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<h1><span class="section-number">12.6. </span>Using Memchecker<a class="headerlink" href="#using-memchecker" title="Permalink to this heading"></a></h1>
<p>The Memchecker functionality in Open MPI provides MPI semantic
checking for your application (as well as internals of Open MPI), with
the help of memory checking tools such as the <code class="docutils literal notranslate"><span class="pre">memcheck</span></code> component of
<a class="reference external" href="https://www.valgrind.org/">the Valgrind suite</a>.</p>
<hr class="docutils" />
<div class="section" id="types-of-errors-detected-by-memchecker">
<h2><span class="section-number">12.6.1. </span>Types of Errors Detected by Memchecker<a class="headerlink" href="#types-of-errors-detected-by-memchecker" title="Permalink to this heading"></a></h2>
<p>Open MPI’s Memchecker is based on the <code class="docutils literal notranslate"><span class="pre">memcheck</span></code> tool included with
Valgrind, so it takes all the advantages from it. Firstly, it checks
all reads and writes of memory, and intercepts calls to
<code class="docutils literal notranslate"><span class="pre">malloc(3)</span></code>/<code class="docutils literal notranslate"><span class="pre">free(3)</span></code> and C++’s <code class="docutils literal notranslate"><span class="pre">new</span></code>/<code class="docutils literal notranslate"><span class="pre">delete</span></code> operators.
Most importantly, Memchecker is able to detect
the user buffer errors in both non-blocking and one-sided
communications, e.g. reading or writing to buffers of active
non-blocking receive operations and writing to buffers of active
non-blocking send operations.</p>
<p>Here are some example problems that Memchecker can detect:</p>
<p>Accessing buffer under control of non-blocking communication:</p>
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="kt">int</span><span class="w"> </span><span class="n">buf</span><span class="p">;</span>
<span class="n">MPI_Irecv</span><span class="p">(</span><span class="o">&</span><span class="n">buf</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_INT</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span><span class="w"> </span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_COMM_WORLD</span><span class="p">,</span><span class="w"> </span><span class="o">&</span><span class="n">req</span><span class="p">);</span>
<span class="c1">// The following line will produce a memchecker warning</span>
<span class="n">buf</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">4711</span><span class="p">;</span>
<span class="n">MPI_Wait</span><span class="w"> </span><span class="p">(</span><span class="o">&</span><span class="n">req</span><span class="p">,</span><span class="w"> </span><span class="o">&</span><span class="n">status</span><span class="p">);</span>
</pre></div>
</div>
<p>Wrong input parameters, e.g., wrong-sized send buffers:</p>
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="kt">char</span><span class="w"> </span><span class="o">*</span><span class="n">send_buffer</span><span class="p">;</span>
<span class="n">send_buffer</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">malloc</span><span class="p">(</span><span class="mi">5</span><span class="p">);</span>
<span class="n">memset</span><span class="p">(</span><span class="n">send_buffer</span><span class="p">,</span><span class="w"> </span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="mi">5</span><span class="p">);</span>
<span class="c1">// The following line will produce a memchecker warning</span>
<span class="n">MPI_Send</span><span class="p">(</span><span class="n">send_buffer</span><span class="p">,</span><span class="w"> </span><span class="mi">10</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_CHAR</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span><span class="w"> </span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_COMM_WORLD</span><span class="p">);</span>
</pre></div>
</div>
<p>Accessing a window in a one-sided communication:</p>
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="n">MPI_Get</span><span class="p">(</span><span class="n">A</span><span class="p">,</span><span class="w"> </span><span class="mi">10</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_INT</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span><span class="w"> </span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_INT</span><span class="p">,</span><span class="w"> </span><span class="n">win</span><span class="p">);</span>
<span class="n">A</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">4711</span><span class="p">;</span>
<span class="n">MPI_Win_fence</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="n">win</span><span class="p">);</span>
</pre></div>
</div>
<p>Uninitialized input buffers:</p>
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="kt">char</span><span class="w"> </span><span class="o">*</span><span class="n">buffer</span><span class="p">;</span>
<span class="n">buffer</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">malloc</span><span class="p">(</span><span class="mi">10</span><span class="p">);</span>
<span class="c1">// The following line will produce a memchecker warning</span>
<span class="n">MPI_Send</span><span class="p">(</span><span class="n">buffer</span><span class="p">,</span><span class="w"> </span><span class="mi">10</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_INT</span><span class="p">,</span><span class="w"> </span><span class="mi">1</span><span class="p">,</span><span class="w"> </span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_COMM_WORLD</span><span class="p">);</span>
</pre></div>
</div>
<p>Usage of the uninitialized <code class="docutils literal notranslate"><span class="pre">MPI_Status</span></code> field in <code class="docutils literal notranslate"><span class="pre">MPI_ERROR</span></code>
structure: (the MPI-1 standard defines the <code class="docutils literal notranslate"><span class="pre">MPI</span> <span class="pre">ERROR</span></code> field to be
undefined for single-completion calls such as <a class="reference internal" href="../man-openmpi/man3/MPI_Wait.3.html#mpi-wait"><span class="std std-ref">MPI_Wait(3)</span></a> or
<a class="reference internal" href="../man-openmpi/man3/MPI_Test.3.html#mpi-test"><span class="std std-ref">MPI_Test(3)</span></a>, see MPI-1 p. 22):</p>
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="n">MPI_Wait</span><span class="p">(</span><span class="o">&</span><span class="n">request</span><span class="p">,</span><span class="w"> </span><span class="o">&</span><span class="n">status</span><span class="p">);</span>
<span class="c1">// The following line will produce a memchecker warning</span>
<span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">status</span><span class="p">.</span><span class="n">MPI_ERROR</span><span class="w"> </span><span class="o">!=</span><span class="w"> </span><span class="n">MPI_SUCCESS</span><span class="p">)</span>
<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="n">ERROR</span><span class="p">;</span>
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="building-open-mpi-with-memchecker-support">
<h2><span class="section-number">12.6.2. </span>Building Open MPI with Memchecker Support<a class="headerlink" href="#building-open-mpi-with-memchecker-support" title="Permalink to this heading"></a></h2>
<p>To use Memchecker, you need Valgrind 3.2.0 or later, and have an Open
MPI that was configured with the <code class="docutils literal notranslate"><span class="pre">--enable-memchecker</span></code> and
<code class="docutils literal notranslate"><span class="pre">--enable-debug</span></code> flags.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The Memchecker functionality is off by default, because it
incurs a performance penalty.</p>
</div>
<p>When <code class="docutils literal notranslate"><span class="pre">--enable-memchecker</span></code> is specified, <code class="docutils literal notranslate"><span class="pre">configure</span></code> will check
for a recent-enable valgrind distribution. If found, Open MPI will
build Memchecker support.</p>
<p>For example:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>shell$<span class="w"> </span>./configure<span class="w"> </span>--prefix<span class="o">=</span>/path/to/openmpi<span class="w"> </span>--enable-debug<span class="w"> </span><span class="se">\</span>
<span class="w"> </span>--enable-memchecker<span class="w"> </span>--with-valgrind<span class="o">=</span>/path/to/valgrind
</pre></div>
</div>
<p>You can check that Open MPI was built with Memchecker support by using
the <a class="reference internal" href="../man-openmpi/man1/ompi_info.1.html#man1-ompi-info"><span class="std std-ref">ompi_info(1)</span></a> command.</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span><span class="c1"># The exact version numbers shown may be different for your Open</span>
<span class="c1"># MPI installation</span>
shell$<span class="w"> </span>ompi_info<span class="w"> </span><span class="p">|</span><span class="w"> </span>grep<span class="w"> </span>memchecker
MCA<span class="w"> </span>memchecker:<span class="w"> </span>valgrind<span class="w"> </span><span class="o">(</span>MCA<span class="w"> </span>v1.0,<span class="w"> </span>API<span class="w"> </span>v1.0,<span class="w"> </span>Component<span class="w"> </span>v1.3<span class="o">)</span>
</pre></div>
</div>
<p>If you do not see the “MCA memchecker: valgrind” line, you probably
did not configure and install Open MPI correctly.</p>
</div>
<hr class="docutils" />
<div class="section" id="running-an-open-mpi-application-with-memchecker">
<h2><span class="section-number">12.6.3. </span>Running an Open MPI Application with Memchecker<a class="headerlink" href="#running-an-open-mpi-application-with-memchecker" title="Permalink to this heading"></a></h2>
<p>After Open MPI was built and installed with Memchecker support,
simply run your application with Valgrind, e.g.:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>shell$<span class="w"> </span>mpirun<span class="w"> </span>-n<span class="w"> </span><span class="m">2</span><span class="w"> </span>valgrind<span class="w"> </span>./my_app
</pre></div>
</div>
<p>If you enabled Memchecker, but you don’t want to check the
application at this time, then just run your application as
usual. E.g.:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>shell$<span class="w"> </span>mpirun<span class="w"> </span>-n<span class="w"> </span><span class="m">2</span><span class="w"> </span>./my_app
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="application-performance-impacts-using-memchecker">
<h2><span class="section-number">12.6.4. </span>Application Performance Impacts Using Memchecker<a class="headerlink" href="#application-performance-impacts-using-memchecker" title="Permalink to this heading"></a></h2>
<p>The configure option <code class="docutils literal notranslate"><span class="pre">--enable-memchecker</span></code> (together with
<code class="docutils literal notranslate"><span class="pre">--enable-debug</span></code>) <em>does</em> cause performance degradation, even if not
running under Valgrind. The following explains the mechanism and may
help in making the decision whether to provide a cluster-wide
installation with <code class="docutils literal notranslate"><span class="pre">--enable-memchecker</span></code>.</p>
<p>There are two cases:</p>
<ol class="arabic">
<li><p>If run without Valgrind, the Valgrind ClientRequests (assembler
instructions added to the normal execution path for checking) do
not affect overall MPI performance. Valgrind ClientRequests are
explained in detail <a class="reference external" href="https://valgrind.org/docs/manual/manual-core-adv.html">in Valgrind’s documentation</a>.
In the case of x86-64, ClientRequests boil down to the following
four rotate-left (ROL) and one xchange (XCHG) assembler instructions
from <code class="docutils literal notranslate"><span class="pre">valgrind.h</span></code>:</p>
<div class="highlight-c notranslate"><div class="highlight"><pre><span></span><span class="cp">#define __SPECIAL_INSTRUCTION_PREAMBLE \</span>
<span class="cp"> "rolq \$3, %%rdi; rolq \$13, %%rdi\\n\\t" \</span>
<span class="cp"> "rolq \$61, %%rdi; rolq \$51, %%rdi\\n\\t"</span>
</pre></div>
</div>
<p>and</p>
<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>__asm__ volatile(__SPECIAL_INSTRUCTION_PREAMBLE \
/* %RDX = client_request ( %RAX ) */ \
"xchgq %%rbx,%%rbx" \
: "=d" (_zzq_result) \
: "a" (& _zzq_args``0``), "0" (_zzq_default) \
: "cc", "memory" \
);
</pre></div>
</div>
<p>for every single ClientRequest. In the case of not running
Valgrind, these ClientRequest instructions do not change the
arithmetic outcome (rotating a 64-bit register left by 128-Bits,
exchanging a register with itself), except for the carry flag.</p>
<p>The first request is checking whether we’re running under Valgrind.
In case we’re not running under Valgrind subsequent checks (a.k.a.
ClientRequests) are not done.</p>
</li>
<li><p>If the application is run under Valgrind, performance is naturally reduced due
to the Valgrind JIT and the checking tool employed.
For costs and overheads of Valgrind’s Memcheck tool on the SPEC 2000 Benchmark,
please see the excellent paper
<a class="reference external" href="https://valgrind.org/docs/valgrind2007.pdf">Valgrind: A Framework for Heavyweight Dynamic Binary Instrumentation</a>.
For an evaluation of various internal implementation alternatives of Shadow Memory, please see
<a class="reference external" href="https://valgrind.org/docs/iiswc2006.pdf">Building Workload Characterization Tools with Valgrind</a>.</p></li>
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