Index: palm/trunk/DOC/app/chapter_3.8.html
===================================================================
--- palm/trunk/DOC/app/chapter_3.8.html	(revision 108)
+++ palm/trunk/DOC/app/chapter_3.8.html	(revision 130)
@@ -3,33 +3,18 @@
 <head>
 
-
-  
   <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252">
-
-  
+  <title>PALM chapter 3.8</title>
 
 
-  
-  <title>PALM chapter 3.8</title>
   <meta name="GENERATOR" content="StarOffice 7 (Win32)">
 
-
-  
   <meta name="AUTHOR" content="Siegfried Raasch">
 
-
-  
   <meta name="CREATED" content="20040809;13460943">
 
-
-  
   <meta name="CHANGED" content="20041112;15085727">
 
-
-  
   <meta name="KEYWORDS" content="parallel LES model">
 
-
-  
   <style>
 <!--
@@ -42,7 +27,5 @@
 <body style="direction: ltr;" lang="en-US">
 
-
 <h3 style="line-height: 100%;">3.8 Coupled model runs</h3>
-
 
 <p style="line-height: 100%;">Starting from version 3.4
@@ -51,5 +34,4 @@
 starts the coupled model as two concurrent executables, the atmosphere
 version and&nbsp;the ocean version of PALM.</p>
-
 
 <p style="line-height: 100%;">Currently, the coupler
@@ -60,5 +42,4 @@
 atmosphere and ocean processors, which does not necessarily guarrantee
 a good load balancing.</p>
-
 
 <p style="line-height: 100%;">The coupler establishes a
@@ -73,6 +54,10 @@
 (see e.g. Steinhorn 1991, JPO 21, p. 1681).</p>
 
-
-<p style="line-height: 100%;">To start a
+<p style="line-height: 100%;">The full MPI-2
+standard must be available in order to use the coupling, and it must be
+activated by adding the preprocessor directive <tt><font style="font-size: 10pt;" size="2">-D__mpi2</font></tt>
+to <tt><font style="font-size: 10pt;" size="2">cpp_options</font></tt>
+in the .mrun.config configuration file. (Note: MPI-2 is
+not available for the IBM-Regatta systems.) To start a
 coupled&nbsp;model run,
 this must be requested with the <b>mrun</b> option <tt><font style="font-size: 10pt;" size="2">-Y</font>.</tt>
@@ -84,24 +69,18 @@
 </p>
 
-
 <ul>
 
-
-  
   <p style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2">mrun </font></tt><font style="font-size: 10pt;" size="2">...</font><tt><font style="font-size: 10pt;" size="2"> -K parallel -r
 &ldquo;d3# d3o# </font></tt><font style="font-size: 10pt;" size="2">...</font><tt><font style="font-size: 10pt;" size="2">&rdquo;</font></tt><tt><font style="font-size: 10pt;" size="2"> </font></tt><tt><font style="font-size: 10pt;" size="2">-X </font></tt><font style="font-size: 10pt;" size="2">...</font><tt><font style="font-size: 10pt;" size="2"> -Y</font></tt><tt>.</tt></p>
 
-
 </ul>
-
 
 <p style="line-height: 100%;">The <tt><font style="font-size: 10pt;" size="2">-X </font></tt><font style="font-size: 10pt;" size="2">...</font><tt><font style="font-size: 10pt;" size="2">&nbsp;</font></tt>option
 here specifies the total number of processors assigned to the coupled
-model. Half of them are assigned to each of the two coupled
+model. Currently, half of them are assigned to each of the two coupled
 executables. Therefore it is advisable to specify an even number
 with&nbsp;<tt><font style="font-size: 10pt;" size="2">-X </font></tt><font style="font-size: 10pt;" size="2">...</font><tt>
 </tt>. Otherwise, in case of an odd total number of processors,
 one processor remains idle.</p>
-
 
 <p style="line-height: 100%;">Each coupled executable has
@@ -114,7 +93,5 @@
 duplicated as follows:</p>
 
-
 <pre style="line-height: 100%;"><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<br>#</font><br><a href="chapter_3.4.html#RUN_CONTROL"><font style="font-size: 10pt;" size="2">RUN_CONTROL</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr d3# ~/palm/current_version/JOBS/$fname/MONITORING _rc</font><br><a href="chapter_3.4.html#HEADER"><font style="font-size: 10pt;" size="2">HEADER</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr d3# ~/palm/current_version/JOBS/$fname/MONITORING _header</font><br><a href="chapter_3.4.html#PLOT1D_PAR"><font style="font-size: 10pt;" size="2">PLOT1D_PAR</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr pr# ~/palm/current_version/JOBS/$fname/OUTPUT _pr_par</font><br><a href="chapter_3.4.html#PLOT1D_DATA"><font style="font-size: 10pt;" size="2">PLOT1D_DATA</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr pr# ~/palm/current_version/JOBS/$fname/OUTPUT _pr_in<br>#<br></font><font style="font-size: 10pt;" size="2">PARIN</font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">_O</span> in:job:npe d3<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/INPUT <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">p3d</font><br><font style="font-size: 10pt;" size="2">PARIN<span style="font-weight: bold;">_O</span> in:job:npe d3<span style="font-weight: bold;">o</span>f ~/palm/current_version/JOBS/$fname/INPUT <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">p3df</font><br><font style="font-size: 10pt;" size="2">BININ</font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">_O</span> in:loc d3<span style="font-weight: bold;">o</span>f ~/palm/current_version/JOBS/$fname/OUTPUT <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">d3d</font><br><font style="font-size: 10pt;" size="2">#</font><br><font style="font-size: 10pt;" size="2">BINOUT</font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">_O</span> out:loc restart ~/palm/current_version/JOBS/$fname/OUTPUT <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">d3d</font><br><font style="font-size: 10pt;" size="2">#</font><br><font style="font-size: 10pt;" size="2">RUN_CONTROL<span style="font-weight: bold;">_O</span></font><font style="font-size: 10pt;" size="2"> out:loc:tr d3<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/MONITORING <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">rc</font><br><font style="font-size: 10pt;" size="2">HEADER</font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">_O</span> out:loc:tr d3<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/MONITORING <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">header</font><br><font style="font-size: 10pt;" size="2">PLOT1D_PAR<span style="font-weight: bold;">_O</span></font><font style="font-size: 10pt;" size="2"> out:loc:tr pr<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/OUTPUT <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">pr_par</font><br><font style="font-size: 10pt;" size="2">PLOT1D_DATA</font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">_O</span> out:loc:tr pr<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/OUTPUT <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">pr_in</font><br></pre>
-
 
 <p style="line-height: 100%;">The coupled ocean model
@@ -125,24 +102,32 @@
 may be changed at the user's discretion.</p>
 
-
-
-
 <p style="line-height: 100%;">The coupler requires the
 following parameters to be equal in both <a href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2"><span style="font-family: mon;"></span>PARIN</font></a>
 and&nbsp;<a href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN_O</font></a>:
 <a href="chapter_4.1.html#dx">dx</a>, <a href="chapter_4.1.html#dy">dy</a>, <a href="chapter_4.1.html#nx">nx</a>, <a href="chapter_4.1.html#ny">ny</a>, <a href="chapter_4.2.html#dt_coupling">dt_coupling</a>, <a href="chapter_4.2.html#end_time">end_time</a>, <a href="chapter_4.2.html#restart_time">restart_time</a>,
-<a href="chapter_4.2.html#dt_restart">dt_restart</a>. In the coupled atmosphere executable,&nbsp;<a href="chapter_4.2.html#bc_pt_b">bc_pt_b</a> is internally set and does not need to be prescribed; in the coupled ocean executable, <a href="chapter_4.2.html#bc_uv_t">bc_uv_t</a>&nbsp;is internally set ('neumann') and does not need to be prescribed. The coupled ocean parameter file&nbsp;<a href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN_O</font></a> should include dummy REAL value assignments to both <a href="chapter_4.1.html#top_momentumflux_u">top_momentumflux_u</a> and&nbsp;<a href="chapter_4.1.html#top_momentumflux_v">top_momentumflux_v</a> (e.g.&nbsp;top_momentumflux_u = 0.0, top_momentumflux_v = 0.0) to enable the momentum flux coupling.</p>
-<p style="line-height: 100%;">The coupling interval  <a href="chapter_4.2.html#dt_coupling">dt_coupling</a> must be explicity set. In order to ensure synchronous coupling throughout the simulation, <a href="chapter_4.2.html#dt_coupling">dt_coupling</a> should be chosen larger than
+<a href="chapter_4.2.html#dt_restart">dt_restart</a>.
+In the coupled atmosphere executable,&nbsp;<a href="chapter_4.2.html#bc_pt_b">bc_pt_b</a> is
+internally set and does not need to be prescribed; in the coupled ocean
+executable, <a href="chapter_4.2.html#bc_uv_t">bc_uv_t</a>&nbsp;is
+internally set ('neumann') and does not need to be prescribed. The
+coupled ocean parameter file&nbsp;<a href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN_O</font></a>
+should include dummy REAL value assignments to both <a href="chapter_4.1.html#top_momentumflux_u">top_momentumflux_u</a>
+and&nbsp;<a href="chapter_4.1.html#top_momentumflux_v">top_momentumflux_v</a>
+(e.g.&nbsp;top_momentumflux_u = 0.0, top_momentumflux_v = 0.0) to
+enable the momentum flux coupling.</p>
+
+<p style="line-height: 100%;">The coupling interval <a href="chapter_4.2.html#dt_coupling">dt_coupling</a>
+must be explicity set. In order to ensure synchronous coupling
+throughout the simulation, <a href="chapter_4.2.html#dt_coupling">dt_coupling</a>
+should be chosen larger than
 <a href="chapter_4.2.html#dt_max">dt_max</a>.</p>
+
 <hr>
 <p style="line-height: 100%;"><br>
 
-
 <font color="#000080"><font color="#000080"><a href="chapter_3.7.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" src="left.gif" name="Grafik1"></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_4.0.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> ++</p>
-
+change:&nbsp;</i> $Id$</p>
 
 </body>
