Accepting request 1002486 from science

OBS-URL: https://build.opensuse.org/request/show/1002486
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/htscodecs?expand=0&rev=2

fix_ix86_build.patch

@@ -0,0 +1,99 @@
+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])

htscodecs-1.2.2.tar.gz

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:d17d7a505da3fc79dcced320c132c5492b5dc78ee70d9ca8218b927070f183ca
-size 3044356

htscodecs-1.3.0.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:696c0affbfa7e59276e0dfc71dcba2f04b0a6db12998f30f1baf2fc21e9113f4
+size 3368716

htscodecs.changes

@@ -1,3 +1,26 @@
+-------------------------------------------------------------------
+Thu Sep  8 21:52:47 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
+
+- Update to 1.3.0:
+  * The primary change in this release is a new SIMD enabled
+    rANS codec.
+    There is a 32-way unrolled rANS implementation. This is accessed
+    using the existing rans 4x16 API with the RANS_ORDER_X32 bit set.
+  * Improved memory allocation via a new htscodecs_tls_alloc function.
+  * Some external functions have been renamed, with the old ones
+    still existing in a deprecated fashion.
+  * Improved test framework with an "entropy" tool that iterates
+    over all entropy encoders.
+  * Reworked fuzzing infrastructure.
+  * Small speed improvements to various rANS encoders and decoders.
+  * Substantial memory reduction to the name tokeniser (tok3).
+  * Fixed undefined behaviour in our use of _builtin_clz().
+  * Fixed a few redundant #includes.
+  * Work around strict aliasing bugs, uncovered with gcc -O2.
+  * Fixed an issue with encoding data blocks close to 2GB in size.
+  * Fix encode error with large blocks using RANS_ORDER_STRIPE.
+- Add fix_ix86_build.patch
+
 -------------------------------------------------------------------
 Wed Apr 20 19:45:48 UTC 2022 - Ferdinand Thiessen <rpm@fthiessen.de>
 

htscodecs.spec

@@ -18,7 +18,7 @@
 
 %define   sonum 2
 Name:           htscodecs
-Version:        1.2.2
+Version:        1.3.0
 Release:        0
 Summary:        C library for custom compression for CRAM and other formats
 License:        MIT
@@ -26,6 +26,9 @@ 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
 BuildRequires:  pkgconfig(bzip2)
@@ -58,9 +61,11 @@ Requires:       lib%{name}%{sonum} = %{version}
 Header files and libraries of the samtools project for compiling against %{name}.
 
 %prep
-%setup -q
+%autosetup -p1
 
 %build
+# Rebuild configure script after Patch0
+autoconf
 %configure --disable-static
 %make_build
 
@@ -76,7 +81,7 @@ rm %{buildroot}%{_libdir}/lib%{name}.la
 %{_libdir}/lib%{name}.so.*
 
 %files devel
-%doc README.md NEWS
+%doc README.md NEWS.md
 %{_includedir}/htscodecs
 %{_libdir}/lib%{name}.so