337 lines
11 KiB
HTML
337 lines
11 KiB
HTML
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<HTML>
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<HEAD>
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<META NAME="GENERATOR" CONTENT="Internet Assistant for Microsoft Word 2.0z">
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<TITLE> lil-gp 1</TITLE>
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</HEAD>
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<BODY BGCOLOR="#FFFFFF">
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<H1>
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<B><FONT SIZE="5">Chapter 3</FONT></B></H1>
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<PRE>
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3.1 <A HREF="#3.1">Preparing the kernel</A>
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3.2 <A HREF="#3.2">Building the Sample Problems</A>
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3.3 <A HREF="#3.3">Running the Sample Problems</A>
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3.3.1 <A HREF="#3.3.1">Symbolic Regression</A>
3.3.2 <A HREF="#3.3.2">Artificial Ant</A>
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3.3.3 <A HREF="#3.3.3">Boolean 11-Multiplexer</A>
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3.3.4 <A HREF="#3.3.4">Two-boxes</A>
3.3.5 <A HREF="#3.3.5">Lawnmower</A>
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3.4 <A HREF="#3.4">Compiling Without the Makefile</A>
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<HR></PRE>
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<P>
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<B><FONT SIZE="5">Compiling lil-gp<BR>
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</FONT></B>
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</P>
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<P>
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When you unpack the distribution, you should get this directory
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tree:<BR>
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</P>
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<P>
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<B>lilgp/</B>
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</P>
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<BLOCKQUOTE><B>app
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<TABLE BORDER="0" ALIGN="DEFAULT" WIDTH="100%">
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"></TD>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>ant/</B> (artificial ant problem)
</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"></TD>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>lawnmower/ </B>(lawnmower problem)
</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"></TD>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>multiplexer/</B> (Boolean 11-multiplexer problem)
</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"></TD>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>regression/</B> (symbolic regression problem)
</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"></TD>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>skeleton/</B> (skeleton code for new problems)
</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"></TD>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>twobox/</B> (two-boxes problem)
</TD>
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</TR>
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</TABLE>
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</B>
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<B>docs/</B> (documentation)
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</BLOCKQUOTE>
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<BLOCKQUOTE>
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<B>kernel/</B> (kernel source)
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</BLOCKQUOTE>
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<BLOCKQUOTE>
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<B> params/</B> (sample parameter files)
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</BLOCKQUOTE>
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<BLOCKQUOTE>
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<B> aux/</B> (miscellany)<BR>
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</BLOCKQUOTE>
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<P>
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This chapter describes how to prepare the kernel, and how to build
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and run the five sample problems included in the distribution.
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It assumes your system is running on some flavor of Unix, and
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has the GNU <B>make</B> utility available. If you don't have
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GNU make, read section 3.4 for tips on writing your own makefile
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or compiling manually.<BR>
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</P>
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<P>
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<B><A NAME="3.1">3.1 Preparing the kernel</A></B></P>
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<P>
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First you should examine the file <B>GNUmakefile.kernel</B> in
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the <B>kernel</B> directory. At the top will be things (such
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as compiler flags) that need to be set for various systems. Look
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to see if you need to make any changes there.</P>
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<P>
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Secondly, you need to customize the timing code, since timing
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relies on system calls which vary from system to system. You
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need to create a pair of files, <B>event.c</B> and <B>event.h</B>.
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There are three pairs of files
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provided:</P>
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<P> </P>
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<P>
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<B>ev_times </B>Use this if your system has the times() system
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call. It will provide wall clock time, in addition to processor
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time spent in user and system spaces, to (on most systems) .01
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second resolution.<BR>
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</P>
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<P>
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<B>ev_time</B> Use this if your system only has the time()
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system call. It will provide wall clock time only, to the nearest
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second.<BR>
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</P>
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<P>
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<B>ev_none</B> Use this if nothing else works. It provides
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no timing information at all, but will work on anything.<BR>
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</P>
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<P>
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Copy the appropriate pair to <B>event.c</B> and <B>event.h.</B>
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Under Unix, that
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would be something like:<BR>
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</P>
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<PRE>
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<B> % cp ev_times.c event.c</B>
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<B> % cp ev_times.h event.h<BR>
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</B></PRE>
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<P>
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If you do not know which to use, try them in the order listed.
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If compilation fails with a message like "Undefined symbol,"
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then try the next one. If all else fails, <B>ev_none </B>will
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always work since it is not system-dependent.<BR>
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</P>
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<P>
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<B><A NAME="3.2">3.2 Building the Sample Problems</A></B></P>
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<P>
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Go into the directory for the problem you want to build. Type
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<B>make</B>. If all goes well, you will be left with an executable
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named <B>gp</B> in the directory. You can type <B>make clean</B>
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to remove all the object files in that directory, leaving only
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the executable.</P>
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<P>
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There is a makefile in the directory of each sample problem.
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Each of these "include"s another file, <B>Makefile.kernel</B>,
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located in the kernel directory, which compiles the kernel code.
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Application- specific makefile changes should be made in the
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problem's directory, while modifications to the kernel should
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be reflected in the kernel makefile, so that they will be visible
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for all applications</P>
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<P>
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The application makefiles included assume use of the <B>gcc</B>
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compiler. If you do not have that, you can change the makefile
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to use something else. Look for the line <B>CC = gcc</B> and
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change <B>gcc</B> to <B>cc</B>, or whatever the name of your C
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compiler is. You may also need to change some of the compiler
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flags found just beneath that.<BR>
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</P>
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<P>
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<B><A NAME="3.3">3.3 Running the Sample Problems</A></B></P>
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<P>
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This section describes specific features and parameters for each
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sample problem.<BR>
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</P>
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<P>
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<B><A NAME="3.3.1">3.3.1 Symbolic Regression</A></B></P>
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<P>
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This uses GP to "discover" the function x<SUP>4</SUP>
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+ x<SUP>3</SUP>+ x<SUP>2</SUP> + x, given some randomly chosen
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sample points in the interval [-1, 1). In addition to the normal
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output files, it creates another (with the extension ".<B>fn</B>"),
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that has the best-of-run function evaluated at 201 points over
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the interval of interest. You can use this file directly in a
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plotting utility such as gnuplot to compare the evolved function
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with the objective function</P>
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<P>
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There are three application-specific parameters.<BR>
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</P>
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<CENTER><TABLE BORDER="2" ALIGN="center" WIDTH="100%">
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>app.use_ercs</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">type: binary </TD>
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<TD ALIGN="LEFT" VALIGN="TOP">If yes, an ephemeral random constant terminal (with the range
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[-1; 1)) is added to the function set.</TD>
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<TD ALIGN="LEFT" VALIGN="TOP">default: yes
</TD>
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</TR>
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<TR>
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<TD><B>app.fitness_cases</B></TD>
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<TD>type: integer </TD>
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<TD>The number of fitness cases generated (sample points in the
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interval).</TD>
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<TD>default: 20
</TD>
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</TR>
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</TABLE></CENTER>
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<P> </P>
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<P>
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When this problem computes the difference between the ideal value
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of the function and the value returned by the individual, large
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values are capped so as not to produce infinite results. A parameter
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controls the value of this cap:<BR>
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</P>
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<CENTER><TABLE BORDER="2" ALIGN="center" WIDTH="100%">
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>app.value_cutoff</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">type: double </TD>
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<TD ALIGN="LEFT" VALIGN="TOP">Maximum allowed value for the difference between objective function
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and evolved individual for any one fitness case. Larger values
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are replaced by this number.</TD>
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<TD ALIGN="LEFT" VALIGN="TOP">default: 1e15
</TD>
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</TR>
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</TABLE></CENTER>
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<P>
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You can change the objective function by editing <B>app.c</B>,
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in the function <B>app_initialize().<BR>
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</B>
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</P>
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<P>
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<B><A NAME="3.3.2">3.3.2 Artificial Ant</A><BR>
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</B>
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</P>
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<P>
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This problem has three parameters:</P>
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<CENTER><TABLE BORDER="2" ALIGN="center" WIDTH="100%">
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<TR>
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<TD><B>app.maxtime</B></TD>
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<TD>type: int </TD>
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<TD>Maximum number of time steps before the ant "times out."
</TD>
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<TD>default: 400
</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>app.trail</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP"> type: filename </TD>
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<TD ALIGN="LEFT" VALIGN="TOP">The name of a file depicting the "trail" of food for
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this run. The first line of the file should have the x and y
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dimensions. Remaining lines should have a "<B>#</B>"
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to indicate a square with food, any other character to indicate
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a blank square.</TD>
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<TD ALIGN="LEFT" VALIGN="TOP">default: none
</TD>
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</TR>
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<TR>
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<TD><B>app.use_progn4</B></TD>
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<TD>type: binary </TD>
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<TD>Whether or not the <B>PROGN4</B> fucntion should be included
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in the function set.</TD>
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<TD>default: no
</TD>
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</TR>
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</TABLE></CENTER>
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<P>
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<BR>
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</P>
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<P>
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Two trail files are provided in the <B>ant/ </B>directory: <B>santafe.trl</B>
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and <B>losaltos.trl</B>, both taken from Koza's first book</P>
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<P>
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In addition to the normal information, the <B>.bst</B> file contains
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the number of time steps used by the ant, the food collected,
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and a picture of the trail. Blank squares are shown by a ".",
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uneaten food is a "<B>#</B>", squares the ant passed
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through have an "<B>x</B>", and the final location and
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facing direction of the ant are indicated by a "<B>N</B>",
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"<B>S</B>", "<B>E</B>", or "<B>W</B>"
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in the appropriate square.<BR>
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</P>
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<P>
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<B><A NAME="3.3.3">3.3.3 Boolean 11-Multiplexer</A></B></P>
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<P>
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This problem has no parameters specific to it. The <B>.bst</B>
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file contains the usual information plus a Koza-esque "scoreboard,"
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with hits indicated by "<B>*</B>" and misses by "<B>.</B>".
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<BR>
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</P>
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<P>
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<B><A NAME="3.3.4">3.3.4 Two-boxes</A><BR>
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</B>
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There are no application-specific parameters, and no problem-specific
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output is generated.<BR>
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</P>
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<P>
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<B><A NAME="3.3.5">3.3.5 Lawnmower</A></B></P>
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<P>
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This problem has three parameters:<BR>
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</P>
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<CENTER><TABLE BORDER="2" ALIGN="center" WIDTH="100%">
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</TABLE></CENTER>
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<P> </P>
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<CENTER><TABLE BORDER="2" ALIGN="center" WIDTH="100%">
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<TR>
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<TD><B>app.use_adfs</B></TD>
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<TD>type: binary </TD>
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<TD>Controls whether the ADFs are used.</TD>
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<TD>default: yes
</TD>
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</TR>
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<TR>
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<TD><B>app.lawn_width</B></TD>
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<TD>type: int </TD>
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<TD>The width of the lawn.</TD>
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<TD>default: 8
</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP"><B>app.lawn_height</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">type: int
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</TD>
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<TD ALIGN="LEFT" VALIGN="TOP">The height of the lawn.</TD>
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<TD ALIGN="LEFT" VALIGN="TOP">default: 8
</TD>
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</TR>
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</TABLE></CENTER>
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<BR>
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<P> </P>
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<P>
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<B><A NAME="3.4">3.4 Compiling Without the Makefile</A><BR>
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</B>
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</P>
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<P>
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You will first need to set up the <B>event.c</B> and <B>event.h</B>
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files just as if you were using a makefile. Look in the file
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<B>GNUmakefile.kernel</B> in the <B>kernel</B> directory. The
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first three lines (beginning <B>kobjects = main.o</B>
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</P>
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<P>
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<B>gp.o eval.o ...</B>) list all the kernel object files that
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need to be built, along with the application objects <B>function.o</B>
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and <B>app.o</B>. Building all those together should produce the
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executable.
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</P>
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</BODY>
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</HTML>
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