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<h3>

Shane Snyder pushed to branch dev-no-mpi

at <a href="https://xgitlab.cels.anl.gov/darshan/darshan">darshan / darshan</a>

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<h4>

Commits:

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<ul>

<li>

<strong><a href="https://xgitlab.cels.anl.gov/darshan/darshan/commit/2d3f980d516bf52a3edf87671f6ddfb9f5962801">2d3f980d</a></strong>

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<span>by Shane Snyder</span>

<i>at 2019-12-10T18:00:52Z</i>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update darshan-runtime doc to reflect non-mpi work

</pre>

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<h4>1 changed file:</h4>

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<a href="#c1f1275094e9957965ea40cf5852335b4164fd05">

darshan-runtime/doc/darshan-runtime.txt

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<h4>Changes:</h4>

<li id="c1f1275094e9957965ea40cf5852335b4164fd05">

<a href="https://xgitlab.cels.anl.gov/darshan/darshan/commit/2d3f980d516bf52a3edf87671f6ddfb9f5962801#c1f1275094e9957965ea40cf5852335b4164fd05"><strong>darshan-runtime/doc/darshan-runtime.txt</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">@@ -13,12 +13,19 @@ application that has been instrumented with Darshan will produce a single</td>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">log file each time it is executed.  This log summarizes the I/O access patterns</span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">used by the application.</span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">The darshan-runtime instrumentation only instruments MPI applications (the</span>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">application must at least call `MPI_Init()` and `MPI_Finalize()`).  However,</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">it captures both MPI-IO and POSIX file access.  It also captures limited</span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">information about HDF5 and PnetCDF access. Darshan also exposes an API that</span>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">can be used to develop and add new instrumentation modules (for other I/O library</span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">interfaces or to gather system-specific data, for instance), as detailed in</span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">The darshan-runtime instrumentation has traditionally only supported MPI</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">applications (specifically, those that call `MPI_Init()` and `MPI_Finalize()`),</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">but, as of version 3.2.0, Darshan also supports instrumentation of non-MPI</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">applications. Regardless of whether MPI is used, Darshan provides detailed</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">statistics about POSIX level file accesses made by the application.</span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">In the case of MPI applications, Darshan additionally captures detals on MPI-IO</span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">level access, as well as limited information about HDF5 and PnetCDF access.</span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Note that instrumentation of non-MPI applications is currently only supported</span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">in Darshan's shared library, which applications must `LD_PRELOAD`.</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Starting in version 3.0.0, Darshan also exposes an API that can be used to develop</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">and add new instrumentation modules (for other I/O library interfaces or to gather</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">system-specific data, for instance), as detailed in</span>

</pre>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">http://www.mcs.anl.gov/research/projects/darshan/docs/darshan-modularization.html[this document].</span>

</pre>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Newly contributed modules include a module for gathering system-specific parameters</span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">for jobs running on BG/Q systems, a module for gathering Lustre striping data for</span>

</pre>

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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">@@ -42,12 +49,12 @@ http://www.mcs.anl.gov/darshan[Darshan web site].</td>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">== Requirements</span>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">* <span class="idiff left right">MPI C compiler</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">* <span class="idiff left right">C compiler (preferrably GCC-compatible)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">* zlib development headers and library</span>

</pre>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">== Compilation</span>

</pre>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">.Configure and build example</span>

</pre>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.Configure and build example<span class="idiff left right"> (with MPI support)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">----</span>

</pre>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">tar -xvzf darshan-<version-number>.tar.gz</span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">cd darshan-<version-number>/darshan-runtime</span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="63" 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">@@ -56,6 +63,15 @@ make</td>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">make install</span>

</pre>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">----</span>

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<td class="diff-line-num old_line" data-linenumber="58" 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">

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>

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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.Configure and build example (without MPI support)</span>

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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">----</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">tar -xvzf darshan-<version-number>.tar.gz</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">cd darshan-<version-number>/darshan-runtime</span>

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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">./configure --with-mem-align=8 --with-log-path=/darshan-logs --with-jobid-env=PBS_JOBID --without-mpi CC=gcc</span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">make</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">make install</span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">----</span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="75" 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">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">.Explanation of configure arguments:</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="76" 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">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">* `--with-mem-align=` (mandatory): This value is system-dependent and will be</span>

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<td class="diff-line-num old_line" data-linenumber="61" 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">

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<td class="diff-line-num new_line" data-linenumber="77" 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">

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext">used by Darshan to determine if the buffer for a read or write operation is</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="77" 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="93" 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">@@ -77,7 +93,9 @@ file.  See `./configure --help` for details.</td>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">active Darshan instrumentation modules can collectively consume.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">* `--with-zlib=`: specifies an alternate location for the zlib development</span>

</pre>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">header and library.</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="80" 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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<td class="diff-line-num new_line old" data-linenumber="96" 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="LC80" class="line" lang="plaintext">* `CC=`: specifies the MPI C compiler to use for compilation.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">* `CC=`: specifies the C compiler to use for compilation.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">* `--without-mpi`: disables MPI support when building Darshan - MPI support is</span>

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">assumed if not specified.</span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">* `--enable-mmap-logs`: enables the use of Darshan's mmap log file mechanism.</span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">* `--disable-cuserid`: disables use of cuserid() at runtime.</span>

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<td class="diff-line-num new_line" data-linenumber="101" 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">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">* `--disable-ld-preload`: disables building of the Darshan LD_PRELOAD library</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">@@ -147,22 +165,22 @@ administrators group</td>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext">=== Instrumentation method</span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext">The instrumentation method to use depends on whether the executables</span>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext">produced by your <span class="idiff left right">MPI </span>compiler are statically or dynamically linked.  If you</span>

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">produced by your compiler are statically or dynamically linked.  If you</span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext">are unsure, you can check by running `ldd <executable_name>` on an example</span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext">executable.  Dynamically-linked executables will produce a list of shared</span>

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<td class="diff-line-num new_line" data-linenumber="171" 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">

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext">libraries when this command is executed.</span>

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<td class="diff-line-num new_line" data-linenumber="172" 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">

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="155" 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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<td class="diff-line-num new_line old" data-linenumber="173" 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="LC155" class="line" lang="plaintext"><span class="idiff left right">Most MPI</span> compilers allow you to toggle dynamic or static linking via options</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="173" 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="LC156" class="line" lang="plaintext">such as `-dynamic` or `-static`.  Please check your <span class="idiff left right">MPI </span>compiler man page</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"><span class="idiff left right">Some</span> compilers allow you to toggle dynamic or static linking via options</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">such as `-dynamic` or `-static`.  Please check your compiler man page</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="175" 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">

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext">for details if you intend to force one mode or the other.</span>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="177" 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="LC159" class="line" lang="plaintext">== Instrumenting statically-linked applications</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">== Instrumenting statically-linked <span class="idiff left right">MPI </span>applications</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" 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">

160

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<td class="diff-line-num new_line" data-linenumber="178" 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">

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" 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">

161

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<td class="diff-line-num new_line" data-linenumber="179" 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">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext">Statically linked executables must be instrumented at compile time.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="162" 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">

162

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<td class="diff-line-num new_line" data-linenumber="180" 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">

180

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="plaintext">The simplest methods to do this are to either generate a customized</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="163" 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">

163

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<td class="diff-line-num new_line" data-linenumber="181" 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">

181

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext">MPI compiler script (e.g. `mpicc`) that includes the link options and</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="164" 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">

164

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<td class="diff-line-num new_line" data-linenumber="182" 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">

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">libraries needed by Darshan, or to use existing profiling configuration</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" 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">

165

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<td class="diff-line-num new_line old" data-linenumber="183" 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="LC165" class="line" lang="plaintext">hooks for <span class="idiff left right">existing </span>MPI compiler scripts.  Once this is done, Darshan</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">hooks for MPI compiler scripts.  Once this is done, Darshan</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" 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">

166

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<td class="diff-line-num new_line" data-linenumber="184" 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">

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="plaintext">instrumentation is transparent; you simply compile applications using</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="167" 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">

167

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<td class="diff-line-num new_line" data-linenumber="185" 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">

185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext">the darshan-enabled MPI compiler scripts.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="168" 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">

168

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<td class="diff-line-num new_line" data-linenumber="186" 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">

186

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" 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="242" 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">@@ -224,9 +242,9 @@ add the necessary link options and libraries.  Please see the</td>

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<td class="diff-line-num old_line" data-linenumber="224" 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">

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<td class="diff-line-num new_line" data-linenumber="242" 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">

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="plaintext">`darshan-gen-*` scripts for examples or contact the Darshan users mailing</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="225" 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">

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<td class="diff-line-num new_line" data-linenumber="243" 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">

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="plaintext">list for help.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="226" 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">

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<td class="diff-line-num new_line" data-linenumber="244" 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">

244

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="227" 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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<td class="diff-line-num new_line old" data-linenumber="245" 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="LC227" class="line" lang="plaintext">== Instrumenting dynamically-linked applications</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">== Instrumenting dynamically-linked <span class="idiff left right">MPI </span>applications</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="228" 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">

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<td class="diff-line-num new_line" data-linenumber="246" 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">

246

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="229" 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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<td class="diff-line-num new_line old" data-linenumber="247" 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="LC229" class="line" lang="plaintext">For dynamically-linked executables, <span class="idiff left right">d</span>arshan relies on the `LD_PRELOAD`</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">For dynamically-linked executables, <span class="idiff left right">D</span>arshan relies on the `LD_PRELOAD`</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="230" 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">

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<td class="diff-line-num new_line" data-linenumber="248" 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">

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext">environment variable to insert instrumentation at run time.  The executables</span>

</pre>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext">should be compiled using the normal, unmodified MPI compiler.</span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"></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">@@ -245,7 +263,7 @@ mpiexec -n 4 -env LD_PRELOAD /home/carns/darshan-install/lib/libdarshan.so mpi-i</td>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext">srun -n 4 --export=LD_PRELOAD=/home/carns/darshan-install/lib/libdarshan.so mpi-io-test</span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext">----</span>

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<td class="diff-line-num old_line" data-linenumber="247" 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">

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="plaintext">For sequential programs, the following will set LD_PRELOAD for process duration only:</span>

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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">For sequential <span class="idiff left right">invocations of MPI </span>programs, the following will set LD_PRELOAD for process duration only:</span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext">----</span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="plaintext">env LD_PRELOAD=/home/carns/darshan-install/lib/libdarshan.so mpi-io-test</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">@@ -288,6 +306,35 @@ exclusively by the executable itself.  You can check the rpath of the</td>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="plaintext">darshan library by running `objdump -x</span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="plaintext">/home/carns/darshan-install/lib/libdarshan.so |grep RPATH`.</span>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">== Instrumenting dynamically-linked non-MPI applications</span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">Similar to the process described in the previous section, Darshan relies on the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">`LD_PRELOAD` mechanism for instrumenting dynamically-linked non-MPI applications.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">This allows Darshan to instrument dynamically-linked binaries produced by non-MPI</span>

</pre>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">compilers (e.g., gcc or clang), extending Darshan instrumentation to new contexts</span>

</pre>

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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">(like instrumentation of arbitrary Python programs or instrumenting serial</span>

</pre>

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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">file transfer utilities like `cp` and `scp`).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">The only additional step required of Darshan non-MPI users is to also set the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">DARSHAN_ENABLE_NONMPI environment variable to signal to Darshan that non-MPI</span>

</pre>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">instrumentation is requested:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">----</span>

</pre>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">export DARSHAN_ENABLE_NONMPI=1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">----</span>

</pre>

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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">As described in the previous section, it may be desirable to users to limit the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">scope of Darshan's instrumentation by only enabling LD_PRELOAD on the target</span>

</pre>

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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">executable:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">----</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">env LD_PRELOAD=/home/carns/darshan-install/lib/libdarshan.so io-test</span>

</pre>

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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">----</span>

</pre>

</td>

</tr>

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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">[NOTE]</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="335" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">Recall that Darshan instrumentation of non-MPI applications is only possible with </span>

</pre>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">dynamically-linked applications.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="plaintext">== Darshan installation recipes</span>

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<td class="diff-line-num old_line" data-linenumber="292" 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">

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="plaintext">The following recipes provide examples for prominent HPC systems.</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="557" 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="604" 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">@@ -557,6 +604,7 @@ behavior at runtime:</td>

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="plaintext">* DARSHAN_MMAP_LOGPATH: if Darshan's mmap log file mechanism is enabled, this variable specifies what path the mmap log files should be stored in (if not specified, log files will be stored in `/tmp`).</span>

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<td class="diff-line-num new_line" data-linenumber="605" 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">

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="plaintext">* DARSHAN_EXCLUDE_DIRS: specifies a list of comma-separated paths that Darshan will not instrument at runtime (in addition to Darshan's default blacklist)</span>

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559

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<td class="diff-line-num new_line" data-linenumber="606" 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">

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<pre style="margin: 0;"> <span id="LC606" class="line" lang="plaintext">* DXT_ENABLE_IO_TRACE: setting this environment variable enables the DXT (Darshan eXtended Tracing) modules at runtime. Users can specify a numeric value for this variable to set the number of MiB to use for tracing per process; if no value is specified, Darshan will use a default value of 4 MiB.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext">* DARSHAN_ENABLE_NONMPI: setting this environment variable is required to generate Darshan logs for non-MPI applications</span>

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC609" class="line" lang="plaintext">== Debugging</span>

</pre>

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<pre style="margin: 0;"> <span id="LC610" class="line" lang="plaintext"></span>

</pre>

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