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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/kalign">Debian Med / kalign</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kalign/-/commit/239226d6712d8625c1a4966c7bc9baf38cfae718">239226d6</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-03-30T13:42:50+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add simde flags
</pre>
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<strong><a href="https://salsa.debian.org/med-team/kalign/-/commit/63c805a3507636cbded1f31e3c3c115176cb6161">63c805a3</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-03-30T14:19:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Don't break the Debian architecture baseline
</pre>
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<strong><a href="https://salsa.debian.org/med-team/kalign/-/commit/33ae524ad1ec634fb8ee7b76db53c83c6f518c26">33ae524a</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-03-30T14:52:52+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix the _mm_malloc fallback
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#9005f0e55a67ca063e7cafdce75000f6d207c3c9">
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+
debian/patches/no-native-build
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2">
debian/patches/simde
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kalign/-/compare/809731ac34775a5318425402bdaa23bd61743213...33ae524ad1ec634fb8ee7b76db53c83c6f518c26#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">kalign (1:3.2.3-2) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * Add non-<span class="idiff left right">x86</span> compatability using the SIMD Everywhere library</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add non-<span class="idiff left right">AVX2</span> compatability using the SIMD Everywhere library</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 30 Mar 2020 12:13:37 +0200</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kalign/-/compare/809731ac34775a5318425402bdaa23bd61743213...33ae524ad1ec634fb8ee7b76db53c83c6f518c26#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,6 +13,7 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Package: kalign</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">#Architecture: any-amd64 any-i386</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Enhances: t-coffee,</span>
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<li id="9005f0e55a67ca063e7cafdce75000f6d207c3c9">
<a href="https://salsa.debian.org/med-team/kalign/-/compare/809731ac34775a5318425402bdaa23bd61743213...33ae524ad1ec634fb8ee7b76db53c83c6f518c26#9005f0e55a67ca063e7cafdce75000f6d207c3c9"><strong>debian/patches/no-native-build</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Description: Don't build with all the SIMD compiler flags</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">This breaks the Debian baseline</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kalign.orig/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kalign/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -16,13 +16,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> AC_CONFIG_MACRO_DIR([m4])</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-m4_include([m4/ax_ext.m4])</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> m4_include([m4/ax_valgrind_check.m4])</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> m4_include([m4/ax_check_compile_flag.m4])</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> m4_include([m4/ax_set_compile_flags.m4])</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-AX_EXT</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> AX_ENABLE_DEBUG</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> AC_ARG_ENABLE(openmp, [AC_HELP_STRING([--enable-openmp],[use OpenMP directives for parallelism])], enable_openmp=$enableval, enable_openmp=no)</span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/809731ac34775a5318425402bdaa23bd61743213...33ae524ad1ec634fb8ee7b76db53c83c6f518c26#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">simde</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">no-native-build</span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/809731ac34775a5318425402bdaa23bd61743213...33ae524ad1ec634fb8ee7b76db53c83c6f518c26#4c0e18367b4a4c2fb5a4fb13dd30c8d2df5876b2"><strong>debian/patches/simde</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,23 +13,29 @@ Description: leverage the SIMD Everywhere library</td>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> #include "pick_anchor.h"</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kalign.orig/src/bisectingKmeans.c</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kalign/src/bisectingKmeans.c</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -20,7 +20,<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -20,7 +20,<span class="idiff left right">12</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> */</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <xmmintrin.h></span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "../debian/include/simde/x86/sse.h"</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if !defined(SIMDE_SSE_NATIVE)</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #include <stdlib.h></span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #define _mm_malloc(size, align) aligned_alloc(align, size)</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #define _mm_free free</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> </span>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> #include "msa.h"</span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kalign.orig/src/bpm.c</span></span>
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kalign/src/bpm.c</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -28,15 +28,15 @@</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -27,16 +27,16 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "../debian/include/simde/x86/avx2.h"</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"> #ifdef HAVE_AVX2</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <immintrin.h></span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "../debian/include/simde/x86/avx2.h"</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-__m256i BROADCAST_MASK[16];</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+simde__m256i BROADCAST_MASK[16];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -310,7 +316,7 @@ Description: leverage the SIMD Everywhere library</td>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kalign.orig/src/euclidean_dist.c</span></span>
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kalign/src/euclidean_dist.c</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="diff"><span class="p">@@ -22,15 +22,<span class="idiff left right">15</span> @@</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="p">@@ -22,15 +22,<span class="idiff left right">20</span> @@</span></span>
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314
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="diff"> </span>
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315
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="diff"> #include "euclidean_dist.h"</span>
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316
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="diff"> #include "rng.h"</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,6 +324,11 @@ Description: leverage the SIMD Everywhere library</td>
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318
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <immintrin.h></span></span>
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319
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "../debian/include/simde/x86/sse.h"</span></span>
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320
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "../debian/include/simde/x86/avx.h"</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if !defined(SIMDE_SSE_NATIVE)</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #include <stdlib.h></span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #define _mm_malloc(size, align) aligned_alloc(align, size)</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #define _mm_free free</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="diff"> #include "float.h"</span>
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322
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="diff"> </span>
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="diff"> #include "esl_stopwatch.h"</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -330,7 +341,7 @@ Description: leverage the SIMD Everywhere library</td>
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330
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="diff"> </span>
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342
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="diff"> </span>
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332
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="diff"> #ifdef ITEST_EDIST</span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff"><span class="p">@@ -163,18 +16<span class="idiff left right">3</span>,18 @@</span></span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"><span class="p">@@ -163,18 +16<span class="idiff left right">8</span>,18 @@</span></span>
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334
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="diff"> </span>
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335
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="diff"> float d = 0.0f;</span>
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336
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="diff"> register int i;</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -357,7 +368,7 @@ Description: leverage the SIMD Everywhere library</td>
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357
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="diff"> a+=8;</span>
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358
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="diff"> b+=8;</span>
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359
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="diff"> }</span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="diff"><span class="p">@@ -187,22 +1<span class="idiff left right">87</span>,22 @@</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="p">@@ -187,22 +1<span class="idiff left right">92</span>,22 @@</span></span>
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361
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="diff"> </span>
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362
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="diff"> </span>
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363
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374
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -403,12 +414,17 @@ Description: leverage the SIMD Everywhere library</td>
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403
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="diff"> #include <stdalign.h></span>
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404
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- kalign.orig/src/sequence_distance.c</span></span>
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405
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ kalign/src/sequence_distance.c</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="diff"><span class="p">@@ -21,7 +21,<span class="idiff left right">7</span> @@</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="p">@@ -21,7 +21,<span class="idiff left right">12</span> @@</span></span>
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407
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="diff"> </span>
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408
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="diff"> */</span>
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409
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="diff"> </span>
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410
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#include <xmmintrin.h></span></span>
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411
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422
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include "../debian/include/simde/x86/sse.h"</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#if !defined(SIMDE_SSE_NATIVE)</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #include <stdlib.h></span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #define _mm_malloc(size, align) aligned_alloc(align, size)</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ #define _mm_free free</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif</span></span>
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="diff"> #include "sequence_distance.h"</span>
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413
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="diff"> </span>
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414
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="diff"> #include "alphabet.h"</span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/compare/809731ac34775a5318425402bdaa23bd61743213...33ae524ad1ec634fb8ee7b76db53c83c6f518c26#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,8 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># -*- makefile -*-</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Build rules for the Debian package kalign</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_CFLAGS_MAINT_APPEND</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-DSIMDE_ENABLE_OPENMP</span> <span class="nt" style="color: #000080;">-fopenmp-simd</span> <span class="nt" style="color: #000080;">-O3</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_CXXFLAGS_MAINT_APPEND</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-DSIMDE_ENABLE_OPENMP</span> <span class="nt" style="color: #000080;">-fopenmp-simd</span> <span class="nt" style="color: #000080;">-O3</span></span>
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5
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="k" style="font-weight: 600;">export </span><span class="nv" style="color: #008080;">DEB_BUILD_MAINT_OPTIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">hardening</span><span class="o" style="font-weight: 600;">=</span>+all</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span></span>
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