
#endif
|
||||
diff --git a/htscodecs/rANS_static32x16pr_sse4.c b/htscodecs/rANS_static32x16pr_sse4.c
|
||||
index fe0345f..88bcbe0 100644
|
||||
--- a/htscodecs/rANS_static32x16pr_sse4.c
|
||||
+++ b/htscodecs/rANS_static32x16pr_sse4.c
|
||||
@@ -1423,7 +1423,7 @@ unsigned char *rans_uncompress_O1_32x16_sse4(unsigned char *in,
|
||||
uint16_t *sp = (uint16_t *)ptr;
|
||||
const uint32_t mask = ((1u << TF_SHIFT_O1_FAST)-1);
|
||||
__m128i maskv = _mm_set1_epi32(mask); // set mask in all lanes
|
||||
- uint8_t tbuf[32][32];
|
||||
+ uint8_t tbuf[32][32] __attribute__((aligned(32)));
|
||||
int tidx = 0;
|
||||
LOAD128(Rv, R);
|
||||
LOAD128(Lv, l);
|
||||
diff --git a/m4/ax_check_compile_flag.m4 b/m4/ax_check_compile_flag.m4
|
||||
index bd753b3..c2bd2c6 100644
|
||||
--- a/m4/ax_check_compile_flag.m4
|
||||
+++ b/m4/ax_check_compile_flag.m4
|
||||
@@ -36,13 +36,17 @@
|
||||
|
||||
#serial 6
|
||||
|
||||
+# LOCAL modification; change AC_COMPILE_IFELSE to AC_LINK_IFELSE so
|
||||
+# _mm256_extract_epi64 tests on a x86_64 running under -m32 still
|
||||
+# fails. (Otherwise it compiles, but fails to link.)
|
||||
+
|
||||
AC_DEFUN([AX_CHECK_COMPILE_FLAG],
|
||||
[AC_PREREQ(2.64)dnl for _AC_LANG_PREFIX and AS_VAR_IF
|
||||
AS_VAR_PUSHDEF([CACHEVAR],[ax_cv_check_[]_AC_LANG_ABBREV[]flags_$4_$1])dnl
|
||||
AC_CACHE_CHECK([whether _AC_LANG compiler accepts $1], CACHEVAR, [
|
||||
ax_check_save_flags=$[]_AC_LANG_PREFIX[]FLAGS
|
||||
_AC_LANG_PREFIX[]FLAGS="$[]_AC_LANG_PREFIX[]FLAGS $4 $1"
|
||||
- AC_COMPILE_IFELSE([m4_default([$5],[AC_LANG_PROGRAM()])],
|
||||
+ AC_LINK_IFELSE([m4_default([$5],[AC_LANG_PROGRAM()])],
|
||||
[AS_VAR_SET(CACHEVAR,[yes])],
|
||||
[AS_VAR_SET(CACHEVAR,[no])])
|
||||
_AC_LANG_PREFIX[]FLAGS=$ax_check_save_flags])
|
||||
@ -1,3 +0,0 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:696c0affbfa7e59276e0dfc71dcba2f04b0a6db12998f30f1baf2fc21e9113f4
|
||||
size 3368716
|
||||
3
htscodecs-1.5.0.tar.gz
Normal file
3
htscodecs-1.5.0.tar.gz
Normal file
@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:34def7341d01a374583d61c9012a80f6b40af078b11bfcaacba1a2412e34dab3
|
||||
size 3498542
|
||||
@ -1,3 +1,23 @@
|
||||
-------------------------------------------------------------------
|
||||
Thu May 4 14:47:16 UTC 2023 - Andrea Manzini <andrea.manzini@suse.com>
|
||||
|
||||
- Update to 1.5.0:
|
||||
* Significant speed ups to the fqzcomp codec via code restructuring
|
||||
and use of memory prefetch instructions. Encode is 30-40% faster
|
||||
and decode 5-8% faster.
|
||||
* Remove unused ax_with_libdeflate.m4 file from build system
|
||||
|
||||
- removed patch fix_ix86_build.patch already merged in upstream
|
||||
|
||||
- Update to 1.4.0:
|
||||
* This is almost entirely minor bug fixing with a few small updates.
|
||||
* Optimise compression / speed of the name tokeniser
|
||||
* Improvements for Intel -m32 builds, including better AVX2 validation
|
||||
* Detect Neon capability at runtime via operating system APIs.
|
||||
* Update hts_pack to operate in line with CRAMcodecs spec, where the number of symbols > 16.
|
||||
* Fixed too-stringent buffer overflow checking in O1 rans decoder.
|
||||
|
||||
|
||||
-------------------------------------------------------------------
|
||||
Thu Sep 8 21:52:47 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
|
||||
|
||||
|
||||
@ -1,7 +1,7 @@
|
||||
#
|
||||
# spec file for package htscodecs
|
||||
#
|
||||
# Copyright (c) 2022 SUSE LLC
|
||||
# Copyright (c) 2023 SUSE LLC
|
||||
#
|
||||
# All modifications and additions to the file contributed by third parties
|
||||
# remain the property of their copyright owners, unless otherwise agreed
|
||||
@ -18,7 +18,7 @@
|
||||
|
||||
%define sonum 2
|
||||
Name: htscodecs
|
||||
Version: 1.3.0
|
||||
Version: 1.5.0
|
||||
Release: 0
|
||||
Summary: C library for custom compression for CRAM and other formats
|
||||
License: MIT
|
||||
@ -26,8 +26,6 @@ Group: Productivity/Scientific/Other
|
||||
URL: https://github.com/samtools/htscodecs
|
||||
Source0: https://github.com/samtools/htscodecs/releases/download/v%{version}/htscodecs-%{version}.tar.gz
|
||||
Source100: baselibs.conf
|
||||
# PATCH-FIX-UPSTREAM
|
||||
Patch0: https://github.com/samtools/htscodecs/commit/843d4f63b1c64905881b4648916a4d027baa1a1c.patch#/fix_ix86_build.patch
|
||||
BuildRequires: autoconf
|
||||
BuildRequires: gcc-c++
|
||||
BuildRequires: pkgconfig
|
||||
@ -64,8 +62,6 @@ Header files and libraries of the samtools project for compiling against %{name}
|
||||
%autosetup -p1
|
||||
|
||||
%build
|
||||
# Rebuild configure script after Patch0
|
||||
autoconf
|
||||
%configure --disable-static
|
||||
%make_build
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user