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<h3>
Philip Carns pushed to branch carns/dev-dyn-link-updates
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/fd47cee438040d0ced86bc11ea67e0b1780592b1">fd47cee4</a></strong>
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<span>by Phil Carns</span>
<i>at 2020-03-25T17:13:29-04:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add mpich recipe back in, fix misc spelling
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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/fd47cee438040d0ced86bc11ea67e0b1780592b1#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">@@ -17,7 +17,7 @@ applications (specifically, those that call `MPI_Init()` and `MPI_Finalize()`),</td>
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<pre style="margin: 0;"> <span id="LC17" 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="LC18" 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="LC19" 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="LC20" 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="LC20" class="line" lang="plaintext">In the case of MPI applications, Darshan additionally captures deta<span class="idiff left right">i</span>ls on MPI-IO</span>
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<pre style="margin: 0;"> <span id="LC21" 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="LC22" 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="LC23" class="line" lang="plaintext">in Darshan's shared library, which applications must `LD_PRELOAD`.</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="48" 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">@@ -48,7 +48,7 @@ http://www.mcs.anl.gov/darshan[Darshan web site].</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">== Requirements</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">* C compiler (prefer<span class="idiff left right">r</span>ably GCC-compatible)</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">* C compiler (preferably GCC-compatible)</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">* zlib development headers and library</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">== Compilation</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">@@ -205,7 +205,7 @@ darshan-config --dyn-ld-flags</td>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext"># linker options to use for static linking</span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext"># The first set of arguments should go early in the link command line</span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext"># (before MPI, while the second set should go at the end <span class="idiff left right">fo</span> the link command</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"># (before MPI, while the second set should go at the end <span class="idiff left right">of</span> the link command</span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext"># line</span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext">darshan-config --pre-ld-flags</span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">darshan-config --post-ld-flags</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">@@ -244,7 +244,7 @@ you need examples for static linking.</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="plaintext">=== Option 2: Instrumenting MPI applications at run time</span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext">This method is applicable to pre-compiled dynamically linked executables</span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="plaintext">as well as interpret<span class="idiff left right">t</span>ed languages such as Python. You do not need to</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">as well as interpreted languages such as Python. You do not need to</span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext">change your compile options in any way. This method works by injecting</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="plaintext">instrumentation at run time. It will not work for statically linked</span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext">executables.</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">@@ -340,7 +340,7 @@ export DXT_ENABLE_IO_TRACE=1</td>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="plaintext">----</span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="plaintext">To enable tracing for particular files, DXT additionally offers a trace</span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="plaintext">triggering mechan<span class="idiff left right">si</span>m, with users specifying triggers used to decide whether or</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">triggering mechan<span class="idiff left right">is</span>m, with users specifying triggers used to decide whether or</span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="plaintext">not to trace a particular file at runtime. Files that do not match any trace</span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="plaintext">trigger will not store trace data in the Darshan log. Currently, DXT supports</span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="plaintext">the following types of trace triggers:</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">@@ -351,7 +351,7 @@ the following types of trace triggers:</td>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="plaintext">Users simply need to specify one or more of these triggers in a text file that is passed</span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="plaintext">to DXT at runtime -- when multiple triggers are specified, DXT will keep any file traces</span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="plaintext">that match at least one trigger (i.e., the trace decision is a logical OR ac<span class="idiff left right">c</span>ross given triggers).</span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">that match at least one trigger (i.e., the trace decision is a logical OR across given triggers).</span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext">An example configuration file is given below, illustrating the syntax to use for currently</span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext">supported triggers:</span>
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<pre style="margin: 0;"> <span id="LC357" 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">@@ -475,6 +475,28 @@ module use /soft/darshan-2.2.3/share/craype-<VERSION>/modulefiles</td>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="plaintext">From this point, Darshan instrumenation can be enabled for all future</span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="plaintext">application compilations by running "module load darshan".</span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext">=== Linux clusters using MPICH</span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext">Most Intel MPI installations produce dynamic executables by default. To</span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext">configure Darshan in this environment you can use the following example:</span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext"></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext">----</span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext">./configure --with-log-path=/darshan-logs --with-jobid-env=PBS_JOBID CC=mpicc</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext">----</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext"></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext">.Rationale</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext">[NOTE]</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext">====</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">There is nothing unusual in this configuration except that you should use</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext">the underlying GNU compilers rather than the Intel ICC compilers to compile</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext">Darshan itself.</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext">====</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext">We recommend using the darshan-gen-* script described earlier in this</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext">document to create variants of the standard mpicc/mpicxx/mpif77/mpif90</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext">scipts that are Darshan enabled. These scripts will work correctly for both</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext">dynamic and statically linked executables.</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext"></span>
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478
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500
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="plaintext">=== Linux clusters using Intel MPI</span>
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501
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="plaintext"></span>
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="plaintext">Most Intel MPI installations produce dynamic executables by default. To</span>
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