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Mar 13, 2007 2:52:40 AM (18 years ago)
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raasch
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  • palm/trunk/DOC/app/chapter_3.3.html

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    6   <title>PALM chapter 3.3</title>
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    8   <meta name="AUTHOR" content="Marcus Oliver Letzel">
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    19 <h3 style="line-height: 100%;">3.3 Initialization and restart runs</h3>
    20 <p style="line-height: 100%;">A job started by <b>mrun</b> will
     2<html><head>
     3<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
     4chapter 3.3</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Marcus Oliver Letzel"> <meta name="CREATED" content="20040728;14053490"> <meta name="CHANGED" content="20041112;14150257"> <meta name="KEYWORDS" content="parallel LES model"> <style>
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     9
     10<body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">3.3 Initialization and restart
     11runs</h3>
     12<p style="line-height: 100%;">A job started by <b>mrun</b>
     13will
    2114- according to its requested computing time, its memory size
    2215requirement and
    … …  
    3528very fast, jobs with higher requirements must wait longer (sometimes
    3629several days). </p>
    37 <p style="line-height: 100%;">Before the start of a model run the user
     30<p style="line-height: 100%;">Before the start of a model
     31run the user
    3832must estimate how much CPU time the model will need for the simulation.
    3933The necessary time in seconds has to be indicated with the mrun
    40 <b>option</b> <tt><a
    41  href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#Opt-t">-t</a></tt>
     34<b>option</b> <tt><a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#Opt-t">-t</a></tt>
    4235and has an influence on the job class into which the job is queued. Due
    4336to the fact that the model usually uses a variable
    … …  
    4942which normally leads to an abort of the job as soon as the available
    5043CPU time is consumed. In principle one could solve this problem by
    51 setting a very generously estimated value for <u><font
    52  style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-t</font></font></u>,
     44setting a very generously estimated value for <u><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-t</font></font></u>,
    5345but this will possibly lead to the disadvantage that the queued job has
    5446to wait longer for execution.<br>
    55 </p>
    56 <p style="line-height: 100%;">To avoid this problem <b>mrun </b>offers
    57 the possibility of so-called <b>restart runs</b>. During the model
     47</p><p style="line-height: 100%;">To avoid this
     48problem <b>mrun </b>offers
     49the possibility of so-called <b>restart runs</b>. During
     50the model
    5851run PALM continuously examines how much time is left for the
    5952execution of the job. If the run is not completed and finished shortly
    … …  
    7568first run of this chain (model start at t=0) is called
    7669<b>initial run</b>. </p>
    77 <p style="line-height: 100%;">Working with restart runs and their
    78 generation through <b>mrun</b> requires certain entries in the
     70<p style="line-height: 100%;">Working with restart runs
     71and their
     72generation through <b>mrun</b> requires certain entries in
     73the
    7974mrun-configuration file and in the parameter file, which are
    8075described and explained in the following. The configuration file must
    8176contain the following entries (example for the IBM Regatta of the
    8277HLRN): </p>
    83 <ul>
    84   <pre style="line-height: 100%;"><font style="font-size: 10pt;"
    85  size="2">%write_binary    true    restart</font><br><font
    86  style="font-size: 10pt;" size="2">#</font><br><a
    87  href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN</font></a><font
    88  style="font-size: 10pt;" size="2">   in:job:npe   d3#   ~/palm/current_version/JOBS/$fname/INPUT    _p3d</font><br><font
    89  style="font-size: 10pt;" size="2">PARIN   in:job:npe   d3f   ~/palm/current_version/JOBS/$fname/INPUT    _p3df</font><br><a
    90  href="chapter_3.4.html#BININ"><font style="font-size: 10pt;" size="2">BININ</font></a><font
    91  style="font-size: 10pt;" size="2">   in:loc       d3f   ~/palm/current_version/JOBS/$fname/OUTPUT   _d3d</font><br><font
    92  style="font-size: 10pt;" size="2">#</font><br><a
    93  href="chapter_3.4.html#BINOUT"><font style="font-size: 10pt;" size="2">BINOUT</font></a><font
    94  style="font-size: 10pt;" size="2">  out:loc   restart  ~/palm/current_version/JOBS/$fname/OUTPUT   _d3d</font></pre>
    95 </ul>
    96 <p style="line-height: 100%;">The <b>mrun</b> call for the
     78<ul> <pre style="line-height: 100%;"><font style="font-size: 10pt;" size="2">%write_binary true restart</font><br><font style="font-size: 10pt;" size="2">#</font><br><a href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN</font></a><font style="font-size: 10pt;" size="2"> in:job:npe d3# ~/palm/current_version/JOBS/$fname/INPUT _p3d</font><br><font style="font-size: 10pt;" size="2">PARIN in:job:npe d3f ~/palm/current_version/JOBS/$fname/INPUT _p3df</font><br><a href="chapter_3.4.html#BININ"><font style="font-size: 10pt;" size="2">BININ</font></a><font style="font-size: 10pt;" size="2"> in:loc d3f ~/palm/current_version/JOBS/$fname/OUTPUT _d3d</font><br><font style="font-size: 10pt;" size="2">#</font><br><a href="chapter_3.4.html#BINOUT"><font style="font-size: 10pt;" size="2">BINOUT</font></a><font style="font-size: 10pt;" size="2"> out:loc restart ~/palm/current_version/JOBS/$fname/OUTPUT _d3d</font></pre></ul>
     79<p style="line-height: 100%;">The <b>mrun</b>
     80call for the
    9781initialization run of the job chain must look as follows: </p>
    98 <ul>
    99   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    100  style="font-size: 10pt;" size="2">mrun -h ibmh -d abcde -t 900 -r "d3# restart"</font></pre>
    101 </ul>
    102 <p style="line-height: 100%;">The specification of the environment
    103 variable <tt><tt><font style="font-size: 10pt;" size="2">writ</font></tt></tt><tt><tt><font
    104  style="font-size: 10pt;" size="2">e_binary</font><font
    105  style="font-size: 11pt;" size="2">, </font></tt></tt>which must be
     82<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h ibmh -d abcde -t 900 -r "d3# restart"</font></pre></ul>
     83<p style="line-height: 100%;">The specification of the
     84environment
     85variable <tt><tt><font style="font-size: 10pt;" size="2">writ</font></tt></tt><tt><tt><font style="font-size: 10pt;" size="2">e_binary</font><font style="font-size: 11pt;" size="2">, </font></tt></tt>which
     86must be
    10687assigned the value <tt><tt><font style="font-size: 10pt;" size="2">true</font></tt></tt>,
    10788is essential. Only in this case the model writes
    108 binary-coded data for a possible restart run to the local file <tt><tt><a
    109  href="chapter_3.4.html#BINOUT">BINOUT</a></tt></tt>
     89binary-coded data for a possible restart run to the local file <tt><tt><a href="chapter_3.4.html#BINOUT">BINOUT</a></tt></tt>
    11090at the end of the run. Then of course this output file must be stored
    11191on a permanent file with an appropriate file connection statement
    11292(last line of the example above). As you can see, both instructions
    11393(variable declaration and connection statements) are only carried out
    114 by <b>mrun</b>, if the character string <tt><tt><font
    115  style="font-size: 10pt;" size="2">restart</font></tt></tt>
     94by <b>mrun</b>, if the character string <tt><tt><font style="font-size: 10pt;" size="2">restart</font></tt></tt>
    11695is given for the option <tt><font style="font-size: 10pt;" size="2">-r</font>
    117 </tt>in the <span style="font-weight: bold;">mrun</span> call. Thus
     96</tt>in the <span style="font-weight: bold;">mrun</span>
     97call. Thus
    11898the example above can also be used
    11999if no restart runs are intended. In such cases the character string
    … …  
    122102can simply be omitted. </p>
    123103<p style="line-height: 100%;">Only by the specification of
    124 <tt><font style="font-size: 10pt;" size="2">write_binary=true</font><font
    125  style="font-size: 11pt;" size="2">
    126 </font><font face="Thorndale, serif">the</font></tt> model is
     104<tt><font style="font-size: 10pt;" size="2">write_binary=true</font><font style="font-size: 11pt;" size="2">
     105</font><font face="Thorndale, serif">the</font></tt>
     106model is
    127107instructed to compute the remaining CPU time after each time step and
    128108stop, if the run is not going to be completed and finished briefly
    … …  
    130110this time. Actually the stop takes place when the
    131111difference from the available job time (determined by the <b>mrun</b>
    132 option <tt><font style="font-size: 10pt;" size="2">-t</font></tt>) and
     112option <tt><font style="font-size: 10pt;" size="2">-t</font></tt>)
     113and
    133114the time used so far by the job becomes smaller than the time given
    134 by the model variable <a
    135  href="chapter_4.2.html#termination_time_needed">termination_time_needed</a>.
    136 With the variable <b>termination_time_needed </b>the user determines,
     115by the model variable <a href="chapter_4.2.html#termination_time_needed">termination_time_needed</a>.
     116With the variable <b>termination_time_needed </b>the user
     117determines,
    137118how much time is needed for binary copying of the data for restart
    138119runs, as
    139120well as for the following data archiving and transfer of result data
    140121etc. (as long as this is part of the job). Thus, as soon as the
    141 remaining job time is less than <b>termination_time_needed</b>, the
     122remaining job time is less than <b>termination_time_needed</b>,
     123the
    142124model stops
    143125the time step procedure and copies the data for a restart run to the
    … …  
    148130the fact that a restart run must be started and leads to the
    149131start of an appropriate job. </p>
    150 <p style="line-height: 100%;"><font color="#000000">During the initial
    151 phase of a restart ru</font>n different actions than during the initial
     132<p style="line-height: 100%;"><font color="#000000">During
     133the initial
     134phase of a restart ru</font>n different actions than during the
     135initial
    152136phase of an initial run of the model are neccessary. In this
    153137case the model must read in the binary data written by the preceding
    154138run at the beginning of the run. Beyond that it also reads the
    155139initialization parameters from this file. Therefore these do not need
    156 to be indicated in the parameter file (local name <a
    157  href="chapter_3.4.html#PARIN">PARIN</a>).
     140to be indicated in the parameter file (local name <a href="chapter_3.4.html#PARIN">PARIN</a>).
    158141If they are indicated nevertheless and if their value deviates from
    159142their value of the initial run, then this is ignored. There is
    160143exactly one exception to this rule: with the help of the
    161 initialization parameter <a
    162  href="chapter_4.1.html#initializing_actions">initializing_actions</a>
     144initialization parameter <a href="chapter_4.1.html#initializing_actions">initializing_actions</a>
    163145it is determined whether the job is a restart run or an
    164146initial run. If <b>initializing_actions</b> =
    165 “<i>read_restart_data”</i>, then it is a restart
     147&ldquo;<i>read_restart_data&rdquo;</i>, then it is
     148a restart
    166149run, otherwise an initial run. The previous remarks make it
    167150clear that the model obviously needs two different parameter files
    … …  
    173156parameters with values different from the initial run may appear in
    174157this file, but they will be ignored), which
    175 must have the value “<i>read_restart_data”</i>.
     158must have the value &ldquo;<i>read_restart_data&rdquo;</i>.
    176159Therefore the user must produce two different parameter files if he
    177160wants to operate job chains. Since the model always expects the
    178 parameter file on the local file <tt>PARIN</tt>, two different file
     161parameter file on the local file <tt>PARIN</tt>, two
     162different file
    179163connection statements must be given for this file in the
    180164configuration file. One may be active only at the initial run,
    181 the other one only at restart runs. The <b>mrun </b>call for the
     165the other one only at restart runs. The <b>mrun </b>call
     166for the
    182167initial run shown above activates the first of the two
    183 specified connection statements, because the character string <tt><font
    184  style="font-size: 10pt;" size="2">d3#</font></tt>
     168specified connection statements, because the character string <tt><font style="font-size: 10pt;" size="2">d3#</font></tt>
    185169with the option <tt><font style="font-size: 10pt;" size="2">-r</font></tt>
    186170coincides with the character
    187171string in the third column of the connection statement. Obviously
    188172the next statement must be active</p>
    189 <ul>
    190   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    191  style="font-size: 10pt;" size="2">PARIN in:job:npe d3f ~/palm/current_version/JOBS/$fname/INPUT _p3df</font></pre>
    192 </ul>
    193 <p style="line-height: 100%;">with the restart runs. Given that t<font
    194  color="#000000">his statement only gets</font> active if the option <tt><font
    195  style="font-size: 10pt;" size="2">-r</font></tt> is given the value
    196 <tt><font style="font-size: 11pt;" size="2">d3f</font></tt> and that
     173<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">PARIN in:job:npe d3f ~/palm/current_version/JOBS/$fname/INPUT _p3df</font></pre></ul>
     174<p style="line-height: 100%;">with the restart runs. Given
     175that t<font color="#000000">his statement only gets</font>
     176active if the option <tt><font style="font-size: 10pt;" size="2">-r</font></tt> is given the value
     177<tt><font style="font-size: 11pt;" size="2">d3f</font></tt>
     178and that
    197179the <b>mrun</b> call for this restart run is produced
    198 automatically (thus not by the user), <b>mrun</b> obviously has to
     180automatically (thus not by the user), <b>mrun</b>
     181obviously has to
    199182replace <tt><font style="font-size: 10pt;" size="2">"d3#"</font></tt>
    200183of the initial run with <tt><tt><font style="font-size: 10pt;" size="2">"d3f"</font>
    201 </tt></tt>within the call of this restart run. Actually, with restart
     184</tt></tt>within the call of this restart run. Actually,
     185with restart
    202186runs all <tt><font style="font-size: 10pt;" size="2">"#"</font></tt>
    203 characters within the strings given for the options <tt><font
    204  style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-r</font></font></tt><font
    205  style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">
    206 , </font></font><tt><font style="font-size: 10pt;" size="2"><font
    207  face="Cumberland, monospace">-i</font></font></tt>
    208 and <tt><font style="font-size: 10pt;" size="2">-o</font></tt> are
    209 replaced by <tt><font style="font-size: 10pt;" size="2">“f”</font></tt>.
     187characters within the strings given for the options <tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-r</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">
     188, </font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-i</font></font></tt>
     189and <tt><font style="font-size: 10pt;" size="2">-o</font></tt>
     190are
     191replaced by <tt><font style="font-size: 10pt;" size="2">&ldquo;f&rdquo;</font></tt>.
    210192</p>
    211 <p style="line-height: 100%;">For example, for the initial run
     193<p style="line-height: 100%;">For example, for the initial
     194run
    212195the permanent file </p>
    213 <ul>
    214   <pre style="margin-bottom: 0.5cm; line-height: 100%;">~/palm/current_version/JOBS/abcde/INPUT/abcde_p3d</pre>
    215 </ul>
    216 <p style="line-height: 100%;">and for restart runs the permanent file<span
    217  style="font-family: monospace;"> </span></p>
    218 <ul style="font-family: monospace;">
    219   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    220  style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/abcde/INPUT/abcde_p3df</font></pre>
    221 </ul>
    222 <p style="line-height: 100%;">is used. Only with restart runs the
    223 local file <tt>BININ</tt> is made available as input file, because
     196<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;">~/palm/current_version/JOBS/abcde/INPUT/abcde_p3d</pre></ul>
     197<p style="line-height: 100%;">and for restart runs the
     198permanent file<span style="font-family: monospace;"> </span></p>
     199<ul style="font-family: monospace;"> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/abcde/INPUT/abcde_p3df</font></pre></ul>
     200<p style="line-height: 100%;">is used. Only with restart
     201runs the
     202local file <tt>BININ</tt> is made available as input file,
     203because
    224204the appropriate file connection statement also contains the
    225205character string <tt><font style="font-size: 10pt;" size="2">"d3f"</font></tt>
    … …  
    230210the corresponding output file (local name BINOUT) are identical and
    231211read </p>
    232 <ul>
    233   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    234  style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/abcde/OUTPUT/abcde_d3d.</font></pre>
    235 </ul>
    236 <p style="line-height: 100%;">However, after the file produced by the
     212<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/abcde/OUTPUT/abcde_d3d.</font></pre></ul>
     213<p style="line-height: 100%;">However, after the file
     214produced by the
    237215previous job was read in by the model and after at the local file
    238216<tt>BINOUT </tt>was produced at the end of the job, the
    239 restart job does not overwrite this permanent file (<tt>
    240 /<font
    241  style="font-size: 10pt;" size="2">abcde_d3d</font></tt>)
     217restart job does not overwrite this permanent file (<tt>&hellip;/<font style="font-size: 10pt;" size="2">abcde_d3d</font></tt>)
    242218with the new data. Instead of that, it is examined whether already
    243 a permanent file with the name <tt><font style="font-size: 10pt;"
    244  size="2">
    245 /abcde_d3d</font>
    246 <font face="Thorndale, serif">exists </font></tt>when copying the
     219a permanent file with the name <tt><font style="font-size: 10pt;" size="2">&hellip;/abcde_d3d</font>
     220<font face="Thorndale, serif">exists </font></tt>when
     221copying the
    247222output file (<tt><font style="font-size: 10pt;" size="2">BINOUT</font></tt>)
    248 of <b>mrun</b>. If this is the case, <tt><font
    249  style="font-size: 10pt;" size="2">BINOUT</font></tt>
    250 is copied to the file<font style="font-size: 10pt;" size="2"><font
    251  face="Cumberland, monospace">
    252 </font></font><tt><font style="font-size: 10pt;" size="2"><font
    253  face="Cumberland, monospace">
    254 /abcde_d3d.1</font></font></tt><font
    255  style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">.</font></font>
    256 Even if this file is already present, <tt><font
    257  style="font-size: 10pt;" size="2">
    258 /abcde_d3d.2</font></tt>
     223of <b>mrun</b>. If this is the case, <tt><font style="font-size: 10pt;" size="2">BINOUT</font></tt>
     224is copied to the file<font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">
     225</font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">&hellip;/abcde_d3d.1</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">.</font></font>
     226Even if this file is already present, <tt><font style="font-size: 10pt;" size="2">&hellip;/abcde_d3d.2</font></tt>
    259227is tried etc. For an input file the highest existing cycle
    260228of the respective permanent file is copied. In the example above this
    261229means: the initial run creates the permanent file
    262 <tt><font style="font-size: 10pt;" size="2">
    263 /abcde_d3d</font></tt><font
    264  style="font-size: 11pt;" size="2">,</font>
    265 the first restart run uses this file and creates <tt>
    266 /<font
    267  style="font-size: 10pt;" size="2">abcde_d3d.1</font></tt>,
    268 the second restart run creates <tt><font style="font-size: 10pt;"
    269  size="2">
    270 /abcde_d3d.2</font></tt><font style="font-size: 10pt;"
    271  size="2">
     230<tt><font style="font-size: 10pt;" size="2">&hellip;/abcde_d3d</font></tt><font style="font-size: 11pt;" size="2">,</font>
     231the first restart run uses this file and creates <tt>&hellip;/<font style="font-size: 10pt;" size="2">abcde_d3d.1</font></tt>,
     232the second restart run creates <tt><font style="font-size: 10pt;" size="2">&hellip;/abcde_d3d.2</font></tt><font style="font-size: 10pt;" size="2">
    272233</font>etc. After completion of the job chain the user can still
    273234access all files created by the jobs. This makes it possible for the
    274235user for example to restart the model run of a certain job of the job
    275236chain again. </p>
    276 <p style="line-height: 100%;">Therefore restart jobs can not only be
    277 started automatically through <b>mrun</b>, but also manually by the
     237<p style="line-height: 100%;">Therefore restart jobs can
     238not only be
     239started automatically through <b>mrun</b>, but also
     240manually by the
    278241user. This is necessary e.g. whenever after the end of a job chain
    279242it is decided that the simulation must be continued further, because
    280243the phenomenon which should be examined did not reach the desired
    281 state yet. In such cases the <b>mrun</b> options completely
    282 correspond to those of the initial call; simply the <tt><font
    283  style="font-size: 10pt;" size="2">"#"</font></tt> characters in the
    284 arguments of options <tt><font style="font-size: 10pt;" size="2"><font
    285  face="Cumberland, monospace">-r</font></font></tt><font
    286  style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">,
    287 </font></font><tt><font style="font-size: 10pt;" size="2"><font
    288  face="Cumberland, monospace">-i</font></font></tt>
    289 and <tt><font style="font-size: 10pt;" size="2">-o</font></tt> must be
     244state yet. In such cases the <b>mrun</b> options
     245completely
     246correspond to those of the initial call; simply the <tt><font style="font-size: 10pt;" size="2">"#"</font></tt>
     247characters in the
     248arguments of options <tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-r</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">,
     249</font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-i</font></font></tt>
     250and <tt><font style="font-size: 10pt;" size="2">-o</font></tt>
     251must be
    290252replaced by <tt><font style="font-size: 10pt;" size="2">"f"</font></tt>.
    291253</p>
    292 <hr>
    293 <p style="line-height: 100%;"><br>
    294 <font color="#000080"><font color="#000080"><a href="chapter_3.2.html"><font
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    301 <p style="line-height: 100%;"><i>Last change:&nbsp;</i> 14/04/05 (SR)</p>
    302 </body>
    303 </html>
     254<hr><p style="line-height: 100%;"><br>
     255<font color="#000080"><font color="#000080"><a href="chapter_3.2.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_3.4.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;"><i>Last change:&nbsp;</i>
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