Index: palm/trunk/DOC/app/chapter_3.5.5.html
===================================================================
--- palm/trunk/DOC/app/chapter_3.5.5.html	(revision 5)
+++ palm/trunk/DOC/app/chapter_3.5.5.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 3.5.5</title>
-  <meta name="GENERATOR" content="StarOffice 7  (Win32)">
+<html><head>
+  <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252">
+  
+  <title>PALM chapter 3.5.5</title><meta name="GENERATOR" content="StarOffice 7  (Win32)">
   <meta name="AUTHOR" content="Siegfried Raasch">
   <meta name="CREATED" content="20040802;14050943">
@@ -14,113 +12,20 @@
 		@page { size: 21cm 29.7cm }
 	-->
-	</style>
-</head>
+	</style></head>
+
 <body dir="ltr" lang="en-US">
 <h3 style="line-height: 100%;"><font size="4">3.5.5 Compiling and
 linking user-defined code<br>
 </font></h3>
-<p style="line-height: 100%;">The compiling and linking of
-user-defined code into a model run is done via the shellscript
-<a
- href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html">mrun</a>.
-The simplest (however not the most comfortable) way is by giving the
-filenames of the files containing the user-defined code as an argument
-of the shellscript option <a
- href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#Opt-s">-s</a>.
-If the user-defined subroutines are located e.g. on the two files <span
- style="font-family: monospace;">user1.f90</span> and <span
- style="font-family: monospace;">user2.f90</span>, then
-the <b>mrun</b> call has to be:<br>
-</p>
-<p style="line-height: 100%; margin-left: 40px;"><span
- style="font-family: monospace;">mrun... -s "user1.f90 user2.f90" ... .</span><br>
-</p>
-<p style="line-height: 100%;">For this call the user has to be in the
-working directory <tt><tt><font style="font-size: 10pt;" size="2">~/palm/current_version/SOURCE</font></tt></tt>,
-because the file with the source code of the main program is located
-here. The main program is compiled with
-each model run (without the appropriate filename given as argument for
-the
-option -s). </p>
-<p style="line-height: 100%;">The call </p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- style="font-size: 10pt;" size="2">mrun
- -s TEST
-,</font></pre>
-</ul>
-<p style="line-height: 100%;">is simpler and causes the compilation
-of all files with suffix <tt><font style="font-size: 10pt;" size="2">.f90</font></tt>
-located in the working
-directory <font face="Thorndale, serif">a</font>nd having
-user write permissions.&nbsp; Unchanged sources of the default model
-have read permission only and therefore are not compiled with that
-call. </p>
-<p style="line-height: 100%;">Typically, users may have different
-versions
-of user-defined code which are to be used for different model runs.
-According to the method just described for starting a certain model
-run,
-the associated user-defined code would have to be copied into the
-working directory and code for other runs may have to be
-removed (otherwise theses files would be compiled as well and the
-routines like <tt><font style="font-size: 10pt;" size="2">user_actions</font></tt>
-would occur twice or several times which would lead to compiling
-errors). This procedure is quite tedious and can lead to errors if
-different
-model runs with restarts are to be carried out at the same time. It is
-better
-to store the different versions of user-defined code in different
-subdirectories
-using the base file name of the respective model run as subdirectory
-name. In this case a line like </p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- style="font-size: 10pt;" size="2">% </font><a
- href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#add_source_path"><font
- style="font-size: 10pt;" size="2">add_source_path</font></a><font
- style="font-size: 10pt;" size="2"> $HOME/palm/current_version/SOURCE/USER_CODE/$fname</font></pre>
-</ul>
-<p style="line-height: 100%;">has to be added to the <b>mrun</b>
-configuration file. If you call <b>mrun</b> now with </p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- style="font-size: 10pt;" size="2">mrun -d run1  -s user1.f90 user2.f90
-,</font></pre>
-</ul>
-<p style="line-height: 100%;">the additional entry in the configuration
-file
-causes that the files given as argument of the option -s are also
-looked
-for in the directory <tt><font style="font-size: 10pt;" size="2">$HOME/palm/current_version/SOURCE/USER_CODE/run1</font></tt><font
- style="font-size: 10pt;" size="2">,</font>
-in case they are not found in the current working directory. The
-specification of <tt><font style="font-size: 10pt;" size="2">-s</font><font
- size="2">
-TEST</font></tt> in the <b>mrun</b> call now causes compilation of all
-files with suffix <tt><font style="font-size: 10pt;" size="2">.f90</font></tt>
-and user write permissions which are located in the working
-directory or in the directory indicated by <span
- style="font-family: monospace;">add_source_path</span>. In
-this case no files with the same name are allowed to be in these two
-directories. </p>
-<p style="line-height: 100%;">Further detailed information for linking
-user-defined code with <b>mrun</b> can be found in <a
- href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#chapter7">chapter
-7</a> of the <b>mrun </b>documentation (only in German). </p>
-<p style="line-height: 100%;">While programming user-defined code,
+<p style="line-height: 100%;">Users can add their own (modified) user-interface to a PALM-run by carrying out the following steps:</p><ol><li>Copy the default (empty) user-interface (file<span style="font-family: Courier New,Courier,monospace;"> user_interface.f90</span>) to a directory of your choice, e.g.:<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;cd ~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;mkdir -p USER_CODE/example</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;cp trunk/SOURCE/user_interface.f90&nbsp; USER_CODE/example/user_example.f90</span><br></li><li>Set an additional path in the configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config </span>to allow <span style="font-weight: bold;">mrun </span>to find and include this file:<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;%add_source_path&nbsp;&nbsp; $base_directory/USER_CODE/$fname</span><br><br>The default configuration file (<span style="font-family: Courier New,Courier,monospace;">trunk/SCRIPTS/.mrun.config.default</span>) already includes this setting.</li><li>Modify the interface routines according to your needs.</li><li>Start a PALM run by executing<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;mrun -d example ...</span><br><br>The file<span style="font-family: Courier New,Courier,monospace;"> user_example.f90 </span>will be automatically compiled within the job and will replace PALM&lsquo;s default user-interface.<br></li></ol>The above method with including<span style="font-family: Courier New,Courier,monospace;"> $fname </span>in
+the additional source path allows to use different user-interfaces for
+different runs at the same time. Just store the respective
+interface-files in subdirectories<span style="font-family: Courier New,Courier,monospace;"> USER_CODE/abcd</span>,<span style="font-family: Courier New,Courier,monospace;"> USER_CODE/cdef</span>, etc. and start <span style="font-weight: bold;">mrun</span> with option &ldquo;<span style="font-family: Courier New,Courier,monospace;">-d abcd</span>&ldquo;, &ldquo;<span style="font-family: Courier New,Courier,monospace;">-d cdef</span>&ldquo;, etc.<br><br><span style="font-weight: bold;">The modified user-interface file cannot be pre-compiled by using mbuild!</span><br><br>While programming user-defined code,
 errors are frequently made. Possible ways of error
-tracing are described in the next chapter. <br>
+tracing are described in the next chapter. <br><p style="line-height: 100%;">
 &nbsp; </p>
 <hr>
 <p style="line-height: 100%;"><br>
-<font color="#000080"><font color="#000080"><a href="chapter_3.5.3.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_3.6.html"><font
- color="#000080"><img src="right.gif" name="Grafik3" align="bottom"
- border="2" height="32" width="32"></font></a></font></font></p>
+<font color="#000080"><font color="#000080"><a href="chapter_3.5.3.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_3.6.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>
+</body></html>
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>
Index: palm/trunk/DOC/app/chapter_4.1.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.1.html	(revision 5)
+++ palm/trunk/DOC/app/chapter_4.1.html	(revision 40)
@@ -1786,5 +1786,5 @@
 
 
-      <td style="vertical-align: top;"><span style="font-style: italic;">'neumann'</span></td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">'initial gradient'</span></td>
 
 
@@ -1831,12 +1831,11 @@
       
       <p>Allowed are the values <span style="font-style: italic;">'dirichlet'
-      </span>(pt(k=nz) and pt(k=nz+1)
-do not change during the run) and <span style="font-style: italic;">'neumann'</span>.
-With the Neumann boundary
-condition the value of the temperature gradient at the top is
+      </span>(pt(k=nz+1)
+does not change during the run), <span style="font-style: italic;">'neumann'</span> (pt(k=nz+1)=pt(k=nz)), and <span style="font-style: italic;">'initial_gradient'</span>.
+With the 'initial_gradient'-condition the value of the temperature gradient at the top is
 calculated from the initial
 temperature profile (see <a href="#pt_surface">pt_surface</a>, <a href="#pt_vertical_gradient">pt_vertical_gradient</a>)
-by bc_pt_t_val = (pt_init(k=nz) -
-pt_init(k=nz-1)) / dzu(nz).<br>
+by bc_pt_t_val = (pt_init(k=nz+1) -
+pt_init(k=nz)) / dzu(nz+1).<br>
 
 
@@ -1871,69 +1870,26 @@
       
       
-      <ul>
-
-
-
-
-
-
-
-
-
-
-        
-        
-        
-        
-        
-        
-        
-        
-        
-        
-        <p style="font-style: normal;">pt(k=nz) = pt(k=nz-1) +
-bc_pt_t_val * dzu(nz)</p>
-
-
-
-
-
-
-
-
-
-
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      </ul>
-
-
-
-
-
-
-
-
-
-
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      <p style="font-style: normal;">and&nbsp; </p>
+      
+
+
+
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
 
 
@@ -2020,6 +1976,19 @@
       
       
-      <p style="font-style: normal;">(up to k=nz-1 the prognostic
-equation for the temperature is solved).</p>
+      <p style="font-style: normal;">(up to k=nz the prognostic
+equation for the temperature is solved).<br>
+
+
+
+
+
+
+
+
+
+
+When a constant sensible heat flux is used at the top boundary (<a href="chapter_4.1.html#top_heatflux">top_heatflux</a>), <b>bc_pt_t</b> = <span style="font-style: italic;">'neumann'</span>
+must be used, because otherwise the resolved scale may contribute to
+the top flux so that a constant value cannot be guaranteed.</p>
 
 
@@ -2345,69 +2314,26 @@
       
       
-      <ul>
-
-
-
-
-
-
-
-
-
-
-        
-        
-        
-        
-        
-        
-        
-        
-        
-        
-        <p style="font-style: normal;">q(k=nz) = q(k=nz-1) +
-bc_q_t_val * dzu(nz)</p>
-
-
-
-
-
-
-
-
-
-
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      </ul>
-
-
-
-
-
-
-
-
-
-
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      <p style="font-style: normal;">and&nbsp; </p>
+      
+
+
+
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
 
 
@@ -2494,5 +2420,5 @@
       
       
-      <p style="font-style: normal;">(up tp k=nz-1 the prognostic
+      <p style="font-style: normal;">(up tp k=nz the prognostic
 equation for q is solved). </p>
 
@@ -2819,69 +2745,26 @@
       
       
-      <ul>
-
-
-
-
-
-
-
-
-
-
-        
-        
-        
-        
-        
-        
-        
-        
-        
-        
-        <p style="font-style: normal;">s(k=nz) = s(k=nz-1) +
-bc_s_t_val * dzu(nz)</p>
-
-
-
-
-
-
-
-
-
-
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      </ul>
-
-
-
-
-
-
-
-
-
-
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      
-      <p style="font-style: normal;">and&nbsp; </p>
+      
+
+
+
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
 
 
@@ -2968,5 +2851,5 @@
       
       
-      <p style="font-style: normal;">(up to k=nz-1 the prognostic
+      <p style="font-style: normal;">(up to k=nz the prognostic
 equation for the scalar concentration is
 solved).</p>
@@ -14687,5 +14570,5 @@
 logarithmic wind and temperature
 profiles between k=0 and k=1. In this case a Dirichlet condition (see <a href="#bc_pt_b">bc_pt_b</a>)
-must be used as bottom boundary condition for the potential temperature.</p>
+must be used as bottom boundary condition for the potential temperature.</p><p>See also <a href="#top_heatflux">top_heatflux</a>.</p>
 
 
@@ -16807,5 +16690,59 @@
 
 
-    <tr>
+    <tr><td style="vertical-align: top;"><a name="top_heatflux"></a><span style="font-weight: bold;">top_heatflux</span></td><td style="vertical-align: top;">R</td><td style="vertical-align: top;"><span style="font-style: italic;">no prescribed<br>
+heatflux</span></td><td style="vertical-align: top;"><p>Kinematic sensible heat flux at the top boundary (in K m/s).&nbsp; </p>
+
+
+
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <p>If a value is assigned to this parameter, the internal two-dimensional surface heat flux field <span style="font-family: monospace;">tswst</span> is initialized with the value of <span style="font-weight: bold;">top_heatflux</span>&nbsp;as top (horizontally homogeneous) boundary condition for the
+temperature equation. This additionally requires that a Neumann
+condition must be used for the potential temperature (see <a href="chapter_4.1.html#bc_pt_t">bc_pt_t</a>),
+because otherwise the resolved scale may contribute to
+the top flux so that a constant value cannot be guaranteed.<span style="font-style: italic;"></span>&nbsp;</p>
+
+
+
+      
+      
+      
+      <p><span style="font-weight: bold;">Note:</span><br>The application of a top heat flux additionally requires the setting of initial parameter <a href="#use_top_fluxes">use_top_fluxes</a> = .T..<span style="font-style: italic;"></span><span style="font-weight: bold;"></span> </p><p>No Prandtl-layer is available at the top boundary so far.</p><p>See also <a href="#surface_heatflux">surface_heatflux</a>.</p>
+
+
+
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      </td></tr><tr>
 
 
@@ -18336,5 +18273,71 @@
 
 
-    <tr>
+    <tr><td style="vertical-align: top;"><a name="use_top_fluxes"></a><span style="font-weight: bold;">use_top_fluxes</span></td><td style="vertical-align: top;">L</td><td style="vertical-align: top;"><span style="font-style: italic;">.F.</span></td><td style="vertical-align: top;">
+
+
+
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+
+
+
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+
+
+
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      
+      <p>Parameter to steer the treatment of the subgrid-scale vertical
+fluxes within the diffusion terms at k=nz (top boundary).</p><p>By default, the fluxes at nz are calculated using the gradient approach. If <b>use_top_fluxes</b>
+= <i>.TRUE.</i>, the user-assigned top fluxes are used instead
+(see <a href="chapter_4.1.html#top_heatflux">top_heatflux</a>).</p><p>Currently, only a value for the sensible heatflux can be assigned. In case of <span style="font-weight: bold;">use_top_fluxes</span> = <span style="font-style: italic;">.TRUE.</span>, the latent heat flux at the top will be automatically set to zero.</p></td></tr><tr>
 
 
Index: palm/trunk/DOC/app/chapter_4.6.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.6.html	(revision 5)
+++ palm/trunk/DOC/app/chapter_4.6.html	(revision 40)
@@ -1,5 +1,4 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<html>
-<head>
+<html><head>
 
 
@@ -16,5 +15,5 @@
   
   <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252">
-  <title>PALM chapter 4.6</title>
+  
 
 
@@ -37,5 +36,5 @@
   
   
-  <meta name="GENERATOR" content="StarOffice 7 (Win32)">
+  <title>PALM chapter 4.6</title><meta name="GENERATOR" content="StarOffice 7 (Win32)">
 
 
@@ -111,6 +110,5 @@
 @page { size: 21cm 29.7cm }
 -->
-  </style>
-</head>
+  </style></head>
 
 <body style="direction: ltr;" lang="en-US">
@@ -22046,5 +22044,5 @@
 
 
-    <tr>
+    <tr><td><a style="font-weight: bold;" href="chapter_4.1.html#top_heatflux">top_heatflux</a></td><td>I</td><td>R</td><td><span style="font-style: italic;">no prescribed heatflux</span></td><td>Kinematic sensible heat flux at the top surface (in K m/s).</td></tr><tr>
 
 
@@ -23204,5 +23202,7 @@
 
 
-    <tr valign="top">
+    <tr><td><a style="font-weight: bold;" href="chapter_4.1.html#use_top_fluxes">use_top_fluxes</a></td><td>I</td><td>L</td><td><span style="font-style: italic;">.F.</span></td><td>Parameter to steer the treatment of the subgrid-scale
+vertical
+fluxes within the diffusion terms at k=nz (top boundary).</td></tr><tr valign="top">
 
 
@@ -24373,4 +24373,3 @@
 
 
-</body>
-</html>
+</body></html>
Index: palm/trunk/DOC/app/chapter_5.0.html
===================================================================
--- palm/trunk/DOC/app/chapter_5.0.html	(revision 5)
+++ palm/trunk/DOC/app/chapter_5.0.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 5.0</title>
-  <meta name="GENERATOR" content="StarOffice 7  (Win32)">
+<html><head>
+  <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252">
+  
+  <title>PALM chapter 5.0</title><meta name="GENERATOR" content="StarOffice 7  (Win32)">
   <meta name="AUTHOR" content="Siegfried Raasch">
   <meta name="CREATED" content="20041103;12380720">
@@ -14,28 +12,26 @@
 		@page { size: 21cm 29.7cm }
 	-->
-	</style>
-</head>
+	</style></head>
+
 <body dir="ltr" lang="en-US">
 <h2 style="line-height: 100%;"><font size="4">5.0 Installation of the
 model</font></h2>
 <p style="line-height: 100%;"><font color="#000000">This chapter
-describes the installation of PALM on the Linux workstation
-cluster of IMUK and a suitable remote computer (host), on which the
-model runs are actually carried out. The local cluster is used to
-start the batch job with <b>mrun</b> and to analyze the results
-produced by the model. In batch mode, runs can be carried on the
-IBM-Regatta
-system of the HLRN, on an IBM-Regatta at KISTI, Korea </font><font
- color="#000000">(via a local
-DEC-Alpha-workstation at the Department of Atmospheric Sciences of the
-Yonsei University, Seoul)</font><font color="#000000">, and on an
-NEC-SX6 at DKRZ. The examples given in this chapter refer to an
-installation of PALM on the IMUK cluster, considering the IBM-Regatta
+describes the installation of PALM on a Linux workstation (local host) and a suitable remote computer, on which the
+model runs are to be carried out. The local host is used to
+start batch jobs with <b>mrun</b> and to analyze the results
+which are produced by the model on the remote host and send back to the local host. Alternatively, <span style="font-weight: bold;">mrun</span> can also be used to start PALM on the local host in interactive mode or as a batch job.</font></p><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Requirements</span></font></p><p style="line-height: 100%;"><font color="#000000">The installation and operation of PALM requires at mimimum (on both, the local and the remote host, unless stated otherwise):</font></p><ol><li><font color="#000000">The AT&amp;T Korn-shell (ksh) must be available under<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">. Most of the current Linux distributions are using the public domain Korn-shell (pdksh). The PALM scripts <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span> do not work with the pdksh! Please replace it by the AT&amp;T ksh. If the AT&amp;T ksh path is different from<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">/bin/ksh</font><font color="#000000">, please modify the first lines in <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>, respectively.</font></li><li><font color="#000000">The NetCDF-library with version number not earlier than 3.6.0-p1 (for NetCDF, see under <a href="http://www.unidata.ucar.edu/software/netcdf/">www.unidata.ucar.edu</a>).</font></li><li><font color="#000000">A FORTRAN90/95 compiler.</font></li><li><font color="#000000">The Message Passing Interface (MPI), at least on the remote host, if the parallel version of PALM shall be used.</font></li><li><font color="#000000">On the local host, the revision control system <span style="font-weight: bold;">subversion</span> (see <a href="http://subversion.tigris.org/">subversion.tigris.org</a>).
+This is already included in many Linux distributions (e.g. SuSe). The
+user needs a permit to access the PALM repository. For getting a permit
+please contact the PALM group (<a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>)
+and define a username under which you like to access the repository.
+You will then receive a password which allows the access under this
+name.</font></li><li><font color="#000000">A job queueing system must be available on the remote host. Currently, <span style="font-weight: bold;">mrun</span> can handle LoadLeveler (IBM-AIX) and NQS/PBS (Linux-Clusters, NEC-SX).</font></li><li><font color="#000000">ssh/scp-connections to and from the remote host must not be blocked by a firewall.<br></font></li></ol><font color="#000000"><span style="font-weight: bold;"></span></font><font color="#000000"> Currently, <span style="font-weight: bold;">mrun</span> is configured to be used on a limited number of selected machines. These are IBM-Regatta at computing center HLRN in Hannover (<span style="font-style: italic;">ibmh</span>), Berlin (<span style="font-style: italic;">ibmb</span>), at KISTI, Korea (<span style="font-style: italic;">ibms</span>), at Yonsei University, Seoul (<span style="font-style: italic;">ibms</span>), on NEC-SX6/8 systems at DKRZ, Hamburg (<span style="font-style: italic;">nech</span>) and RIAM, Kyushu University, Fukuoka (<span style="font-style: italic;">neck</span>), as well as on the Linux cluster of IMUK (<span style="font-style: italic;">lcmuk</span>) and Tokyo Institute of Technology (<span style="font-style: italic;">lctit</span>). The strings given in brackets are the systems names under which <span style="font-weight: bold;">mrun</span> indentifies the different hosts. mrun should also work on other systems, but this requires some modifications in the scripts <span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>, and <span style="font-weight: bold;">subjob</span>. Future PALM versions will allow to configure the scripts for different kinds of systems by just using a configuration file.</font><p style="line-height: 100%;"><font color="#000000">The examples given in this chapter refer to an
+installation of PALM on an IMUK Linux workstation and the IBM-Regatta
 system of
-the HLRN as the remote computer. </font>
+the HLRN used as&nbsp;remote host. They are just called local and remote host from now on. </font>
 </p>
 <p style="line-height: 100%;">The installation process requires a valid
-account on the IMUK cluster and on the remote host as well. In the
-following the IMUK workstation is called the local host. <br>
+account on the local and on the remote host as well.<br>
 &nbsp; </p>
 <ul>
@@ -49,137 +45,54 @@
 out e.g. on the local host:</p>
   <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
-ssh&nbsp; &lt;username on remote host&gt;@&lt;remote IP-address&gt;</span><br>
+</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on remote host&gt;@&lt;remote IP-address&gt;</span><br>
   </p>
   <p style="line-height: 100%;">and on the remote host:<br>
   </p>
   <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
-ssh&nbsp; &lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
+</span><span style="font-family: Courier New,Courier,monospace;">ssh&nbsp; &lt;username on local host&gt;@&lt;local IP-adddress&gt;</span><br>
   </p>
-  <p style="line-height: 100%;">In both cases you should nnot be
+  <p style="line-height: 100%;">In both cases you should&nbsp;not be
 prompted for a password. <b>Before continuing the further installation
 process, this must be absolutely guaranteed!</b> This must also be
 guaranteed for <b>all</b> other remote hosts, on which PALM shall run.</p>
 </ul>
-<p style="line-height: 100%;">In the <b>first installation step</b> a
+<p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold; text-decoration: underline;">Package Installation</span></p><p style="line-height: 100%;">In the <b>first installation step</b> a
 set of directories must be created both on the local and on the
-remote host. These directories are: </p>
-<ul>
-  <pre style="line-height: 100%;"><font size="2">~/job_queue</font><br><font
- size="2">~/palm</font><br><font size="2">~/palm/current_version</font><br><font
- size="2">~/palm/current_version/SOURCE</font><br><font size="2">~/palm/current_version/JOBS</font></pre>
-</ul>
-<p style="line-height: 100%;">The names of these directories are
+remote host. These directories are:</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/job_queue<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm<br></div><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version<br></div><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS</span><br></div><p style="line-height: 100%;">The names of these directories are
 freely selectable (except <tt><font size="2">~/job_queue</font></tt>),
 however new users should use them as suggested, since many
 examples in this documentation as well as all example files are
-assuming these settings. </p>
+assuming these settings. The directory <span style="font-family: monospace;">~/palm/current_version</span> on the local host will be called the working directory from now on. </p>
 <p style="line-height: 100%;"><font color="#000000">In the <b>second
-step</b> the PALM source code must be copied into directory </font><tt><font
- size="2"><font color="#000000">~/palm/current_version/SOURCE</font></font></tt><font
- color="#000000"> on the local host by carrying out the following
-commands: </font>
-</p>
-<ul>
-  <pre style="line-height: 100%;"><font color="#000000">cd ~/palm/current_version/SOURCE</font><br><font
- color="#000000">ln -s /home/raasch/public_html/PALM_group/INSTALL/RCS .</font><br><font
- color="#000000">cp RCS/*,v .</font><br><font color="#000000">co *,v</font><br><font
- color="#000000">rm -rf *,v</font></pre>
-</ul>
-<p style="line-height: 100%;"><font color="#000000">Afterwards, the
-directory</font><font color="#000000"> </font><tt><font size="2"><font
- color="#000000">~/palm/current_version/SOURCE</font></font></tt><font
- color="#000000">
-should contain</font><font color="#000000"> all PALM routines as well
-as a file with the name </font><tt><font size="2"><font color="#000000">Makefile</font></font></tt><font
- color="#000000">. </font><font color="#000000">All files are
-write-protected, the source code files end on </font><tt><font
- style="font-size: 11pt;" size="2"><font color="#000000">.f90</font></font></tt><font
- color="#000000">.
-The user should never modify these files without further knowledge of
-the PALM code. </font>
-</p>
+step</b>
+a working copy of the recent version of the PALM software package,
+including the source code, scripts, documentation, etc.&nbsp; must be
+copied to the working directory (</font><font color="#000000">local host!) by executing the following
+commands. Replace &lt;your username&gt; by the name that you choosed to access the repository.</font></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">cd ~/palm/current_version</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/trunk</span><br></div><p style="line-height: 100%;"><font color="#000000">You will then be prompted for your password. After finishing, the subdirectory</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> trunk </font><font color="#000000">should
+appear in your working directory. It contains a number of further
+subdirectories which contain e.g. the PALM source code (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SOURCE</font><font color="#000000">) and the scripts for running PALM (</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">SCRIPTS</font><font color="#000000">).</font></p><p style="line-height: 100%;">Alternatively,&nbsp;executing</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/trunk abcde</pre><p style="line-height: 100%;">will place your working copy in a directory named<span style="font-family: Courier New,Courier,monospace;"> abcde </span>instead of a directory named<span style="font-family: Courier New,Courier,monospace;"> trunk</span>. But keep in mind that you will have to adjust several paths given below, if you do not use the default directory<span style="font-family: Courier New,Courier,monospace;"> trunk</span>.</p><p style="line-height: 100%;">Please never touch any file in your working copy of PALM, unless you&nbsp;know exactly what you are doing.</p><p style="line-height: 100%; font-weight: bold;">In future PALM releases, repository access to the most recent PALM version will
+probably be restricted because this is a test version. However, access
+to the last (and earlier) stable version(s) will still be possible with
+(e.g.)</p><pre style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45/palm/tags/release-3.1c trunk</pre><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Package Configuration</span></font></p><p style="line-height: 100%;"><font color="#000000">To
+use the PALM scripts, the PATH variable has to be extended and the
+environment variable PALM_BIN has to be set (on local and remote host)
+in the respective profile of the users default shell (e.g. in<span style="font-family: Courier New,Courier,monospace;"> .profile</span>, if<span style="font-family: Courier New,Courier,monospace;"> ksh </span>is used):</font></p><p style="line-height: 100%; margin-left: 40px;"><font style="font-family: Courier New,Courier,monospace;" color="#000000">export PATH=$HOME/palm/current_version/trunk/SCRIPTS:$PATH</font><font color="#000000"><br><span style="font-family: Courier New,Courier,monospace;">export PALM_BIN=</span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">$HOME/palm/current_version/trunk/SCRIPTS</font></p><p style="line-height: 100%;"><font color="#000000">You may habe to login again in order to activate these settings.</font></p><p style="line-height: 100%;"><font color="#000000">On the local and on the remote host, some small helper/utility programs have to be installed, which are e.g. later used by <span style="font-weight: bold;">mrun</span> or for PALM data postprocessing. The installation is done by <span style="font-weight: bold;">mbuild</span>. This script requires a configuration file<span style="font-family: Courier New,Courier,monospace;"> .mrun.config</span>, which will be also used by <span style="font-weight: bold;">mrun</span> in the following. A copy has to be put into the working directory under the name<span style="font-family: Courier New,Courier,monospace;"> .mrun.config </span>by</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">cp trunk/SCRIPTS/.mrun.config.default .mrun.config</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside many other things, this file contains typical installation parameters
+like compiler name, compiler options, etc.
+for a set of different remote hosts. Please edit this file, uncomment lines like</font></p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">#%remote_username &nbsp;&lt;replace by your ... username&gt; &nbsp; &lt;remote-computer-shortcut&gt;</div><p style="line-height: 100%;"><font color="#000000">by removing the first hash (<span style="font-family: Courier New,Courier,monospace;">#</span>) character and replace the string "<span style="font-family: Courier New,Courier,monospace;">&lt;replace by ...&gt;</span>" by your username on the respective host given in the <span style="font-family: Courier New,Courier,monospace;">&lt;remote-computer-shortcut&gt;</span>. You only have to uncomment lines for those hosts on which you intend to use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">After modifying the configuration file, the respective executables are generated by executing</font></p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild -u -h lcmuk<br>mbuild -u -h ibmh</font></p><p style="line-height: 100%;"><font color="#000000">The second call also copies the PALM scripts like <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span> to the remote host.</font></p><p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold; text-decoration: underline;">Pre-Compilation of PALM Code</span></font></p><font color="#000000">
+</font>
 <p style="line-height: 100%;"><font color="#000000">To avoid the
 re-compilation of the complete source code for each model run, PALM
-willl be pre-compiled once on the remote host. Due to the use of
+willl be pre-compiled once on the remote host by again using the script <span style="font-weight: bold;">mbuild</span>. Due to the use of
 FORTRAN modules in the source code, the subroutines must be compiled
-in a certain sequence. Therefore the so-called <i>make</i> mechanism
+in a certain order. Therefore the so-called <i>make</i> mechanism
 is used (see the respective man-page of the Unix operating system),
-requiring the file </font><tt><font color="#000000">Makefile</font></tt><font
- color="#000000">,
-in which the dependencies are described. The compiled sources (object
+requiring a<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">Makefile</font><font color="#000000">,
+in which the dependencies are described. This file is found in subdirectory <span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE<span style="font-family: Times New Roman,Times,serif;">, where also the PALM code is stored</span></span>. The compiled sources (object
 files) are
-stored on the remote computer in the directory
-</font><tt><font color="#000000">~/palm/current_version/SOURCE/MAKE_DEPOSITORY</font></tt><font
- color="#000000">.<br>
-&nbsp;<br>
-For pre-compilation the user has to</font> call <font color="#000000">the
-command <b>mbuild</b>, which requires some pre-settings. The path
-variable must be extended on <b>both</b> computers, so that the
-commands <b>mbuild</b> and <b>mrun</b> as well as further routines
-needed by <span style="font-weight: bold;">mrun</span> can be found.
-This is achieved on the local computer via:: </font>
-</p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- color="#000000">PATH=$PATH:/home/raasch/pub,</font></pre>
-</ul>
-<p style="line-height: 100%;"><font color="#000000">and on the IBM
-Regatta
-system of the HLRN via</font></p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- color="#000000">PATH=$PATH:/home/h/niksiraa/pub.</font></pre>
-</ul>
-<p style="line-height: 100%;"><font color="#000000">These path
-extensions must be automatically set in the profiles of the local and
-remote host (file "~/.myprofile" at IMUK, file "~/.profile" at HLRN)</font><font
- color="#000000">.
-</font></p>
-<p style="line-height: 100%;"><font color="#000000">It is now assumed
-that the working directory is
-</font><tt><font color="#000000">~/palm/current_version/SOURCE</font></tt><font
- color="#000000">
-on the local host. Compilation of the PALM code via <b>mbuild </b>needs
-a </font><a
- href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config"><font
- color="#000080">configuration
-file</font></a><font color="#000080">,</font><font color="#000000">
-which must be copied to the working directory under name
-</font><tt><font color="#000000">.mrun.config</font></tt><font
- color="#000000">
-(please click on the link with &lt;SHIFT&gt; + left mouse button)</font><font
- color="#000000">. This file contains typical installation parameters
-like compiler name, compiler options, etc.
-for a set of different remote hosts. This file is also needed later on
-for starting the model runs. </font>
-</p>
-<p style="line-height: 100%;"><font color="#000000">In the
-configuration file </font><tt><font color="#000000">.mrun.config</font></tt><font
- color="#000000">
-the user name on the respective remote host must be entered. In lines
-like</font>
-</p>
-<ul>
-  <p style="line-height: 100%;"><tt><font color="#000000">%
-remote_username &lt;username&gt; &lt;remote-computer-shortcut&gt;</font></tt></p>
-</ul>
-the string "<span style="font-family: monospace;">&lt;username&gt;</span>"
-has to be replaced by the actual name of the user on the respective
-remote host (e.g. "nik....." on HLRN).<font color="#000000">
-</font>
-<p style="line-height: 100%;"><font color="#000000">After this, the
-pre-compilation for the IBM-Regatta of HLRN can be started by entering</font><font
- color="#000000"> </font>
-</p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- color="#000000">mbuild - h ibmh  .</font></pre>
-</ul>
-<p style="line-height: 100%;"><span style="font-family: monospace;">mbuild</span>
-will prompt some queries<font color="#000000">, which must all be
-answered "y" by the user. The compiling process </font><font
- color="#000000">will take some time. </font><font color="#000000"><span
- style="font-family: monospace;">mbuild</span></font><font
- color="#000000"> transfers the respective compiler calls to the remote
+stored&nbsp;on the remote computer in the default directory
+</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/palm/current_version/MAKE_DEPOSITORY</font>.<font color="#000000"><span style="font-weight: bold;"></span></font></p><p style="line-height: 100%;"><font color="#000000">The
+pre-compilation for the remote host (here the IBM-Regatta of HLRN) is done by</font><span style="font-family: monospace;"></span></p><div style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mbuild -h ibmh&nbsp;&nbsp;</span></div><p style="line-height: 100%;"><span style="font-family: Courier New,Courier,monospace;">mbuild
+</span>will prompt some queries<font color="#000000">, which must all be
+answered "y" by the user. The compiling process </font><font color="#000000">will take some time.<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">mbuild</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>transfers the respective compiler calls to the remote
 host where they are carried out interactively. You can follow the
 progress at the terminal window, where also error messages
@@ -187,76 +100,51 @@
 entering </font>
 </p>
-<blockquote style="line-height: 100%;"><tt><font color="#000000">mbuild</font></tt></blockquote>
+<blockquote style="line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mbuild</font></blockquote>
 <p style="line-height: 100%;"><font color="#000000">PALM will
 be (consecutively) pre-compiled for all remote hosts listed in
-the configuration file. </font>
+the configuration file. If you want to compile for the local host only, please enter</font></p><p style="line-height: 100%; margin-left: 40px;"><font color="#000000"><span style="font-family: Courier New,Courier,monospace;">mbuild -h lcmuk</span> </font>
 </p>
-<p style="line-height: 100%;"><font color="#000000">As a last step,
+<p style="line-height: 100%;"><font color="#000000"></font></p><p style="line-height: 100%; font-weight: bold; text-decoration: underline;"><font color="#000000">Installation Verification</font></p><p style="line-height: 100%;"><font color="#000000">As a last step,
 after the compilation has been finished, the PALM installation has to
 be verified. For this
 purpose a simple test run is carried out. This once again requires the <b>mrun
-</b>configuration file (described in </font><a href="chapter_3.2.html"><font
- color="#000080">chapter
-3.2</font></a><font color="#000000">), as well as the </font><a
- href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font
- color="#000080">parameter
-file</font></a><font color="#000000"> (described in </font><a
- href="chapter_4.4.html"><font color="#000080">chapter
-4.4</font></a>)<font color="#000000">. The parameter file must be&nbsp;
-copied to<br>
+</b>configuration file (described in </font><a href="chapter_3.2.html"><font color="#000080">chapter
+3.2</font></a><font color="#000000">), as well as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font color="#000080">parameter
+file</font></a><font color="#000000"> (described in </font><a href="chapter_4.4.html"><font color="#000080">chapter
+4.4</font></a>)<font color="#000000">. The parameter file must be
+copied from the PALM working copy by<br>
 </font></p>
-<p style="line-height: 100%;"><tt><font color="#000000">&nbsp;&nbsp;&nbsp;
-~/palm/current_version/JOBS/example/INPUT/example_p3d</font></tt><font
- color="#000000">&nbsp;&nbsp; .
-</font></p>
+<div style="margin-left: 40px;"><span style="font-family: monospace;"></span><font style="font-family: Courier New,Courier,monospace;" color="#000000">mkdir -p JOBS/example/INPUT<br>cp trunk/INSTALL/example_p3d&nbsp;JOBS/example/INPUT/example_p3d</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"></span></font></div>
 <p style="line-height: 100%;"><font color="#000000">The test run can
-now be started by entering the command: </font>
+now be started by executing the command </font>
 </p>
-<pre
- style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%;"><font
- color="#000000">mrun -d example -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r d3# pr#</font></pre>
+<pre style="margin-left: 1cm; margin-right: 1cm; margin-bottom: 0.5cm; line-height: 100%; font-family: Courier New,Courier,monospace;"><font color="#000000">mrun -d example -h ibmh -K parallel -X 8 -T 8 -t 500 -q cdev -r &ldquo;d3# pr#&rdquo;</font></pre>
 <p style="line-height: 100%;"><font color="#000000">This specific run
 will be carried out on 8 PEs and is allowed to use up to 500 seconds
 CPU time. After pressing &lt;return&gt;, the most important settings of
 the job are displayed at the terminal window
-and the user is prompted for o.k. (</font><tt><font color="#000000">y</font></tt><font
- color="#000000">).
-Afterwards a message of the queuing system like <i>Request</i> 
-
-<i>Submitted to queue
- by
- </i>should be displayed. Now the job is
-queued either started immediately or at a later time, depending on the
+and the user is prompted for o.k. (&ldquo;</font><font style="font-family: Courier New,Courier,monospace;" color="#000000">y</font><font color="#000000">&rdquo;). Next, a message of the queuing system like &ldquo;<i>Request</i> &hellip;
+<i>Submitted to queue&hellip; by&hellip;&rdquo; </i>should be displayed. Now the job is
+queued and either started immediately or at a later time, depending on the
 current workload of the remote host. Provided that it is executed
 immediately and that all things work as designed, the job protocol of
-this run will appear under the file name </font><tt><font
- color="#000000">~/job_queue/ibmh_example</font></tt><font
- color="#000000"> no more than 3 minutes later. The content of this
+this run will appear under the file name<span style="font-family: Courier New,Courier,monospace;"> </span></font><font style="font-family: Courier New,Courier,monospace;" color="#000000">~/job_queue/ibmh_example</font><font color="#000000"><span style="font-family: Courier New,Courier,monospace;"> </span>no more than a few minutes later. The content of this
 file should be carefully examined for any error messages.</font>
 </p>
+
+
 <p style="line-height: 100%;">Beside the job protocol and according to
 the configuration file and arguments given for <b>mrun</b>
-options <tt>-d</tt> and <tt>-r,</tt>further files should be found in
+options<span style="font-family: Courier New,Courier,monospace;"> -d </span>and<span style="font-family: Courier New,Courier,monospace;"> -r</span><tt>,</tt>further files should be found in
 the
-directories<br>
-</p>
-<p style="line-height: 100%; font-family: monospace;">&nbsp;&nbsp;&nbsp;
-~/palm/current_version/JOBS/example/MONITORING
-<br>
-</p>
-<p style="line-height: 100%;">and</p>
+directories</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING</div><p style="line-height: 100%;">and</p>
 <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
-~/palm/current_version/JOBS/example/OUTPUT&nbsp; .
-</span><br>
+</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/OUTPUT</span><span style="font-family: monospace;"></span><br>
 </p>
 <p style="line-height: 100%;">Please compare the contents of file</p>
 <p style="line-height: 100%;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
-~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
+</span><span style="font-family: Courier New,Courier,monospace;">~/palm/current_version/JOBS/example/MONITORING/ibmh_example_rc</span><br>
 </p>
-<p style="line-height: 100%;">with those of the <a
- href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_rc">result
-example file</a> (e.g. with the help of the UNIX-command <span
- style="font-family: monospace;">diff</span>). There should be not a
-single difference between these two files. <font color="#000000">If
+<p style="line-height: 100%;">with those of the example result file which can be found under<span style="font-family: Courier New,Courier,monospace;"> trunk/INSTALL/example_rc</span>., e.g. by using the<span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"> standard</span> diff </span>command:</p><p style="line-height: 100%; margin-left: 40px; font-family: Courier New,Courier,monospace;">diff &nbsp;JOBS/example/MONITORING/ibmh_example_rc trunk/INSTALL/example_rc</p><p style="line-height: 100%;">where it is assumed that your working directory is<span style="font-family: Courier New,Courier,monospace;"> ~/palm/current_version</span>.</p><p style="line-height: 100%;"><span style="font-weight: bold;">You should not find any difference between these two files</span>, except of the run date and time displayed at the top of the file header. <font color="#000000">If
 the file contents are identical, the installation is successfully
 completed.</font> </p>
@@ -265,13 +153,5 @@
 help you. &nbsp; </p>
 <hr>
-<p style="line-height: 100%;"><font color="#000080"><font
- color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img
- src="left.gif" name="Grafik1" align="bottom" border="2" height="32"
- width="32"></font></a><a href="Inhaltsverzeichnis.html"><font
- color="#000080"><img src="up.gif" name="Grafik2" align="bottom"
- border="2" height="32" width="32"></font></a><a href="chapter_5.1.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> 20/04/05 (SR) </p>
-</body>
-</html>
+<p style="line-height: 100%;"><font color="#000080"><font color="#000080"><a href="chapter_4.6.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="Inhaltsverzeichnis.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_5.1.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>
Index: palm/trunk/DOC/app/chapter_5.1.html
===================================================================
--- palm/trunk/DOC/app/chapter_5.1.html	(revision 5)
+++ palm/trunk/DOC/app/chapter_5.1.html	(revision 40)
@@ -1,3 +1,4 @@
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"><html><head>
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html><head>
   <meta content="text/html; charset=windows-1252" http-equiv="CONTENT-TYPE"><title>PALM chapter 5.1</title>
   
@@ -6,33 +7,31 @@
   <meta content="20041103;12395815" name="CREATED">
   <meta content="20041119;12321236" name="CHANGED">
-  <meta content="parallel LES model" name="KEYWORDS"></head>
-
-<body lang="en-US" dir="ltr">
-<h3>5.1 Installation of new versions</h3>
-<p>The PALM developer group announces code revisions within the
+  <meta content="parallel LES model" name="KEYWORDS"></head><body dir="ltr" lang="en-US">
+<h3>5.1 Installation of new / other versions</h3>
+<p>The PALM&nbsp;group announces code revisions by emails send to the
+PALM mailing list. If you like to be put on this list, just send an
+email to <a href="mailto:raasch@muk.uni-hannover.de">raasch@muk.uni-hannover.de</a>. Details about new releases can be found in the
 <a href="../tec/technical_documentation.html">technical/numerical
-documentation</a>. Users can carry out version updates by changing into
-the working directory
-<span style="font-family: monospace;">~/palm/current_version/SOURCE</span>
-and entering </p>
-<ul>
-  <pre style="margin-bottom: 0.5cm;">co *.f90.</pre>
-</ul>
-<p>This updates all source code files. </p>
-<p><b>Note:</b> if the user should have changed this source code, then
-these changes are certainly lost! This is one reason why
-modifications of the basic source code should be omitted and
+documentation</a>. Users can easily make version updates by changing into
+the working directory<span style="font-family: Courier New,Courier,monospace;">
+~/palm/current_version
+</span>and executing<span style="font-family: Courier New,Courier,monospace;"></span></p><p style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">svn update</span></p><p><span style="font-family: Courier New,Courier,monospace;"></span>This updates all files in the PALM working copy in subdirectory<span style="font-family: Courier New,Courier,monospace;"> trunk</span>. The update may fail due&nbsp;the&nbsp;<span style="font-weight: bold;">subversion</span> rules, if you have modified the contents of<span style="font-family: Courier New,Courier,monospace;"> trunk</span>. In case of any conflicts, please refer to the <span style="font-weight: bold;">subversion</span> documentation on how to remove them.&nbsp;In order to avoid such conflicts, modifications of the default PALM code should be omitted and
 be restricted to the user-interface only
 (see <a href="chapter_3.5.html">chapter
-3.5</a>). </p>
-<p>After updating the source code the pre-compiled code must be updated
-via </p>
-<ul>
-  <pre style="margin-bottom: 0.5cm;">mbuild -h ibmh</pre>
+3.5</a>).</p>
+<ul style="font-family: Courier New,Courier,monospace;">
 </ul>
-<p>on the IBM-Regatta "hanni" of the HLRN or via</p>
-<blockquote style="font-family: monospace;">mbuild</blockquote>
-<p>on all remote hosts listed in the configuration file
-<span style="font-family: monospace;">.mrun.config</span>. </p>
+
+<p>Alternatively, you can install new or other releases in a different directory, eg.</p><p style="margin-left: 40px;"><span style="font-family: Courier New,Courier,monospace;">mkdir ~/palm/release-3.1c</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">cd ~/palm/release-3.1c</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">svn checkout --username &lt;your username&gt; svn://130.75.105.45:palm/tags/release-3.1c trunk</span></p>
+<p>However, this would require to carry out again the complete
+installation process described in chapter 5.0. So far, differet
+versions of PALM cannot be used at the same time.</p><p>After updating the working copy, please check for any differences between your current configuration file (<span style="font-family: Courier New,Courier,monospace;">.mrun.config</span>) and the default configuration file under<span style="font-family: Courier New,Courier,monospace;"> trunk/SCRIPTS/.mrun.config.default </span>and adjust your current file, if neccessary.</p><p>The scripts and the pre-compiled code must then be updated
+via</p><div style="margin-left: 40px; font-family: Courier New,Courier,monospace;">mbuild -u -h lcmuk<br>mbuild -u -h ibmh<br>mbuild -h ibmh</div><p>or via</p>
+<ul style="font-family: Courier New,Courier,monospace;">
+</ul>
+
+<blockquote style="font-family: Courier New,Courier,monospace;">mbuild -u<br>mbuild</blockquote>
+<p>on all remote hosts listed in the configuration file<span style="font-family: Courier New,Courier,monospace;">
+.mrun.config</span>. </p>
 <p>As a last step, a suitable test run should be carried out. It should
 be carefully examined whether and how the results created by the new
@@ -40,12 +39,12 @@
 which go beyond the ones announced in the <a href="../tec/technical_documentation.html">technical/numerical
 documentation</a>
-should be communicated as soon as possible to the PALM developer group.
+should be communicated as soon as possible to the PALM group.
 </p>
 <hr>
 <p><br>
-<font color="#000080"><font color="#000080"><a href="chapter_5.0.html"><font color="#000080"><img width="32" height="32" border="2" align="bottom" name="Grafik1" src="left.gif"></font></a><a href="index.html"><font color="#000080"><img width="32" height="32" border="2" align="bottom" name="Grafik2" src="up.gif"></font></a></font></font><br>
+<font color="#000080"><font color="#000080"><a href="chapter_5.0.html"><font color="#000080"><img name="Grafik1" src="left.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img name="Grafik2" src="up.gif" align="bottom" border="2" height="32" width="32"></font></a></font></font><br>
 &nbsp;
 <br>
-&nbsp;<span style="font-style: italic;">Last change:</span> 20/04/05
+&nbsp;<span style="font-style: italic;">Last change:</span> 02/03/07
 (SR)<br>
 </p>
