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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/bio-eagle">Debian Med / bio-eagle</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/bio-eagle/-/commit/bb3394a255475c84dc76e6babd76c269b1fbb79e">bb3394a2</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-12-05T21:49:16+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add patch for compilation on systems without SSE.
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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debian/patches/non_x86_malloc
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bio-eagle/-/commit/bb3394a255475c84dc76e6babd76c269b1fbb79e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">bio-eagle (2.4.1-3) 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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Add patch for compilation on systems without SSE.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Use of "rdtsc" assembly still makes it x86 specific.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Sat, 05 Dec 2020 16:58:11 +0100</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">bio-eagle (2.4.1-2) unstable; urgency=medium</span>
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<li id="1a0e2a73dd3553e604656f9ea96e8364b81a367e">
<a href="https://salsa.debian.org/med-team/bio-eagle/-/commit/bb3394a255475c84dc76e6babd76c269b1fbb79e#1a0e2a73dd3553e604656f9ea96e8364b81a367e"><strong>debian/patches/non_x86_malloc</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: allow compilation on non-x86</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bio-eagle.orig/src/MemoryUtils.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bio-eagle/src/MemoryUtils.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -25,8 +25,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> void *ALIGNED_MALLOC(uint64 size) {</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> #ifdef USE_MKL_MALLOC</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> void *p = mkl_malloc(size, MEM_ALIGNMENT);</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__SSE__)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> void *p = _mm_malloc(size, MEM_ALIGNMENT);</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <stdlib.h></span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ void *p = aligned_alloc(MEM_ALIGNMENT, size);</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> // TODO: change to assert() or dispense with altogether and change ALIGNED_MALLOC to macro?</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> if (p == NULL) {</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- bio-eagle.orig/src/MemoryUtils.hpp</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ bio-eagle/src/MemoryUtils.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -30,9 +30,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> #ifdef USE_MKL_MALLOC</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> #include <mkl.h></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> #define ALIGNED_FREE mkl_free</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#else</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#elif defined(__SSE__)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> #include <xmmintrin.h></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> #define ALIGNED_FREE _mm_free</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#else</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define ALIGNED_FREE free</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> #endif</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> #define ALIGNED_MALLOC_DOUBLES(numDoubles) (double *) ALIGNED_MALLOC((numDoubles)*sizeof(double))</span></pre>
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<a href="https://salsa.debian.org/med-team/bio-eagle/-/commit/bb3394a255475c84dc76e6babd76c269b1fbb79e#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Makefile_config.patch</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">non_x86_malloc</span></pre>
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