source: tags/3.2.2/doc/test/performance/index.html @ 8053

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1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
2<!--
3  $Id: index.html 4889 2009-04-06 12:52:39Z nicklas $
4
5  Copyright (C) 2007 Nicklas Nordborg
6  Copyright (C) 2008 Jari Häkkinen
7
8  This file is part of BASE - BioArray Software Environment.
9  Available at http://base.thep.lu.se/
10
11  BASE is free software; you can redistribute it and/or
12  modify it under the terms of the GNU General Public License
13  as published by the Free Software Foundation; either version 3
14  of the License, or (at your option) any later version.
15
16  BASE is distributed in the hope that it will be useful,
17  but WITHOUT ANY WARRANTY; without even the implied warranty of
18  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
19  GNU General Public License for more details.
20
21  You should have received a copy of the GNU General Public License
22  along with BASE. If not, see <http://www.gnu.org/licenses/>.
23-->
24<html>
25  <head>
26    <title>BASE - Performance testing of BASE</title>
27  <link rel=stylesheet type="text/css" href="../../historical/styles.css">
28  </head>
29<body>
30
31<div class="navigation">
32  <a href="../../index.html">BASE</a>
33  <img src="../../historical/next.gif">
34  <a href="../index.html">Test procedures</a>
35  <img src="../../historical/next.gif">
36  Performance
37</div>
38
39  <h1>Performance testing of BASE</h1>
40
41  <div class="abstract">
42    <p>
43      This document defines a procedure for testing the performance
44      of BASE. The intention is that BASE should be compared to the
45      earlier BASE version 1 with respect to performance. The tests on
46      a BASE version 1 server must be done by hand. For later BASE
47      versions, there is a test program. The current test program
48      includes the following tests:
49    </p>
50   
51    <ul>
52    <li>Import raw data</li>
53    <li>Create a root bioassayset</li>
54    <li>Create a filtered bioassayset</li>
55    <li>Create a normalized bioassayset with LOWESS</li>
56    <li>Export bioassay set data in Serial and Matrix BASEFile format and MeV format</li>
57    </ul>
58   
59 
60    <b>Contents</b><br>
61    <ol>
62    <li><a href="#program">Running the test program</a></li>
63    <li><a href="#typical">A typical test sequence</a></li>
64    </ol>
65   
66    <p class="authors">
67    <b>Last updated:</b> $Date: 2009-04-06 12:52:39 +0000 (Mon, 06 Apr 2009) $
68    </p>
69  </div>
70
71 
72  <a name="program"></a>
73  <h2>1. Running the test pgoram</h2>
74
75  <p>
76    The data files needed by the tests are NOT included in the subversion repository.
77    The main reason is that they are too large, and that we don't have permission to
78    make them publicly available for download. To get the test file you need to be a
79    core developer. Read the instructions on the
80    <a href="http://base.thep.lu.se/wiki/DeveloperInformation">DeveloperInformation</a>
81    page, <code>Test data</code> section on the Base 2 web site.
82  </p>
83 
84  <p>
85    To run the test do the following:
86  </p>
87  <ol>
88   
89    <li>Compile the core and the test programs: <code>ant test</code>.</li>
90
91    <li>Change to the <code>build/test/</code> directory.</li>
92
93    <li>Run test program:
94      <pre class="code">
95./test.sh performace &lt;options&gt; &lt;cmd&gt;
96</pre>
97  </ol>
98
99     
100      <p>
101      <b>Test program options</b>
102
103      <ul>
104      <li>global options:
105        <ul>
106        <li><code>-u</code>: Username to run the test as. The default value is "root".
107        <li><code>-p</code>: Password for the user. The default value is "root".
108        <li><code>-x</code>: If present, the tests are executed immediately. Otherwise
109          they are added as jobs to the job queue.
110        </ul>
111        <p>
112       
113      <li><code>raw</code>: import raw data
114        <ul>
115        <li><code>-i</code>: Number of raw bioassays to create.
116          The default value is 1.
117        <li><code>-c</code>: Name prefix for the created raw bioassays. A
118          running number is appended to the name automatically. The
119          default value is "Raw".
120        </ul>
121        <p>
122     
123      <li><code>root</code>: create root bioassay sets
124        <ul>
125        <li><code>-s</code>: Name prefix of raw bioassays that should be used.
126          If no value is given, all raw bioassays in the experiment are used.
127        <li><code>-c</code>: Name prefix for the created bioassay sets. The
128          iteration number and number of raw data sets is appended to the name
129          automatically. The default value is "Root".
130        <li><code>-i</code>: Number of root bioassay sets to create in each
131          iteration. The default value is 1.
132        <li><code>-mi</code>: Number of source raw bioassays to use in the first
133          iteration. The default value is 1. The number of source raw bioassays
134          are double in each iteration.
135        <li><code>-mx</code>: Number of source raw bioassays to use in the last
136          iteration. The default value is 1.
137        </ul>
138        Note! With the -i, -mi and -mx parameters it is possible to specify that
139        multiple root bioassay sets are created. Here is an example:
140        <code>-i 2 -mi 10 -mx 80</code>. This creates 2 root bioassays with
141        10, 20, 40 and 80 source raw bioassays each.
142        <p>
143       
144      <li><code>filter</code>: create filtered bioassay sets
145        <ul>
146        <li><code>-s</code>: Name prefix of bioassay sets that should be
147          filtered. The default value is "Root".
148        <li><code>-c</code>: Name prefix for the created bioassay sets.
149          The default value is "Filtered".
150        </ul>
151        <p>
152     
153      <li><code>lowess</code>: create normalized bioassay sets using lowess
154        <ul>
155        <li><code>-s</code>: Name prefix of bioassay sets that should be
156          normalized. The default value is "Filtered".
157        <li><code>-c</code>: Name prefix for the created bioassay sets.
158          The default value is "Lowess".
159        </ul>
160        <p>
161     
162      <li><code>export</code>: export bioassay set data
163        <ul>
164        <li><code>-s</code>: Name prefix of bioassay sets that should be
165          exported. There is no default value.
166        </ul>
167        <p>
168 
169      <li><code>clean</code>: delete all test data, except reporters
170        <p>
171     
172    </ul>
173    </ol>
174
175  <p>
176    The test doesn't program doesn't require an empty database. Running the
177    test program multiple times will simply add more data to the experiment.
178  </p>
179 
180  <p>
181    Parameters to plug-ins are read from the performance.properties
182    configuration file. It should be located in either /config/test or
183    /config/local directory. If you want to change the parameters
184    put the changed file in /config/local. Don't put this file into
185    the subversion repository.
186  </p>
187 
188  <a name="typical"></a>
189  <h2>2. A typical test sequence</h2>
190 
191  <p>
192    In this case we assume a fresh, empty database.
193  </p>
194 
195  <pre class="code">
196# Import raw data to 10 raw bioassays.
197./test.sh performace -i 10 raw
198
199# Create 2 root bioassay sets each with 1, 2, 4, and 8
200# raw bioassays
201./test.sh performance -i 2 -mi 1 -mx 8 root
202
203# Filter all root bioassay sets
204./test.sh performance -s Root -c Filtered filter
205
206# Normalize all filtered bioassay sets
207./test.sh performance -s Filtered -c Lowess lowess
208
209# Export all root bioassay sets
210./test.sh performance -s Root export
211
212# Export all filtered bioassay sets
213./test.sh performance -s Filtered export
214</pre>
215
216 
217</body>
218</html>
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