Index: palm/trunk/DOC/app/chapter_3.6.html
===================================================================
--- palm/trunk/DOC/app/chapter_3.6.html	(revision 5)
+++ palm/trunk/DOC/app/chapter_3.6.html	(revision 40)
@@ -1,9 +1,7 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<html>
-<head>
-  <meta http-equiv="CONTENT-TYPE"
- content="text/html; charset=windows-1252">
-  <title>PALM chapter 3.6</title>
-  <meta name="GENERATOR" content="StarOffice 7  (Win32)">
+<html><head>
+  <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252">
+  
+  <title>PALM chapter 3.6</title><meta name="GENERATOR" content="StarOffice 7  (Win32)">
   <meta name="AUTHOR" content="Siegfried Raasch">
   <meta name="CREATED" content="20040809;10583400">
@@ -14,6 +12,6 @@
 		@page { size: 21cm 29.7cm }
 	-->
-	</style>
-</head>
+	</style></head>
+
 <body dir="ltr" lang="en-US">
 <h3 style="line-height: 100%;">3.6 Interactive mode and debugging</h3>
@@ -23,21 +21,12 @@
 this computer the subroutines of the model must have
 been precompiled (see <a href="chapter_5.0.html">chapter
-5.0</a>). Furthermore, the working directory
-(<tt><font style="font-size: 10pt;" size="2">~/palm/current_version/SOURCE</font></tt>)
-must contain all default source code files of the model (<span
- style="font-family: monospace;">*.f90</span>), the <b>mrun</b>
-configuration file (<span style="font-family: monospace;">.mrun.config</span>)
-the Makefile (<span style="font-family: monospace;">Makefile</span>)
-and the files which contain the user-defined code (the default
-user-interface file <span style="font-family: monospace;">user_interface.f90</span>
-have to be removed from the directory). All output-files possibly
+5.0</a>). Files containing user-defined code must be stored in the directory given by the variable<span style="font-family: Courier New,Courier,monospace;"> %add_source_path </span>in the mrun-configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>.<span style="font-family: monospace;"></span> All output-files possibly
 created by the model and requested by the user to be kept after the run
 are copied to
 directories on the local host corresponding to the specifications
-in the configuration file (in this case the file attribute <a
- href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#tr">tr</a>
+in the configuration file (in this case the file attribute <a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#tr">tr</a>
 does not cause transfer to another computer). </p>
 <p style="line-height: 100%;">Since model runs usually require large
-amounts of CPU time, interactive runs are usually not feasible, since
+amounts of CPU time, interactive runs may not be feasible, since
 in interactive mode CPU time
 is strongly limited on many hosts and runs will be aborted
@@ -54,21 +43,20 @@
 the model, including the user-defined code, must be compiled
 with special debug compiler options. For this purpose, at least the
-following three lines must be included in the <span
- style="font-weight: bold;">mrun </span>configuration file:<br>
+following three lines must be included in the <span style="font-weight: bold;">mrun </span>configuration file:<br>
 </p>
-<p style="line-height: 100%;"><span style="font-family: monospace;">%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
+<p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">%compiler_name&nbsp;&nbsp;&nbsp;&nbsp;
 mpxlf95_r&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-ibmh parallel debug</span><br style="font-family: monospace;">
-<span style="font-family: monospace;">%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
--g:-C:-qinitauto=FF:-qrealsize=8:-Q:-q64:-qmaxmem=-1:-qtune=pwr4:<br>
+ibmh parallel debug</span><br style="font-family: Courier New,Courier,monospace;">
+<span style="font-family: Courier New,Courier,monospace;">%fopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+-g:-C:-qinitauto=FF:-qrealsize=8:-Q:-q64:-qmaxmem=-1:-qtune=pwr4:</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
--qarch=pwr4:-qnosave:-qnoescape:-qflttrap=overflow::zerodivide:<br>
+-qarch=pwr4:-qnosave:-qnoescape:-qflttrap=overflow::zerodivide:</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 :invalid::enable:-qsigtrap&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-ibmh parallel debug</span><br style="font-family: monospace;">
-<span style="font-family: monospace;">%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
--g:-C:-qinitauto=FF:-qrealsize=8:-Q:-q64:-qmaxmem=-1:-qtune=pwr4:<br>
+ibmh parallel debug</span><br style="font-family: Courier New,Courier,monospace;">
+<span style="font-family: Courier New,Courier,monospace;">%lopts&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+-g:-C:-qinitauto=FF:-qrealsize=8:-Q:-q64:-qmaxmem=-1:-qtune=pwr4:</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
--qarch=pwr4:-qnosave:-qnoescape:-qflttrap=overflow::zerodivide:<br>
+-qarch=pwr4:-qnosave:-qnoescape:-qflttrap=overflow::zerodivide:</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 :invalid::enable:-qsigtrap:-lesslsmp&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
@@ -77,17 +65,14 @@
 </p>
 <p style="line-height: 100%;">(Attention: in the configuration file,
-the compiler and linker options (<span style="font-family: monospace;">fopts</span>
-and <span style="font-family: monospace;">lopts</span>) must be
+the compiler and linker options (<span style="font-family: Courier New,Courier,monospace;">fopts
+</span>and<span style="font-family: Courier New,Courier,monospace;"> lopts</span>) must be
 written in one line without any blank space before and after the
 colons!)<br>
 </p>
-<p style="line-height: 100%;">Using the compiler options "<span
- style="font-family: monospace;">-g</span>" and "<span
- style="font-family: monospace;">-C</span>", debugable code is created
+<p style="line-height: 100%;">Using the compiler options "<span style="font-family: Courier New,Courier,monospace;">-g</span>" and "<span style="font-family: Courier New,Courier,monospace;">-C</span>", debugable code is created
 and check of array bounds is
-switched on during run time. Option "-qinitauto=FF" initializes all
+switched on during run time. Option "<span style="font-family: Courier New,Courier,monospace;">-qinitauto=FF</span>" initializes all
 automatic variables (unfortunately not the global values of modules) to
-NaN.The "<span style="font-family: monospace;">-qflttrap</span>" and "<span
- style="font-family: monospace;">-qsigtrap</span>" options are needed
+NaN.The "<span style="font-family: Courier New,Courier,monospace;">-qflttrap</span>" and "<span style="font-family: Courier New,Courier,monospace;">-qsigtrap</span>" options are needed
 in order to terminate the run in case of any floating point errors
 (otherwise the run will not terminate and errors can hardly be
@@ -96,27 +81,15 @@
 <p style="line-height: 100%;">The <b>mrun </b>call for debugging
 needs
-an extended argument for the option <tt><font style="font-size: 10pt;"
- size="2">-K</font></tt><font style="font-size: 10pt;" size="2">:</font>
-</p>
-<ul>
-  <p style="line-height: 100%;"><tt><font style="font-size: 10pt;"
- size="2">mrun ... -K parallel debug -s *.f90" ... .<br>
-  </font></tt></p>
-</ul>
-<p style="line-height: 100%;">The argument of option <tt><font
- style="font-size: 10pt;" size="2">-s</font></tt>
-must list all source code files of the model. </p>
+an extended argument for the option<span style="font-family: Courier New,Courier,monospace;"> </span><font style="font-size: 10pt; font-family: Courier New,Courier,monospace;" size="2">-K</font>:</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">mrun ... -K &ldquo;parallel debug&rdquo; -s &rdquo;*.f90" ... .</div><p style="line-height: 100%;">The argument of option<span style="font-family: Courier New,Courier,monospace;"> -s </span><span style="font-family: Courier New,Courier,monospace;"></span>must list all source code files of the default PALM code. </p>
 <p style="line-height: 100%;">After compiling, the debugger
-<b>TotalView</b> is automatically called by <span
- style="font-weight: bold;">mrun</span>. With its assistance the user
+<b>TotalView</b> is automatically called by <span style="font-weight: bold;">mrun</span>. With its assistance the user
 has to start
 the program execution manually, to set breakpoints, etc.. User manuals
-of <b>TotalView</b> are available <a
- href="http://www.hlrn.de/doc/totalview/index.html">online</a>. </p>
+of <b>TotalView</b> are available <a href="http://www.hlrn.de/doc/totalview/index.html">online</a>. </p>
 <p style="line-height: 100%;">Program crashes caused by errors in the
 user-defined code should usually be found
 unassisted. If the termination point lies outside the user code (in the
-default model code), the PALM developer group had possibly be asked for
-assistance. It is emphasized again that error tracing and programming
+default model code), the PALM&nbsp;group can be asked for
+assistance, but please do not expect any quick response. It is emphasized again that error tracing and programming
 of
 user-defined code requires more or less precise knowledge of the
@@ -126,12 +99,5 @@
 <hr>
 <p style="line-height: 100%;"><br>
-<font color="#000080"><font color="#000080"><a href="chapter_3.5.5.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_3.7.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> 15/04/05 (SR)</p>
-</body>
-</html>
+<font color="#000080"><font color="#000080"><a href="chapter_3.5.5.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_3.7.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> 02/03/07 (SR)</p>
+</body></html>
