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--- palm/trunk/DOC/app/chapter_3.3.html	(revision 54)
+++ palm/trunk/DOC/app/chapter_3.3.html	(revision 108)
@@ -1,22 +1,15 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<html>
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-  <title>PALM chapter 3.3</title>
-  <meta name="GENERATOR" content="StarOffice 7  (Win32)">
-  <meta name="AUTHOR" content="Marcus Oliver Letzel">
-  <meta name="CREATED" content="20040728;14053490">
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-  <meta name="KEYWORDS" content="parallel LES model">
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-<h3 style="line-height: 100%;">3.3 Initialization and restart runs</h3>
-<p style="line-height: 100%;">A job started by <b>mrun</b> will
+<html><head>
+<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
+chapter 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>
+<!--
+@page { size: 21cm 29.7cm }
+-->
+</style></head>
+
+<body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">3.3 Initialization and restart
+runs</h3>
+<p style="line-height: 100%;">A job started by <b>mrun</b>
+will
 - according to its requested computing time, its memory size
 requirement and
@@ -35,9 +28,9 @@
 very fast, jobs with higher requirements must wait longer (sometimes
 several days). </p>
-<p style="line-height: 100%;">Before the start of a model run the user
+<p style="line-height: 100%;">Before the start of a model
+run the user
 must estimate how much CPU time the model will need for the simulation.
 The necessary time in seconds has to be indicated with the mrun
-<b>option</b> <tt><a
- href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#Opt-t">-t</a></tt>
+<b>option</b> <tt><a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#Opt-t">-t</a></tt>
 and has an influence on the job class into which the job is queued. Due
 to the fact that the model usually uses a variable
@@ -49,11 +42,11 @@
 which normally leads to an abort of the job as soon as the available
 CPU time is consumed. In principle one could solve this problem by
-setting a very generously estimated value for <u><font
- style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-t</font></font></u>,
+setting a very generously estimated value for <u><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-t</font></font></u>,
 but this will possibly lead to the disadvantage that the queued job has
 to wait longer for execution.<br>
-</p>
-<p style="line-height: 100%;">To avoid this problem <b>mrun </b>offers
-the possibility of so-called <b>restart runs</b>. During the model
+</p><p style="line-height: 100%;">To avoid this
+problem <b>mrun </b>offers
+the possibility of so-called <b>restart runs</b>. During
+the model
 run PALM continuously examines how much time is left for the
 execution of the job. If the run is not completed and finished shortly
@@ -75,45 +68,32 @@
 first run of this chain (model start at t=0) is called
 <b>initial run</b>. </p>
-<p style="line-height: 100%;">Working with restart runs and their
-generation through <b>mrun</b> requires certain entries in the
+<p style="line-height: 100%;">Working with restart runs
+and their
+generation through <b>mrun</b> requires certain entries in
+the
 mrun-configuration file and in the parameter file, which are
 described and explained in the following. The configuration file must
 contain the following entries (example for the IBM Regatta of the
 HLRN): </p>
-<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>
-<p style="line-height: 100%;">The <b>mrun</b> call for the
+<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>
+<p style="line-height: 100%;">The <b>mrun</b>
+call for the
 initialization run of the job chain must look as follows: </p>
-<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>
-<p style="line-height: 100%;">The specification of the environment
-variable <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 must be
+<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>
+<p style="line-height: 100%;">The specification of the
+environment
+variable <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
+must be
 assigned the value <tt><tt><font style="font-size: 10pt;" size="2">true</font></tt></tt>,
 is essential. Only in this case the model writes
-binary-coded data for a possible restart run to the local file <tt><tt><a
- href="chapter_3.4.html#BINOUT">BINOUT</a></tt></tt>
+binary-coded data for a possible restart run to the local file <tt><tt><a href="chapter_3.4.html#BINOUT">BINOUT</a></tt></tt>
 at the end of the run. Then of course this output file must be stored
 on a permanent file with an appropriate file connection statement
 (last line of the example above). As you can see, both instructions
 (variable declaration and connection statements) are only carried out
-by <b>mrun</b>, if the character string <tt><tt><font
- style="font-size: 10pt;" size="2">restart</font></tt></tt>
+by <b>mrun</b>, if the character string <tt><tt><font style="font-size: 10pt;" size="2">restart</font></tt></tt>
 is given for the option <tt><font style="font-size: 10pt;" size="2">-r</font>
-</tt>in the <span style="font-weight: bold;">mrun</span> call. Thus
+</tt>in the <span style="font-weight: bold;">mrun</span>
+call. Thus
 the example above can also be used
 if no restart runs are intended. In such cases the character string
@@ -122,7 +102,7 @@
 can simply be omitted. </p>
 <p style="line-height: 100%;">Only by the specification of
-<tt><font style="font-size: 10pt;" size="2">write_binary=true</font><font
- style="font-size: 11pt;" size="2">
-</font><font face="Thorndale, serif">the</font></tt> model is
+<tt><font style="font-size: 10pt;" size="2">write_binary=true</font><font style="font-size: 11pt;" size="2">
+</font><font face="Thorndale, serif">the</font></tt>
+model is
 instructed to compute the remaining CPU time after each time step and
 stop, if the run is not going to be completed and finished briefly
@@ -130,14 +110,16 @@
 this time. Actually the stop takes place when the
 difference from the available job time (determined by the <b>mrun</b>
-option <tt><font style="font-size: 10pt;" size="2">-t</font></tt>) and
+option <tt><font style="font-size: 10pt;" size="2">-t</font></tt>)
+and
 the time used so far by the job becomes smaller than the time given
-by the model variable <a
- href="chapter_4.2.html#termination_time_needed">termination_time_needed</a>.
-With the variable <b>termination_time_needed </b>the user determines,
+by the model variable <a href="chapter_4.2.html#termination_time_needed">termination_time_needed</a>.
+With the variable <b>termination_time_needed </b>the user
+determines,
 how much time is needed for binary copying of the data for restart
 runs, as
 well as for the following data archiving and transfer of result data
 etc. (as long as this is part of the job). Thus, as soon as the
-remaining job time is less than <b>termination_time_needed</b>, the
+remaining job time is less than <b>termination_time_needed</b>,
+the
 model stops
 the time step procedure and copies the data for a restart run to the
@@ -148,20 +130,21 @@
 the fact that a restart run must be started and leads to the
 start of an appropriate job. </p>
-<p style="line-height: 100%;"><font color="#000000">During the initial
-phase of a restart ru</font>n different actions than during the initial
+<p style="line-height: 100%;"><font color="#000000">During
+the initial
+phase of a restart ru</font>n different actions than during the
+initial
 phase of an initial run of the model are neccessary. In this
 case the model must read in the binary data written by the preceding
 run at the beginning of the run. Beyond that it also reads the
 initialization parameters from this file. Therefore these do not need
-to be indicated in the parameter file (local name <a
- href="chapter_3.4.html#PARIN">PARIN</a>).
+to be indicated in the parameter file (local name <a href="chapter_3.4.html#PARIN">PARIN</a>).
 If they are indicated nevertheless and if their value deviates from
 their value of the initial run, then this is ignored. There is
 exactly one exception to this rule: with the help of the
-initialization parameter <a
- href="chapter_4.1.html#initializing_actions">initializing_actions</a>
+initialization parameter <a href="chapter_4.1.html#initializing_actions">initializing_actions</a>
 it is determined whether the job is a restart run or an
 initial run. If <b>initializing_actions</b> =
-<i>read_restart_data</i>, then it is a restart
+&ldquo;<i>read_restart_data&rdquo;</i>, then it is
+a restart
 run, otherwise an initial run. The previous remarks make it
 clear that the model obviously needs two different parameter files
@@ -173,53 +156,50 @@
 parameters with values different from the initial run may appear in
 this file, but they will be ignored), which
-must have the value <i>read_restart_data</i>.
+must have the value &ldquo;<i>read_restart_data&rdquo;</i>.
 Therefore the user must produce two different parameter files if he
 wants to operate job chains. Since the model always expects the
-parameter file on the local file <tt>PARIN</tt>, two different file
+parameter file on the local file <tt>PARIN</tt>, two
+different file
 connection statements must be given for this file in the
 configuration file. One may be active only at the initial run,
-the other one only at restart runs. The <b>mrun </b>call for the
+the other one only at restart runs. The <b>mrun </b>call
+for the
 initial run shown above activates the first of the two
-specified connection statements, because the character string <tt><font
- style="font-size: 10pt;" size="2">d3#</font></tt>
+specified connection statements, because the character string <tt><font style="font-size: 10pt;" size="2">d3#</font></tt>
 with the option <tt><font style="font-size: 10pt;" size="2">-r</font></tt>
 coincides with the character
 string in the third column of the connection statement. Obviously
 the next statement must be active</p>
-<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/$fname/INPUT _p3df</font></pre>
-</ul>
-<p style="line-height: 100%;">with the restart runs. Given that t<font
- color="#000000">his statement only gets</font> active if the option <tt><font
- style="font-size: 10pt;" size="2">-r</font></tt> is given the value
-<tt><font style="font-size: 11pt;" size="2">d3f</font></tt> and that
+<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">PARIN in:job:npe d3f ~/palm/current_version/JOBS/$fname/INPUT _p3df</font></pre></ul>
+<p style="line-height: 100%;">with the restart runs. Given
+that t<font color="#000000">his statement only gets</font>
+active if the option <tt><font style="font-size: 10pt;" size="2">-r</font></tt> is given the value
+<tt><font style="font-size: 11pt;" size="2">d3f</font></tt>
+and that
 the <b>mrun</b> call for this restart run is produced
-automatically (thus not by the user), <b>mrun</b> obviously has to
+automatically (thus not by the user), <b>mrun</b>
+obviously has to
 replace <tt><font style="font-size: 10pt;" size="2">"d3#"</font></tt>
 of the initial run with <tt><tt><font style="font-size: 10pt;" size="2">"d3f"</font>
-</tt></tt>within the call of this restart run. Actually, with restart
+</tt></tt>within the call of this restart run. Actually,
+with restart
 runs all <tt><font style="font-size: 10pt;" size="2">"#"</font></tt>
-characters 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">
-, </font></font><tt><font style="font-size: 10pt;" size="2"><font
- face="Cumberland, monospace">-i</font></font></tt>
-and <tt><font style="font-size: 10pt;" size="2">-o</font></tt> are
-replaced by <tt><font style="font-size: 10pt;" size="2">f</font></tt>.
+characters 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">
+, </font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-i</font></font></tt>
+and <tt><font style="font-size: 10pt;" size="2">-o</font></tt>
+are
+replaced by <tt><font style="font-size: 10pt;" size="2">&ldquo;f&rdquo;</font></tt>.
 </p>
-<p style="line-height: 100%;">For example, for the initial run
+<p style="line-height: 100%;">For example, for the initial
+run
 the permanent file </p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;">~/palm/current_version/JOBS/abcde/INPUT/abcde_p3d</pre>
-</ul>
-<p style="line-height: 100%;">and for restart runs the permanent file<span
- style="font-family: monospace;"> </span></p>
-<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>
-<p style="line-height: 100%;">is used. Only with restart runs the
-local file <tt>BININ</tt> is made available as input file, because
+<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;">~/palm/current_version/JOBS/abcde/INPUT/abcde_p3d</pre></ul>
+<p style="line-height: 100%;">and for restart runs the
+permanent file<span style="font-family: monospace;"> </span></p>
+<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>
+<p style="line-height: 100%;">is used. Only with restart
+runs the
+local file <tt>BININ</tt> is made available as input file,
+because
 the appropriate file connection statement also contains the
 character string <tt><font style="font-size: 10pt;" size="2">"d3f"</font></tt>
@@ -230,74 +210,48 @@
 the corresponding output file (local name BINOUT) are identical and
 read </p>
-<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>
-<p style="line-height: 100%;">However, after the file produced by the
+<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>
+<p style="line-height: 100%;">However, after the file
+produced by the
 previous job was read in by the model and after at the local file
 <tt>BINOUT </tt>was produced at the end of the job, the
-restart job does not overwrite this permanent file (<tt>
-/<font
- style="font-size: 10pt;" size="2">abcde_d3d</font></tt>)
+restart job does not overwrite this permanent file (<tt>&hellip;/<font style="font-size: 10pt;" size="2">abcde_d3d</font></tt>)
 with the new data. Instead of that, it is examined whether already
-a permanent file with the name <tt><font style="font-size: 10pt;"
- size="2">
-/abcde_d3d</font>
-<font face="Thorndale, serif">exists </font></tt>when copying the
+a permanent file with the name <tt><font style="font-size: 10pt;" size="2">&hellip;/abcde_d3d</font>
+<font face="Thorndale, serif">exists </font></tt>when
+copying the
 output file (<tt><font style="font-size: 10pt;" size="2">BINOUT</font></tt>)
-of <b>mrun</b>. If this is the case, <tt><font
- style="font-size: 10pt;" size="2">BINOUT</font></tt>
-is copied to the file<font style="font-size: 10pt;" size="2"><font
- face="Cumberland, monospace">
-</font></font><tt><font style="font-size: 10pt;" size="2"><font
- face="Cumberland, monospace">
-/abcde_d3d.1</font></font></tt><font
- style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">.</font></font>
-Even if this file is already present, <tt><font
- style="font-size: 10pt;" size="2">
-/abcde_d3d.2</font></tt>
+of <b>mrun</b>. If this is the case, <tt><font style="font-size: 10pt;" size="2">BINOUT</font></tt>
+is copied to the file<font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">
+</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>
+Even if this file is already present, <tt><font style="font-size: 10pt;" size="2">&hellip;/abcde_d3d.2</font></tt>
 is tried etc. For an input file the highest existing cycle
 of the respective permanent file is copied. In the example above this
 means: the initial run creates the permanent file
-<tt><font style="font-size: 10pt;" size="2">
-/abcde_d3d</font></tt><font
- style="font-size: 11pt;" size="2">,</font>
-the first restart run uses this file and creates <tt>
-/<font
- style="font-size: 10pt;" size="2">abcde_d3d.1</font></tt>,
-the second restart run creates <tt><font style="font-size: 10pt;"
- size="2">
-/abcde_d3d.2</font></tt><font style="font-size: 10pt;"
- size="2">
+<tt><font style="font-size: 10pt;" size="2">&hellip;/abcde_d3d</font></tt><font style="font-size: 11pt;" size="2">,</font>
+the first restart run uses this file and creates <tt>&hellip;/<font style="font-size: 10pt;" size="2">abcde_d3d.1</font></tt>,
+the 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">
 </font>etc. After completion of the job chain the user can still
 access all files created by the jobs. This makes it possible for the
 user for example to restart the model run of a certain job of the job
 chain again. </p>
-<p style="line-height: 100%;">Therefore restart jobs can not only be
-started automatically through <b>mrun</b>, but also manually by the
+<p style="line-height: 100%;">Therefore restart jobs can
+not only be
+started automatically through <b>mrun</b>, but also
+manually by the
 user. This is necessary e.g. whenever after the end of a job chain
 it is decided that the simulation must be continued further, because
 the phenomenon which should be examined did not reach the desired
-state yet. In such cases the <b>mrun</b> options completely
-correspond to those of the initial call; simply the <tt><font
- style="font-size: 10pt;" size="2">"#"</font></tt> characters in the
-arguments 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">,
-</font></font><tt><font style="font-size: 10pt;" size="2"><font
- face="Cumberland, monospace">-i</font></font></tt>
-and <tt><font style="font-size: 10pt;" size="2">-o</font></tt> must be
+state yet. In such cases the <b>mrun</b> options
+completely
+correspond to those of the initial call; simply the <tt><font style="font-size: 10pt;" size="2">"#"</font></tt>
+characters in the
+arguments 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">,
+</font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">-i</font></font></tt>
+and <tt><font style="font-size: 10pt;" size="2">-o</font></tt>
+must be
 replaced by <tt><font style="font-size: 10pt;" size="2">"f"</font></tt>.
 </p>
-<hr>
-<p style="line-height: 100%;"><br>
-<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
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- border="2" height="32" width="32"></font></a><a href="chapter_3.4.html"><font
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- border="2" height="32" width="32"></font></a></font></font></p>
-<p style="line-height: 100%;"><i>Last change:&nbsp;</i> 14/04/05 (SR)</p>
-</body>
-</html>
+<hr><p style="line-height: 100%;"><br>
+<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>
+$Id$</p>
+</body></html>
