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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/libmmmulti">Debian Med / libmmmulti</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libmmmulti/-/commit/08ff8a7dde81f56e3e024b9d49dbf252b810b4c5">08ff8a7d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-26T18:52:18+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Link Dynamically
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libmmmulti/-/commit/360638594a1921b4dc75fd68a5249d6f774997cf">36063859</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-26T18:52:40+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modify Install file
On a look at it, all code actually resides in the "header files" - the
main.cpp just contains a main function which is basically the logic for
the mmmulti binary.
The header files do _not_ seem to be used in the standard way wherein
headers contains mostly the prototypes and the corresponding c/cpp files
contain the definitions and declarations. This is also apparent by the
this package's documentation.
Hence it might be a good idea to simply make it header only (plus installing
corresponding binary) and use it in a way that it's intended to.
That being said, what I did there might be _completely wrong_ consider to revert
this commit if so
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#a050623b065e4fd7f5e1cf1c1ec57af275a12d85">
debian/libmmmulti-dev.install
</a>
</li>
<li class="file-stats">
<a href="#6bb62a224290905eab9f79430adb48a7c2fc02f3">
<span class="deleted-file">
−
debian/libmmmulti0.dirs
</span>
</a>
</li>
<li class="file-stats">
<a href="#a45836bf032785589b1073cf78ed896fc501ab4f">
<span class="deleted-file">
−
debian/libmmmulti0.install
</span>
</a>
</li>
<li class="file-stats">
<a href="#1ed521584073489bddc0c35f4e1e4df0dca25049">
<span class="deleted-file">
−
debian/mmmulti-dev.dirs
</span>
</a>
</li>
<li class="file-stats">
<a href="#0dbdfa862738a5fe0673d7cbcc4cb26aad2a2a7c">
debian/patches/NoExternalSourceTrees.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libmmmulti/-/compare/c2a7285114b8709ec4a76734b9b9543c817581b2...360638594a1921b4dc75fd68a5249d6f774997cf#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="51" 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">@@ -51,34 +51,3 @@ Description: header files for mmmulti library</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> we are virtually guaranteed to be able to complete the compute.</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> This package contains header files and the static library</span></pre>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">Package: libmmmulti0</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">Description: memory-mapped multimap, multiset, and interval tree</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"> Sometimes you have a lot of plain-old data, but you need random access</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> to it. These header-only classes combine memory-mapped files with</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"> high-performance parallel sorting and appropriate indexing strategies</span>
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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> to support very large (>memory but <disk) multimaps, multisets, and</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> interval trees.</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> This implements a memory backed multimap intended for use where:</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"> * your keys are integers, or can be mapped to dense range of integers,</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> * the memory mapped file is on fast storage, like an SSD (although</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> this is not a requirement),</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"> * you have arbitrary values of fixed size (e.g. structs, other POD</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> types) that can be sorted,</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> * you don't need dynamic updates of the table,</span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"> * and you are likely to run out of memory of you use a traditional</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> map or hash table,</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"> * but you can handle approximately 1 bit per record in RAM.</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> .</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> These may seem to be very specific, but many problems can be mapped into</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> a dense integer set. mmmulti::map developed first as a data structure</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> to support seqwish, which uses it to generate precise variation graphs</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> from pairwise alignments between collections of sequences. As this</span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> multimap forms a key data processing kernel in the algorithm, it can</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext"> scale to extremely large problem sizes, limited only by available disk</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"> space. Although performance is much slower than an in-memory structure,</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"> we are virtually guaranteed to be able to complete the compute.</span></pre>
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<a href="https://salsa.debian.org/med-team/libmmmulti/-/compare/c2a7285114b8709ec4a76734b9b9543c817581b2...360638594a1921b4dc75fd68a5249d6f774997cf#a050623b065e4fd7f5e1cf1c1ec57af275a12d85"><strong>debian/libmmmulti-dev.install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="php"><span class="cm" style="color: #998; font-style: italic;">usr/lib/*/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">*.</span><span class="n" style="color: #333;">so</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/*/</span><span class="n" style="color: #333;">pkgconfig</span><span class="o" style="font-weight: 600;">/*</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">pkgconfig</span><span class="o" style="font-weight: 600;">/*</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">src</span><span class="o" style="font-weight: 600;">/*.</span><span class="n" style="color: #333;">hpp</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="k" style="font-weight: 600;">include</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libmmmulti/-/compare/c2a7285114b8709ec4a76734b9b9543c817581b2...360638594a1921b4dc75fd68a5249d6f774997cf#6bb62a224290905eab9f79430adb48a7c2fc02f3"><strong>debian/libmmmulti0.dirs</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/lib</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/*/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">*.</span><span class="n" style="color: #333;">so</span><span class="mf" style="color: #099;">.</span><span class="o" style="font-weight: 600;">*</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/lib</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">usr/include</span></pre>
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<li id="0dbdfa862738a5fe0673d7cbcc4cb26aad2a2a7c">
<a href="https://salsa.debian.org/med-team/libmmmulti/-/compare/c2a7285114b8709ec4a76734b9b9543c817581b2...360638594a1921b4dc75fd68a5249d6f774997cf#0dbdfa862738a5fe0673d7cbcc4cb26aad2a2a7c"><strong>debian/patches/NoExternalSourceTrees.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/CMakeLists.txt</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">@@ -22,110 +22,22 @@</span> set(LIBRARY_OUTPUT_PATH ${CMAKE_SOURCE_D</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -11,8 +11,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> find_package(Threads REQUIRED)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> # Use all standard-compliant optimizations</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -mcx16 -g")</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -mcx16 -g")</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -g -fPIC -fopenmp")</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;">+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -g -fPIC -fopenmp")</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> # Set the output folder where your program will be created</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> set(CMAKE_BINARY_DIR ${CMAKE_SOURCE_DIR}/bin)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -22,110 +22,22 @@</span></span>
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4
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> # The following folder will be included</span>
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5
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> include_directories("${PROJECT_SOURCE_DIR}")</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" 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="130" 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">@@ -119,7 +130,7 @@</td>
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119
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> </span>
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120
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"> # macOS doesn't want you to link in libatomic this way</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")</span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="p">@@ -137,9 +49,9 @@</span><span class="idiff left right"> if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -137,9 +49,9 @@</span></span>
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123
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="diff"> )</span>
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124
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="diff"> elseif (TRUE)</span>
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125
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> target_link_libraries(mmmulti</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" 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="143" 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">@@ -132,3 +143,12 @@</td>
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132
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="diff"> "-latomic"</span>
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133
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> Threads::Threads</span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="p">@@ -150,7 +62,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> elseif (TRUE)</span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> # this was hard to track down</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> # https://stackoverflow.com/questions/35116327/when-g-static-link-pthread-cause-segmentation-fault-why</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- set(CMAKE_EXE_LINKER_FLAGS "-static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive")</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ set (CMAKE_SHARED_LINKER_FLAGS "-lpthread -Wl,--as-needed")</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> endif()</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> </span></pre>
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