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<section class="tex2jax_ignore mathjax_ignore" id="code-management">
<h1>Code Management<a class="headerlink" href="#code-management" title="Link to this heading">#</a></h1>
<p>We list some of the techniques that may be used to increase one’s
efficiency when developing PETSc application codes. We have learned to
use these techniques ourselves, and they have improved our efficiency
tremendously.</p>
<section id="editing-and-compiling">
<h2>Editing and Compiling<a class="headerlink" href="#editing-and-compiling" title="Link to this heading">#</a></h2>
<p>The biggest time sink in code development is generally the cycle of
EDIT-COMPILE-LINK-RUN. We often see users working in a single window
with a cycle such as:</p>
<ul class="simple">
<li><p>Edit a file with <code class="docutils notranslate"><span class="pre">emacs</span></code> or <code class="docutils notranslate"><span class="pre">vim</span></code>.</p></li>
<li><p>Exit <code class="docutils notranslate"><span class="pre">emacs</span></code> or <code class="docutils notranslate"><span class="pre">vim</span></code>.</p></li>
<li><p>Run <code class="docutils notranslate"><span class="pre">make</span></code> and see some error messages.</p></li>
<li><p>Start <code class="docutils notranslate"><span class="pre">emacs</span></code> or <code class="docutils notranslate"><span class="pre">vim</span></code> and try to fix the errors; often starting
the editor hides the error messages so that users cannot remember all
of them and thus do not fix all the compiler errors.</p></li>
<li><p>Run <code class="docutils notranslate"><span class="pre">make</span></code> generating a bunch of object (.o) files.</p></li>
<li><p>Link the executable (which also removes the .o files). Users may
delete the .o files because they anticipate compiling the next time
on a different machine that uses a different compiler.</p></li>
<li><p>Run the executable.</p></li>
<li><p>Detect some error condition and restart the cycle.</p></li>
</ul>
<p>In addition, during this process the user often moves manually among
different directories for editing, compiling, and running.</p>
</section>
<section id="several-easy-ways-to-improve-the-cycle">
<h2>Several easy ways to improve the cycle<a class="headerlink" href="#several-easy-ways-to-improve-the-cycle" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p><code class="docutils notranslate"><span class="pre">emacs</span></code> and <code class="docutils notranslate"><span class="pre">vim</span></code> have a feature to allow the user to compile
using make and have the editor automatically jump to the line of
source code where the compiler detects an error, even when not
currently editing the erroneous file.</p></li>
<li><p>The etags feature of <code class="docutils notranslate"><span class="pre">emacs</span></code> or tags feature of <code class="docutils notranslate"><span class="pre">vim</span></code> enables one
to search quickly through a group of user-defined source files
(and/or PETSc source files) regardless of the directory in which they
are located. <a class="reference external" href="http://www.gnu.org/s/global">GNU Global</a> is a richer
alternative to etags.</p></li>
<li><p>Also, <code class="docutils notranslate"><span class="pre">emacs</span></code> and <code class="docutils notranslate"><span class="pre">vim</span></code> easily enable:</p>
<ul>
<li><p>editing files that reside in any directory and retaining one’s
place within each of them</p></li>
<li><p>searching for files in any directory as one attempts to load them
into the editor</p></li>
</ul>
</li>
</ul>
<p>You might consider using <code class="docutils notranslate"><span class="pre">Microsoft</span> <span class="pre">Visual</span> <span class="pre">Studio</span></code>, <code class="docutils notranslate"><span class="pre">Eclipse</span></code> or
other advanced software development systems. See the <a class="reference internal" href="../manual/other.html#sec-developer-environments"><span class="std std-ref">Users Manual</span></a>.</p>
</section>
<section id="debugging">
<h2>Debugging<a class="headerlink" href="#debugging" title="Link to this heading">#</a></h2>
<p>Most code development for PETSc codes should be done on one processor;
hence, using a standard debugger such as dbx, gdb, xdbx, etc. is fine.
For debugging parallel runs we suggest <strong>Totalview</strong> if it is available
on your machine. Otherwise, you can run each process in a separate
debugger; this is not the same as using a parallel debugger, but in most
cases it is not so bad. The PETSc run-time options
<code class="docutils notranslate"><span class="pre">-start_in_debugger</span></code> [-display xdisplay:0] will open separate windows
and debuggers for each process. You should debug using the debugging
versions of the libraries (run ./configure with the additional option
–with-debugging (the default)).</p>
<p>It really pays to learn how to use a debugger; you will end up writing
more interesting and far more ambitious codes once it is easy for you to
track down problems in the codes.</p>
</section>
<section id="other-suggestions">
<h2>Other suggestions<a class="headerlink" href="#other-suggestions" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p>Choose consistent and obvious names for variables and functions.
(Short variable names may be faster to type, but by using longer
names you don’t have to remember what they represent since it is
clear from the name.)</p></li>
<li><p>Use informative comments.</p></li>
<li><p>Leave space in the code to make it readable.</p></li>
<li><p>Line things up in the code for readability. Remember that any code
written for an application will be visited <strong>over and over</strong> again,
so spending an extra 20 percent of effort on it the first time will
make each of those visits faster and more efficient.</p></li>
<li><p>Realize that you <strong>will</strong> have to debug your code. <strong>No one</strong> writes
perfect code, so always write code that may be debugged and learn how
to use a debugger. In most cases using the debugger to track down
problems is much faster than using print statements.</p></li>
<li><p><strong>Never</strong> hardwire a large problem size into your code. Instead,
allow a command line option to run a small problem. We’ve seen people
developing codes who have to wait 15 minutes after starting a run to
reach the crashing point; this is an inefficient way of developing
code.</p></li>
<li><p>Develop your code on the simplest machine to which you have access.
We have accounts on a variety of large parallel machines, but we
write and initially test all our code on laptops or workstations
because the user interface is friendlier, and the turn-around time
for compiling and running is much faster than for the parallel
machines. We use the parallel machines only for large jobs. Since
PETSc code is completely portable, switching to a parallel machine
from our laptop/workstation development environment simply means
logging into another machine – there are no code or makefile
changes.</p></li>
<li><p>Never develop code directly on a multi-node computing system; your
productivity will be much lower than if you developed on a
well-organized workstation.</p></li>
<li><p>Keep your machines’ operating systems and compilers up-to-date (or
force your systems people to do this :-). You should always work with
whatever tools are currently the best available. It may seem that you
are saving time by not spending the time upgrading your system, but,
in fact, your loss in efficiency by sticking with an outdated system
is probably larger than then the time required to keep it up-to-date.</p></li>
</ul>
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