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468 lines
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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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<BODY BGCOLOR="#FFFFFF">
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<P>
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<B><FONT SIZE="5">Chapter 4</FONT><FONT><BR>
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</FONT></B>
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</P>
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<PRE> 4.1 <A HREF="#4.1">Invoking lil-gp</A>
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4.1.1 <A HREF="#4.1.1">Parameter Files</A>
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4.2 <A HREF="#4.2">Output Files</A>
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<HR></PRE>
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<P>
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<B><FONT SIZE="5">Running lil-gp</FONT></B></P>
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<P>
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This chapter describes how to use lil-gp once you have built the
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executable program, including the various command-line options
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available.</P>
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<P>
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<B><A NAME="4.1">4.1 Invoking lil-gp</A></B></P>
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<P>
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The default executable name produced by the makefile is "gp".
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Once you have built this, you can run it from the command line.
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There are six command-line arguments you can use:<BR>
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</P>
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<P>
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<B> -f</B> <<I>parameter</I>_<I>filename</I>>
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</P>
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<P>
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This loads a parameter file into lil-gp's parameter database.
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The format of this file is explained in section 4.1.1. You can
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have multiple <B>-f</B> options.<BR>
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</P>
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<P>
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<B> -p</B> <<I>parametername</I>=<I>value</I>>
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</P>
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<P>
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This sets the value of an individual parameter. You
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can have multiple <B>-p</B> options.<BR>
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</P>
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<P>
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<B> -c</B> <<I>checkpoint</I>_<I>filename</I>>
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</P>
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<P>
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This restarts lil-gp from the specified checkpoint file. You may
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only have one -c option.<BR>
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</P>
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<P>
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<B> -d</B> <<I>defined</I>_<I>symbo</I>l>
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</P>
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<P>
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This defines the given parameter file symbol. The space between
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the "d" and the symbol is optional.<BR>
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</P>
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<P>
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<B> -u</B> <<I>parameter</I>_<I>file</I>_<I>directive</I>>
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</P>
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<P>
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This undefines the given parameter file symbol. The space between
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the "u" and the symbol is optional.<BR>
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</P>
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<P>
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<B> -q</B>
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</P>
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<P>
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Causes lil-gp to run in quiet mode, producing nothing on standard
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output. Without this option, everything written to the <B>.SYS</B>
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output file is also printed to the terminal.<BR>
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</P>
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<P>
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These options can be specified in any order, but the order <I>is</I>
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significant. Options that modify the parameter database (all
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except <B>-q</B>) are processed in the order they appear on the
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command line. If a parameter is multiply defined, it is the <I>last</I>
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occurrence of it that takes effect. A listing and explanation
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of all parameters available is given in chapter 5. Order of directives
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is important too, so for
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instance</P>
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<PRE>
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<B>% gp -dBLAH -f file1 -uBLAH -f file2</B></PRE>
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<P>
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will cause the symbol "BLAH" to be defined during the
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processing of file1 but not file2.<BR>
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</P>
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<P>
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Note that all parameter settings are saved in the checkpoint files,
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so if you are just restarting an interrupted run you need only
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the<B> -c</B> option. You can, however, use<B> -f</B> and <B>-p</B>
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to modify parameter
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settings--they should, of course, come after the <B>-c</B> option
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or they will have no effect.<BR>
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</P>
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<P>
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<B><A NAME="4.1.1">4.1.1 Parameter Files</A></B></P>
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<P>
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Parameter files have a simple syntax. Comments can begin with
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a <B>'#'</B> or a <B>';'</B> and continue to the end of a line.
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<BR>
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</P>
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<P>
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The file is a series of "name=value" pairs. If the
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last nonwhitespace, noncomment character on a line is a backslash
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then the next nonblank line is considered a continuation of the
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line. Blank lines and lines that contain only comments are completely
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ignored, even in the middle of a continuation. For instance:
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<BR>
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</P>
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<PRE>
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<B>sample = here is \</B></PRE>
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<PRE><B> a single parameter that is continued \</B>
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<B># this comment is followed by a blank line<BR>
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</B><B># this comment is preceded by a blank line</B>
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<B> right through a comment onto this line.<BR></B></PRE>
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<P>
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Whitespace (spaces and tabs) are ignored before the name, on either
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side of the equals sign, and after the value. The following are
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all equivalent:</P>
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<PRE>
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<B>max_generations = 100</B>
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<B> max_generations= 100 ; here is a comment</B>
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<B>max_generations=100 # this is a comment too.<BR>
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</B></PRE>
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<P>
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Both the name and the value of a parameter are just strings.
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In many cases, the names have been chosen to convey the impression
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of a hierarchical structure, but as far as lil-gp is concerned,
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all parameter names are plain strings and no interpretation is
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applied. So, for example, the parameter names <B>breed[1].rate</B>,
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<B>breed[01].rate</B>, and <B>breed[1.0].rate</B> are all different.
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<BR>
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</P>
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<P>
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<B>"Preprocessor" Directives</B></P>
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<P>
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Parameter files also support a simple set of C-preprocessor-like
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directives to allow parts of the file to be processed optionally.
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They all begin with a "%" character, which must occur
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on the first column of the line. They are:<BR>
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</P>
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<P>
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<B>%define</B> <I>symbol</I>
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</P>
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<P>
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Defines the given symbol. Equivalent to the <B>-d</B>
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command line option.<BR>
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</P>
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<P>
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<B>%undefine</B> <I>symbol</I>
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</P>
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<P>
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Undefines the given symbol. Equivalent to the<B> -u</B>
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command line option.<BR>
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</P>
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<P>
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<B> %ifdef</B> <I>symbol</I>
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</P>
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<P>
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If the given symbol is defined, has no effect. Otherwise skips
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all lines up until the next <B>%ifdef</B>, <B>%ifndef</B>, <B>%endif</B>,
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or end-of-file.<BR>
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</P>
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<P>
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<B>%ifndef</B> <I>symbol</I>
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</P>
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<P>
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Same as <B>%ifdef</B>, but reverses the sense of the
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test.<BR>
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</P>
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<P>
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<B>%endif</B>
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</P>
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<P>
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Cancels a previous <B>%ifdef</B> or <B>%ifndef</B>.
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<BR>
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</P>
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<P>
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Symbols are case-sensitive. Leading and trailing whitespace are
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ignored, but internal whitespace is allowed.<SUP>1</SUP> It is
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important to remember that these may look like C preprocessor
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directives, but they don't work the same. In particular, you
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can't nest ifs and there are no Boolean operations (i.e. <B>%ifdef
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FIRST && SECOND </B>is legal, but it tests a single symbol
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named "<B>FIRST && SECOND</B>"). Also, %define
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does not assign a value to the symbol, and no text substitution
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occurs. This is merely meant as a simple mechanism for optionally
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setting groups of parameters, without having to fiddle with lots
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of different parameter files.</P>
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<P>
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The idea is that you can keep multiple sets of parameters in one
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parameter file, and switch among them using directives on the
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command line. You can have a parameter file that looks like:
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</P>
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<PRE><B><some common parameters></B>
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<B>%ifdef FIRST</B>
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<B><one set of parameters></B>
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<B>%endif</B>
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<B>%ifdef SECOND</B>
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<B><another set of parameters></B>
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<B>%endif<BR></B></PRE>
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<P>
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You can then use one set or the other with a command line like:
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</P>
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<PRE>
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<B>gp -d FIRST -f parameter.file</B></PRE>
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<P>
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to select the first set.<BR>
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<BR>
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</P>
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<P>
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<B><A NAME="4.2">4.2 Output Files</A></B></P>
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<P>
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lil-gp produces a number of output files, with statistics on tree
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size and fitness for each generation. The filenames are produced
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by appending a three-character extension to the value of the <B>output.basename</B>
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parameter. They are:</P>
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<CENTER><TABLE BORDER="1" ALIGN="center" WIDTH="80%">
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"><B>.sys</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">general information about the run
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</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"><B>.gen</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">statistics on tree size and depth
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</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"><B>.prg</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">statistics on fitness and hits
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</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"><B>.bst</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">information about the current best-of-run individual(s)
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</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"><B>.his</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">history of the<B> .bst</B> file
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</TD>
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</TR>
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<TR>
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<TD ALIGN="LEFT" VALIGN="TOP" WIDTH="10%"><B>.stt</B></TD>
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<TD ALIGN="LEFT" VALIGN="TOP">condensed version of all statistics</TD>
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</TR>
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</TABLE></CENTER>
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<P>
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</P>
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<P>
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the <B>.bst</B> is rewritten every generation, and all the other
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files are flushed to disk at the completion of every generation.
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This lets you see current information on backgrounded runs.</P>
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<P>
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Each message printed to an output file has an integer priority
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associated with it, ranging from 0 to 100. A given message is
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produced only if its priority is less than or equal to the setting
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of the<B> output.detail</B> parameter. You can experiment to
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find a level of output detail that you like.</P>
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<P>
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The <B>.gen</B> and <B>.prg</B> files can grow very large, and
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are basically just a human-readable form of the information in
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the <B>.stt</B> file. This information is not written to them
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unless you really ask for it (by setting the <B>output.detail</B>
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parameter to at least 90)</P>
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<P>
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The <B>.stt</B> file has one line per subpopulation per generation,
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each line consisting of 20 space- separated numbers. The parameter
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<B>output.stt_interval</B> can be set to modify how often the
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<B>.stt</B> file is written to. The default is 1, meaning every
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generation. For multiple-population problems, a line is written
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for each subpopulation, plus one more line for the population
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as a whole. For single-population problems, only one line (the
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overall population line) is written, since the overall population
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is just the single subpop. The meanings of each column are listed
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in Table 4.</P>
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<P>
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The<B> aux</B> directory in the distribution contains a short
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Perl script called <B>splitstt</B>. This will split an <B>.stt</B>
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file into separate files for each subpopulation. When invoked
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as
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</P>
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<PRE>
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<B>% splitstt myfile.stt<BR>
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</B></PRE>
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<P>
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it will produce files named <B>myfile.stt.pop0, myfile.stt.pop1</B>,
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etc.<BR>
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</P>
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<TABLE BORDER="2" ALIGN="DEFAULT">
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<TR>
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<TH ALIGN="LEFT" VALIGN="MIDDLE" WIDTH="109">
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<P ALIGN="center"> </P>
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<P ALIGN="center"><B>column</B></P>
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</TH>
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<TH ALIGN="LEFT" VALIGN="BOTTOM" WIDTH="481">
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<P ALIGN="left"> </P>
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contents</TH>
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</TR>
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<TR>
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<TD WIDTH="109">
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<P ALIGN="center">1</P>
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<P ALIGN="center">
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2
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</P>
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</TD>
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<TD WIDTH="481">generation number
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<P>
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subpopulation number (0 indicates the overall population)
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</P>
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</TD>
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</TR>
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<TR>
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<TD WIDTH="109">
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<P ALIGN="center">3</P>
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<P ALIGN="center">
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4
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</P>
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<P ALIGN="center">
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5
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</P>
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<P ALIGN="center">
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6
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</P>
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<P ALIGN="center">
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7
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</P>
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<P ALIGN="center">
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8
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</P>
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<P ALIGN="center">
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9
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</P>
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<P ALIGN="center">
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10
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</P>
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<P ALIGN="center">
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11
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</P>
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</TD>
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<TD WIDTH="481">mean standardized fitness of generation
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<P>
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standardized fitness of best-of-generation individual
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</P>
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<P>
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standardized fitness of worst-of-generation individual
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</P>
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<P>
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mean tree size of generation
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</P>
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<P>
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mean tree depth of generation
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</P>
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<P>
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tree size of best-of-generation individual
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</P>
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<P>
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tree depth of best-of-generation individual
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</P>
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<P>
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tree size of worst-of-generation individual
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</P>
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<P>
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tree depth of worst-of-generation individual
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</P>
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</TD>
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</TR>
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<TR>
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<TD WIDTH="109">
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<P ALIGN="center">12</P>
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<P ALIGN="center">
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13
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</P>
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<P ALIGN="center">
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14
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</P>
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<P ALIGN="center">
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15
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</P>
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<P ALIGN="center">
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16
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</P>
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<P ALIGN="center">
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17
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</P>
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<P ALIGN="center">
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18
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</P>
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<P ALIGN="center">
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19
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</P>
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<P ALIGN="center">
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20
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</P>
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</TD>
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<TD WIDTH="481">mean standardized fitness of run
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<P>
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standardized fitness of best-of-run individual
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</P>
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<P>
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standardized fitness of worst-of-run individual
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</P>
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<P>
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mean tree size of run
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</P>
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<P>
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mean tree depth of run
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</P>
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<P>
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tree size of best-of-run individual
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</P>
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<P>
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tree depth of best-of-run individual
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</P>
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<P>
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tree size of worst-of-run individual
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</P>
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<P>
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tree depth of worst-of-run individual
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</P>
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</TD>
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</TR>
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</TABLE>
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<P>
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</P>
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<P>
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Table 4.1: Columns of the <B>.stt</B> output file.<BR>
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<BR>
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</P>
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