source: palm/trunk/DOC/app/chapter_3.2.html @ 97

Last change on this file since 97 was 97, checked in by raasch, 15 years ago

ocean version including prognostic equation for salinity and equation of state for seawater. Routine buoyancy can be used with both temperature and density.
+ inipar-parameters bc_sa_t, bottom_salinityflux, ocean, sa_surface, sa_vertical_gradient, sa_vertical_gradient_level, top_salinityflux

advec_s_bc, average_3d_data, boundary_conds, buoyancy, check_parameters, data_output_2d, data_output_3d, diffusion_e, flow_statistics, header, init_grid, init_3d_model, modules, netcdf, parin, production_e, prognostic_equations, read_var_list, sum_up_3d_data, swap_timelevel, time_integration, user_interface, write_var_list, write_3d_binary

eqn_state_seawater, init_ocean


inipar-parameter use_pt_reference renamed use_reference

hydro_press renamed hyp, routine calc_mean_pt_profile renamed calc_mean_profile

format adjustments for the ocean version (run_control)

advec_particles, buoyancy, calc_liquid_water_content, check_parameters, diffusion_e, diffusivities, header, init_cloud_physics, modules, production_e, prognostic_equations, run_control


Bugfix: height above topography instead of height above level k=0 is used for calculating the mixing length (diffusion_e and diffusivities).

Bugfix: error in boundary condition for TKE removed (advec_s_bc)

advec_s_bc, diffusion_e, prognostic_equations

  • Property svn:keywords set to Id
File size: 22.0 KB
1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
3<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 3.2</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Marcus Oliver Letzel"> <meta name="CREATED" content="20040726;13164873"> <meta name="CHANGED" content="20050119;9245042"> <meta name="KEYWORDS" content="parallel LES model"> <style>
5@page { size: 21cm 29.7cm }
8<body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">3.2 Example of a minimum
11<p style="line-height: 100%;">In this chapter a sample
13file is described. It contains only instructions which are really
14necessary for the execution of a simple model run (configuration
15files can be much more complex). The example presented here is stored
16in an appropriate <a href="">example
17file</a> (containing more than the configuration data presented
19and can be used, together with the <a href="">parameter
20file</a> presented in <a href="chapter_4.4.1.html">chapter
214.4.1</a>, for the execution of a simple model run. In chapter 4.4.1
23complete <b>mrun</b> options which are necessary for the
25parameter file are described. Furthermore not all details of the
26configuration file are described here. Therefore you should take a
27look at the <a href="">mrun</a>
28documentation (sorry: this is only available in German, so far. If you
29think that you
30would profit from an English version, please give a message to the PALM
31group). </p>
32<p style="line-height: 100%;">The following configuration
34exclusively applies to model runs on the IBM Regatta hanni of the
35HLRN when using several processing elements (i.e. for the parallel
36version of the model). The proper installation of the model is
37presumed (see <a href="chapter_5.0.html">chapter
385.0</a>). Furthermore it is supposed that the user is located in
40directory <tt><font style="font-size: 10pt;" size="2">$HOME/palm/current_version/SOURCE</font></tt>
41on its local computer. There are the FORTRAN source codes of the
42model (<tt><font style="font-size: 10pt;" size="2">*.f90</font></tt>)
44well as the configuration file (name: <tt><font style="font-size: 10pt;" size="2">.mrun.config</font></tt>)
45and the make file (name: <tt><font style="font-size: 10pt;" size="2">Makefile</font></tt>).
46The configuration file has the following contents (among other things):
48</p><pre style="line-height: 100%;"><font style="font-size: 10pt;" size="2">% source_path <i>$HOME/palm/current_version/SOURCE</i></font><br><font style="font-size: 10pt;" size="2">% mainprog <i>palm.f90</i></font><br><font style="font-size: 10pt;" size="2">% use_makefile <i>true</i></font><br><font style="font-size: 10pt;" size="2">% fopts <i>-O3:-g:-qrealsize=8:-Q:-q64:-qmaxmem=-1:-qtune=pwr4:-qarch=pwr4:-qnosave:-qnoescape ibmh parallel<span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></i></font><br><font style="font-size: 10pt;" size="2">% lopts <span style="font-style: italic;">-O3:-g:-qrealsize=8:-Q:-q64:-qmaxmem=-1:-qtune=pwr4:-qarch=pwr4:-qnosave:-qnoescape:-lesslsmp ibmh parallel</span></font><br><font style="font-size: 10pt;" size="2">#</font><br><font style="font-size: 10pt;" size="2">EC:[[ \$locat = execution]] &amp; &amp; <i>cat </i>RUN_CONTROL </font><br><font style="font-size: 10pt;" size="2">#</font><br><a href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN</font></a><font style="font-size: 10pt;" size="2"> in:job:npe d3# ~/palm/current_version/JOBS/$fname/INPUT _p3d</font><br><font style="font-size: 10pt;" size="2">#</font><br><a href="chapter_3.4.html#RUN_CONTROL"><font style="font-size: 10pt;" size="2">RUN_CONTROL</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr d3# ~/palm/current_version/JOBS/$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</font></pre>
49<p style="line-height: 100%;"><font face="Thorndale, serif">The first
50five lines specify values of
51so-called environment variables. Such lines begin with a
53sign. After at least one blank the name of the variable</font> <font face="Thorndale, serif">(e.g.
54</font><tt><i><font face="Thorndale, serif">source_path</font></i></tt><font face="Thorndale, serif">)
55follows and then seperated by at least one blank the value of the
56variable. Again separated by blank t<font face="Thorndale, serif">he
57so-called validity domain</font> can be indicated (later more).
58With the first three variables <b>mrun</b> gets to know in
60directory the source code lies (</font><tt><i><font face="Thorndale, serif">source_path</font></i></tt><font face="Thorndale, serif">),
61the file name of the main program (</font><tt><i><font face="Thorndale, serif">mainprog</font></i></tt><font face="Thorndale, serif">)
62and that the <font face="Thorndale, serif">make mechanism
63should be
64used </font>for compiling (</font><tt><font face="Thorndale, serif"><i>use_makefile
65=</i> <i>true</i></font></tt><font face="Thorndale, serif">). <b>mrun
66</b>needs these information, <font color="#000000">because
67for each
68model run the executable is created by compiling the source files.</font>
69Normally, only the main program (palm.f90) will be compiled while all
70other object files are just linked. These object files have already
71been created from the source code files during the installation of the
73(see </font><a href="chapter_5.0.html"><font face="Thorndale, serif">chapter
745.0</font></a><font face="Thorndale, serif">).
75<b>mrun</b> uses
76certain standard options for the compilation process. Beyond that you
78declare additional options with the environment variable </font><tt><i><font face="Thorndale, serif">fopts</font></i></tt><font face="Thorndale, serif">.
79Within the value assignment of an environment variable in the
80configuration file no blanks must be
81used. If blanks are necessary they must <font face="Thorndale, serif">be
82replaced </font>by colons (&ldquo;:&rdquo;). <b>mrun</b>
84interpret these colons as blanks (2 colons written one behind the
85other will be interpreted as a colon). Thus in the example above</font> fopts
86has the value<tt><font face="Thorndale, serif"> </font></tt>&ldquo;<font style="font-size: 10pt; font-family: monospace;" size="2"><i>-O3
88-qrealsize=8 -Q -q64 -qmaxmem=-1 -qtune=pwr4 -qarch=pwr4 -qnosave
89-qnoescape</i></font><tt><i><font face="Thorndale, serif"><font color="#000000">&rdquo;</font></font></i></tt><font face="Thorndale, serif"><font color="#000000">.
90Thus a PALM executable is generated using high level optimization (</font></font><font color="#000000"><span style="font-style: italic; font-family: monospace;">-O3</span></font><font face="Thorndale, serif"><font color="#000000">).</font></font><font color="#000000"><font face="Thorndale, serif">
91For all other options
92see the compiler manual on the IBM (</font><font size="2"><font face="Cumberland, monospace">man</font></font></font><tt><font color="#000000">
93<font size="2"><font face="Cumberland, monospace">f90</font></font></font></tt><font face="Thorndale, serif"><font color="#000000">).
94Additional libraries
95which the compiler should use are described by
96the environment variable </font></font><tt><font size="2"><font face="Cumberland, monospace"><font color="#000000">lopts</font></font></font></tt><font color="#000000">
97<font face="Thorndale, serif">(loader options).</font></font><font color="#800000">
98</font><font face="Thorndale, serif"><font color="#000000">Here you
99have to indicate a special IBM library (ESSL, </font></font>Engineering
100and Scientific Subroutine Library)<font face="Thorndale, serif"><font color="#000000">.</font><font color="#800000">
101</font>On the
102IBM-Regatta, all compiler options have also to be given to the linker.</font><font color="#000000"><font face="Thorndale, serif"> </font></font>
103</p><p style="line-height: 100%;"><font color="#000000">Compiler and
104loader options usually differ from computer to computer. In the
105configuration file therefore several value assignments for the
106variables </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">fopts</font></font></tt><font color="#000000">
107and </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">lopts</font></font></tt><font color="#000000">
108exist which become active for different computers.</font><font color="#800000">
109<font color="#000000">Which value assignment is used is
110described by
111the so-called validity domain which follows in the appropriate
112variable lines after the value of variables.</font></font><font color="#000000">
113In the example above the entry &ldquo;</font><font color="#000000"><font style="font-size: 11pt; font-style: italic; font-family: monospace;" size="2">ibmh</font></font><tt><font color="#000000"><span style="font-style: italic; font-family: monospace;">
114</span></font><font color="#000000"><i><font style="font-size: 11pt;" size="2">parallel</font></i></font></tt><font color="#000000">&rdquo;
115stands for </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">fopts</font></font></tt><font color="#000000">
116and </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">lopts</font></font></tt><font color="#000000">.
117These lines only become active if a run on the parallel computer of
118the HLRN (</font><tt><i><font style="font-size: 10pt;" size="2">ibmh</font></i></tt><font color="#000000">)
119on several <font color="#000000">(</font><tt><i><font style="font-size: 10pt;" size="2"><font color="#000000">parallel</font></font></i></tt><font color="#000000">)
120</font>processors is started. The activation takes place when you
121appropriately specify the <span style="font-weight: bold;">mrun</span>
122options </font><tt><font color="#000000">-h</font></tt><font color="#000000">
123and </font><tt><font color="#000000">-K</font></tt><font color="#000000">
124(see below). This way, the validity domain can be limited also for all
125other environment-variables. If no validity domain
126is indicated then the given values of variables are valid on all
127computers. </font>
128</p><p style="line-height: 100%;">After the value
129assignment for the
130variables the so-called error commands follow which have to begin with
131&ldquo;<tt><font style="font-size: 11pt;" size="2">EC:</font></tt>&rdquo;
132in the first column (comment lines begin with &ldquo;<tt>#</tt>&rdquo;).
134after the colon Unix commands follow (korn shell syntax) which are
135processed by <b>mrun</b> if errors arise during
136the model run. The command described in the example (<tt><font style="font-size: 10pt;" size="2">cat
137RUN_CONTROL</font></tt>) is executed thereby only on the
138condition that errors during the execution of the model (<tt><font style="font-size: 10pt;" size="2">execution</font></tt>)
139arise. An <b>mrun </b>internal environment variable which
142respective abort place in case of errors is <tt><a href="">locat</a></tt>.
143In order to determine the actual value of this variable at the
144execution of <b>mrun</b> the &ldquo;<tt>$</tt>&rdquo;
145- prefix
146must be protected by a &ldquo;\&rdquo; since the configuration
147file has been
148already interpreted once when reading in through <b>mrun</b>
149and the
150value from
151<tt>locat</tt> would then supply the empty character
152string. If
153errors arise during the model run this command
154copies the data written by the model up to then to the local file
155<a href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a>
156on the standard output where they can be checked after
157job end.<font color="#000000"> RUN_CONTROL is an output
158file of the
159model which has to be copied according to the default configuration
161(see below) after the end of the model run to a permanent file of the
162user but this action would not be performed in case of errors
163in the model run, so that the file content would be lost.</font>
165the help of the error command one can secure it nevertheless. </p>
166<p style="line-height: 100%;">Before and/or after
167the error commands in the example file you can find the so-called input
168and/or output commands which are implemented before and/or after the
169model run. </p>
170<p style="line-height: 100%;">After the output commands<font color="#000000">
171<font color="#000000">in the example file t</font>he
172so-called file
173connection statements</font> <font color="#000000">follow
175which tell <span style="font-weight: bold;">mrun</span>
176how to connect
177the local files in the temporary working
178directory of the model with the respective permanent files of the user.
179<b>mrun</b> copies the input and output files in accordance
180with the
181data in these connection statements. The file connection statements are
182explained in detail in the <b>mrun</b>
183description (<a href="">chapter
1846.3</a>, in German) and are described here only as far as
185necessary. A
186file connection statement usually consists of entries in 5 columns
187whereby all columns are separated from each other by one or more blanks
188(the blanks define the individual columns). In the
189first column the local file name (e.g. <tt><font size="2">PARIN</font></tt>)
190is given as it is addressed by the model. It must begin directly at
191the start of the line. In the second column the so-called file
193are given. These determine whether the file is an input file (<tt><font style="font-size: 10pt;" size="2">in</font></tt>)
194or an output file (<tt><font size="2">out</font></tt>),
195whether output
196files are to be transferred to the local computer of the user (<tt><font style="font-size: 10pt;" size="2">tr</font></tt>)
197or whether they are to be archived (<font size="2"><font face="Cumberland, monospace">fl</font></font>).
198If a file has several attributes then they are separated by a <font color="#000000">colon
199in each case .</font> </p>
200<p style="line-height: 100%;">With the entries in the
201third column one
202specifies the conditions under which a file connection statement
203becomes active i.e. under
204which circumstances it is executed by <b>mrun</b>. Then <b>mrun</b>
205copies the appropriate in or output files only if at least one of the
206character strings registered in column 3 (again two or more character
207strings have to be separated from each other by a colon) is
208indicated within the mrun <b>call</b> by the option <a href="">-r</a>.
209Thus a call of the form </p>
210<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun - h ibmh -d abcde -r d3</font></pre></ul>
211<p style="line-height: 100%;">would lead to the fact that
212the input
213file with the local name PARIN is made available and the output files
214RUN_CONTROL and HEADER are copied to permanent files. The output
215files PLOT1D_PAR and PLOT1D_DATA are not copied so that their
216contents are not available to the user after the end of the job. If
217these files are to be copied of <b>mrun</b> then the call
218must be</p>
219<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h ibmh -d abcde -r "d3 pr"</font></pre></ul>
220<p style="line-height: 100%;">Instead of the option -r you
222separately address the file connection statements for input and/or
223output files with the options -i and -o. If one likes to make sure with
224these two options that in the example configuration
225file all file connection statements are actually executed then
226the call must be: </p>
227<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h ibmh -d abcde -i d3 -o "d3 pr"</font></pre></ul>
228<p style="line-height: 100%;"><font color="#000000">The
229names of the
230local files assigned permanent files are build from the entries in
231the 4th and 5th column of the file connection statements and the
232value of the <span style="font-weight: bold;">mrun</span>
233option </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">-d</font></font></tt><font color="#000000">
234in the following way:</font><font color="#800000"> </font>
235</p><ul> <p style="line-height: 100%;">File
236name (inclusive path) = &ldquo;value of
237the 4th column&rdquo; + &ldquo;value of the option <tt><font size="2">-d</font></tt>&rdquo;
238+ &ldquo;value of the 5th column&rdquo;.</p>
239</ul><p style="line-height: 100%;">The 4th column
240contains the path name
241whereby <tt><a href="">$fname</a></tt>
242is replaced by the value indicated for the option <tt><font size="2">-d</font></tt>.
243The 5th column contains the so-called file name extension. The name
244of the permanent file which was copied by <b>mrun</b> to
245the local
246file <tt>PARIN</tt> thereby reads: </p>
247<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/abcde/INPUT/abcde_p3d.</font></pre></ul>
248<p style="line-height: 100%;">In the same way the names of
250permanent files of the remaining <font color="#000000">file
251connection statements </font>can be formed. </p>
252<p style="line-height: 100%;">With this example
253configuration file
254exactly one input file is copied into the temporary working directory
255of the model. This file has the local name <a href="chapter_3.4.html#PARIN">PARIN</a>
256and contains the steering parameters for the model and has to be
257provided by the user for each model run. </p>
258<p style="line-height: 100%;">The example configuration
259file also
260instructs <b>mrun</b> to copy four output files of the
261model to
262appropriate permanent files of the user at the end of the run.
263There are timestep information (local file name <tt><a href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a></tt>),
264the so-called header file, in which the values of the most selected
265parameters for this run (<tt><a href="chapter_3.4.html#HEADER">HEADER</a></tt>)
266are located, as well as a file with data of horizontally averaged
267vertical profiles
268(<tt><a href="chapter_3.4.html#PLOT1D_DATA">PLOT1D_DATA</a></tt>)
269and an associated parameter file (<tt><a href="chapter_3.4.html#PLOT1D_PAR">PLOT1D_PAR</a></tt>),
270which can be used as input files for the plot program <a href="">profil</a>.
271A model run does not presuppose neither the file connection statements
273output files nor their activation. But without declaring AND activating
274them usually the data produced by the model
275are lost after the end of the model run! </p>
276<p style="line-height: 100%;">As already mentioned the
278file offers a variety of further possibilities to steer the
279execution of the model run. Some of them are described in the next
280chapter. Same applies to possible other options of the <b>mrun</b>
281call. For these please refer to the <a href="">mrun</a>
282documentation (in German). An <b>mrun </b>call for the
283execution of a
284model run
285on several processors on the IBM Regatta "hanni" of the HLRN must be
286supplemented by the following options in each case: </p>
287<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun - K parallel -X &hellip; -t &hellip; -m &hellip;</font></pre></ul>
288<p style="line-height: 100%;">Only the indication of <tt><font style="font-size: 11pt;" size="2">-K
289parallel</font></tt> causes the parallel execution of the
290run on
291several processors (otherwise a scalar execution on one processor is
292accomplished). In addition to this the number of the
293processing elements which shall be used has to be pre-scribed with the
294option <tt><font style="font-size: 10pt;" size="2">-X</font>
295</tt><font size="2">(</font><font style="font-size: 10pt;" size="2">e.g.
296</font><tt><font style="font-size: 10pt;" size="2">-X
2974</font></tt><font size="2">).</font>
298In each case the permitted CPU time in seconds and the required memory
299size in MB must be indicated by the options <tt><font style="font-size: 11pt;" size="2">-t</font></tt>
300and <tt><font style="font-size: 11pt;" size="2">-m</font></tt>,
301respectively<font face="Thorndale, serif">.</font>
302Alternatively, these can be set by the appropriate environment
303variables in the configuration file: </p>
304<blockquote style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">%
305memory&nbsp; <i>1630</i> ibmh parallel</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><br> </font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">%
306cputime <i>1000</i> ibmh parallel</font></font></tt></blockquote>
307<p style="line-height: 100%;">The values indicated there
308can be
309overridden with the values of the options <tt><font style="font-size: 10pt;" size="2">-t</font></tt>
310and/or <tt><font style="font-size: 10pt;" size="2">-m</font></tt>,
311respectivly. </p>
312<hr><p style="line-height: 100%;"><br>
313<font color="#000080"><font color="#000080"><a href="chapter_3.1.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_3.3.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>
314$Id: chapter_3.2.html 97 2007-06-21 08:23:15Z raasch $</p>
Note: See TracBrowser for help on using the repository browser.