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<h3>
Shane Snyder pushed to branch master
at <a href="https://xgitlab.cels.anl.gov/darshan/darshan">darshan / darshan</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://xgitlab.cels.anl.gov/darshan/darshan/commit/d88e8161e77fca4545575206d95780f3826c94bc">d88e8161</a></strong>
<div>
<span>by Shane Snyder</span>
<i>at 2019-12-19T21:51:56Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">two darshan_core_wtime fixes
1) make sure wtime_offset is set properly when using MPI
2) fix ifdef logic to properly get wtime in all non-MPI cases
</pre>
</li>
<li>
<strong><a href="https://xgitlab.cels.anl.gov/darshan/darshan/commit/d89229b7b1c04aa4900ec7fa66e95bb678a53839">d89229b7</a></strong>
<div>
<span>by Shane Snyder</span>
<i>at 2019-12-19T21:53:22Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">bug fix for segfaults when reducing hdf5 recs
</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#4022c5f1c049da302e63f7acf3598afadfdfeb89">
darshan-runtime/lib/darshan-core.c
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<li class="file-stats">
<a href="#8db652116ee33e5969aa0dc28d53c50c7fe13a3b">
darshan-runtime/lib/darshan-hdf5.c
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<h4>Changes:</h4>
<li id="4022c5f1c049da302e63f7acf3598afadfdfeb89">
<a href="https://xgitlab.cels.anl.gov/darshan/darshan/compare/2178526ff9412090d9ed9c77de1e83f0540d51b8...d89229b7b1c04aa4900ec7fa66e95bb678a53839#4022c5f1c049da302e63f7acf3598afadfdfeb89"><strong>darshan-runtime/lib/darshan-core.c</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">@@ -279,10 +279,6 @@ void darshan_core_initialize(int argc, char **argv)</td>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">init_core</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">init_core</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">init_core</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* record absolute start time at startup so that we can later</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * generate relative times with this as a reference point.</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">init_core</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">wtime_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">darshan_core_wtime_absolute</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_MPI</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c"> <span class="n" style="color: #333;">PMPI_Initialized</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">using_mpi</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="294" 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">@@ -294,6 +290,11 @@ void darshan_core_initialize(int argc, char **argv)</td>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* record absolute start time at startup so that we can later</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * generate relative times with this as a reference point.</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="c"> <span class="n" style="color: #333;">init_core</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">wtime_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">darshan_core_wtime_absolute</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* TODO: do we alloc new memory as we go or just do everything up front? */</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef __DARSHAN_ENABLE_MMAP_LOGS</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">@@ -2352,11 +2353,11 @@ static double darshan_core_wtime_absolute(void)</td>
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<pre style="margin: 0;"> <span id="LC2353" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_MPI</span></span>
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<pre style="margin: 0;"> <span id="LC2354" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">using_mpi</span><span class="p">)</span></span>
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2355
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<pre style="margin: 0;"> <span id="LC2355" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">PMPI_Wtime</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC2355" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC2356" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2357
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<pre style="margin: 0;">+<span id="LC2357" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2358" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">timeval</span> <span class="n" style="color: #333;">tval</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2359" class="line" lang="c"> <span class="n" style="color: #333;">gettimeofday</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tval</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2360" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">tval</span><span class="p">.</span><span class="n" style="color: #333;">tv_sec</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">tval</span><span class="p">.</span><span class="n" style="color: #333;">tv_usec</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">1000000</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC2359" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC2361" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2362" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2363" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DARSHAN_PRELOAD</span></span>
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<li id="8db652116ee33e5969aa0dc28d53c50c7fe13a3b">
<a href="https://xgitlab.cels.anl.gov/darshan/darshan/compare/2178526ff9412090d9ed9c77de1e83f0540d51b8...d89229b7b1c04aa4900ec7fa66e95bb678a53839#8db652116ee33e5969aa0dc28d53c50c7fe13a3b"><strong>darshan-runtime/lib/darshan-hdf5.c</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">@@ -420,7 +420,7 @@ static void hdf5_mpi_redux(</td>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hdf5_rec_count</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">hdf5_file_record_ref</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rec_ref</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">darshan_hdf5_file</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hdf5_rec_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">darshan_hdf5_file</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span>*</span><span class="p">)</span><span class="n" style="color: #333;">hdf5_buf</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">darshan_hdf5_file</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hdf5_rec_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">darshan_hdf5_file</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">hdf5_buf</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">darshan_hdf5_file</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">red_send_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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425
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">darshan_hdf5_file</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">red_recv_buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="c"> <span class="n" style="color: #333;">MPI_Datatype</span> <span class="n" style="color: #333;">red_type</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="430" 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">@@ -430,6 +430,8 @@ static void hdf5_mpi_redux(</td>
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="c"> <span class="n" style="color: #333;">HDF5_LOCK</span><span class="p">();</span></span>
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">hdf5_runtime</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="c"> <span class="n" style="color: #333;">hdf5_rec_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hdf5_runtime</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">file_rec_count</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* necessary initialization of shared records */</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">shared_rec_count</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="c"> <span class="p">{</span></span>
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