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| 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> |
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| 8 | <body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">3.2 Example of a minimum |
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| 9 | configuration |
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| 10 | file</h3> |
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| 11 | <p style="line-height: 100%;">In this chapter a sample |
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| 12 | configuration |
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| 13 | file is described. It contains only instructions which are really |
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| 14 | necessary for the execution of a simple model run (configuration |
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| 15 | files can be much more complex). The example presented here is stored |
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| 16 | in an appropriate <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config">example |
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| 17 | file</a> (containing more than the configuration data presented |
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| 18 | here) |
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| 19 | and can be used, together with the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">parameter |
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| 20 | file</a> presented in <a href="chapter_4.4.1.html">chapter |
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| 21 | 4.4.1</a>, for the execution of a simple model run. In chapter 4.4.1 |
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| 22 | the |
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| 23 | complete <b>mrun</b> options which are necessary for the |
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| 24 | appropriate |
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| 25 | parameter file are described. Furthermore not all details of the |
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| 26 | configuration file are described here. Therefore you should take a |
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| 27 | look at the <a href="http://www.muk.uni-hannover.de/%7Eraasch/Software/mrun_beschreibung.html">mrun</a> |
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| 28 | documentation (sorry: this is only available in German, so far. If you |
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| 29 | think that you |
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| 30 | would profit from an English version, please give a message to the PALM |
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| 31 | group). </p> |
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| 32 | <p style="line-height: 100%;">The following configuration |
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| 33 | data |
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| 34 | exclusively applies to model runs on the SGI ICE system of the |
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| 35 | HLRN when using several processing elements (i.e. for the parallel |
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| 36 | version of the model). The proper installation of the model is |
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| 37 | presumed (see <a href="chapter_5.0.html">chapter |
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| 38 | 5.0</a>). Furthermore it is supposed that the user is located in |
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| 39 | the |
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| 40 | directory <tt><font style="font-size: 10pt;" size="2">$HOME/palm/current_version</font></tt> |
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| 41 | on its local computer, where the configuration file (<tt><font style="font-size: 10pt;" size="2">.mrun.config</font></tt>) should reside. |
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| 42 | The configuration file has the following contents (among other things): |
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| 43 | <br> |
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| 44 | </p><pre style="line-height: 100%;"><font style="font-size: 10pt;" size="2">%mainprog palm.f90<br>%base_directory $HOME/palm/current_version<br>%base_data ~/palm/current_version/JOBS<br>%source_path $base_directory/trunk/SOURCE<br>#<br></font><font style="font-size: 10pt;" size="2">%fopts -g:-w:-xT:-O3:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian lcsgih parallel<br></font><font style="font-size: 10pt;" size="2">%lopts -g:-w:-xT:-O3:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib lcsgih parallel</font><font style="font-size: 10pt;" size="2"><br>#</font><br><font style="font-size: 10pt;" size="2">EC:[[ \$locat = execution]] & & <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 d3# $base_data/$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# $base_data/$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# $base_data/$fname/MONITORING _header</font><span style="font-family: mon;"><span style="text-decoration: underline;"><br></span><a href="chapter_3.4.html#DATA_1D_PR_NETCDF">DATA_1D_PR_NETCDF</a></span><font style="font-size: 10pt;" size="2"> out:loc:tr pr# ~/palm/current_version/JOBS/$fname/OUTPUT _pr nc</font></pre> |
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| 45 | <p style="line-height: 100%;"><font face="Thorndale, serif">The first |
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| 46 | five lines specify values of |
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| 47 | so-called environment variables. Such lines begin with a |
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| 48 | “%”- |
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| 49 | sign. After at least one blank the name of the variable</font> <font face="Thorndale, serif">(e.g. |
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| 50 | </font><tt><i><font face="Thorndale, serif">source_path</font></i></tt><font face="Thorndale, serif">) |
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| 51 | follows and then seperated by at least one blank the value of the |
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| 52 | variable. Again separated by blank t<font face="Thorndale, serif">he |
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| 53 | so-called validity domain</font> can be indicated (later more). |
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| 54 | With the first four variables <b>mrun</b> gets to know in |
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| 55 | which |
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| 56 | directory the source code lies (</font><tt><i><font face="Thorndale, serif">source_path</font></i></tt><font face="Thorndale, serif">), |
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| 57 | the file name of the main program (</font><tt><i><font face="Thorndale, serif">mainprog</font></i></tt><font face="Thorndale, serif">)</font><font face="Thorndale, serif">. Also, two variables are defined which contain path informations used later in the file (<span style="font-style: italic;">base_directory</span>, <span style="font-style: italic;">base_data</span>). <b>mrun |
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| 58 | </b>needs these information, <font color="#000000">because |
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| 59 | for each |
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| 60 | model run the executable is created by compiling the respective source file.</font> |
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| 61 | Normally, only the main program (palm.f90) will be compiled while all |
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| 62 | other object files are just linked. These object files have already |
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| 63 | been created from the source code files during the installation of the |
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| 64 | model |
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| 65 | (see </font><a href="chapter_5.0.html"><font face="Thorndale, serif">chapter |
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| 66 | 5.0</font></a><font face="Thorndale, serif">). |
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| 67 | <b>mrun</b> uses |
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| 68 | certain standard options for the compilation process. Beyond that you |
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| 69 | can |
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| 70 | declare additional options with the environment variable </font><tt><i><font face="Thorndale, serif">fopts</font></i></tt><font face="Thorndale, serif">. |
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| 71 | Within the value assignment of an environment variable in the |
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| 72 | configuration file no blanks must be |
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| 73 | used. If blanks are necessary they must <font face="Thorndale, serif">be |
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| 74 | replaced </font>by colons (“:”). <b>mrun</b> |
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| 75 | will |
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| 76 | interpret these colons as blanks (2 colons written one behind the |
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| 77 | other will be interpreted as a colon). Thus in the example above</font> fopts |
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| 78 | has the value<tt><font face="Thorndale, serif"> </font></tt>“<tt>-g -w -xT -O3 -cpp -r8 -ftz -fno-alias -no-prec-div -no-prec-sqrt -ip -nbs -convert little_endian<i><font face="Thorndale, serif"><font color="#000000">”</font></font></i></tt><font face="Thorndale, serif"><font color="#000000">. |
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| 79 | Thus a PALM executable is generated using high level optimization (</font></font><font color="#000000"><span style="font-family: monospace;">-O3</span></font><font face="Thorndale, serif"><font color="#000000">).</font></font><font color="#000000"><font face="Thorndale, serif"> |
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| 80 | For all other options |
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| 81 | see the compiler manual on the SGI (</font><font size="2"><font face="Cumberland, monospace">man</font></font></font><tt><font color="#000000"> <span style="font-family: Cumberland,monospace;">ifort</span></font></tt><font face="Thorndale, serif"><font color="#000000">). |
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| 82 | Additional libraries |
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| 83 | which the compiler should use may have to be given by |
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| 84 | the environment variable </font></font><tt><font size="2"><font face="Cumberland, monospace"><font color="#000000">lopts</font></font></font></tt><font color="#000000"> |
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| 85 | <font face="Thorndale, serif">(loader options).</font></font><font color="#000000"><font face="Thorndale, serif"> </font></font> |
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| 86 | </p><p style="line-height: 100%;"><font color="#000000">Compiler and |
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| 87 | loader options usually differ from computer to computer. In the |
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| 88 | configuration file therefore several value assignments for the |
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| 89 | variables </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">fopts</font></font></tt><font color="#000000"> |
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| 90 | and </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">lopts</font></font></tt><font color="#000000"> |
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| 91 | exist which become active for different computers.</font><font color="#800000"> |
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| 92 | <font color="#000000">Which value assignment is used is |
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| 93 | described by |
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| 94 | the so-called validity domain which follows in the appropriate |
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| 95 | variable lines after the value of variables.</font></font><font color="#000000"> |
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| 96 | In the example above the entry “</font><font color="#000000"><font style="font-size: 11pt; font-style: italic; font-family: monospace;" size="2">lcsgih</font></font><tt><font color="#000000"><span style="font-style: italic; font-family: monospace;"> |
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| 97 | </span></font><font color="#000000"><i><font style="font-size: 11pt;" size="2">parallel</font></i></font></tt><font color="#000000">” |
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| 98 | stands for </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">fopts</font></font></tt><font color="#000000"> |
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| 99 | and </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">lopts</font></font></tt><font color="#000000">. |
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| 100 | These lines only become active if a run on the parallel computer of |
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| 101 | the HLRN (</font><tt><i><font style="font-size: 10pt;" size="2">lcsgih</font></i></tt><font color="#000000">) |
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| 102 | on 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">) |
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| 103 | </font>processors is started. The activation takes place when you |
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| 104 | appropriately specify the <span style="font-weight: bold;">mrun</span> |
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| 105 | options </font><tt><font color="#000000">-h</font></tt><font color="#000000"> |
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| 106 | and </font><tt><font color="#000000">-K</font></tt><font color="#000000"> |
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| 107 | (see below). This way, the validity domain can be limited also for all |
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| 108 | other environment-variables. If no validity domain |
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| 109 | is indicated then the given values of variables are valid for all |
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| 110 | computers. </font> |
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| 111 | </p><p style="line-height: 100%;">After the value |
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| 112 | assignment for the |
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| 113 | variables the so-called error commands follow which have to begin with |
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| 114 | “<tt><font style="font-size: 11pt;" size="2">EC:</font></tt>” |
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| 115 | in the first column (comment lines begin with “<tt>#</tt>”). |
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| 116 | Directly |
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| 117 | after the colon Unix commands follow (korn shell syntax) which are |
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| 118 | processed by <b>mrun</b> if errors arise during |
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| 119 | the model run. The command described in the example (<tt><font style="font-size: 10pt;" size="2">cat |
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| 120 | RUN_CONTROL</font></tt>) is executed thereby only on the |
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| 121 | condition that errors during the execution of the model (<tt><font style="font-size: 10pt;" size="2">execution</font></tt>) |
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| 122 | arise. An <b>mrun </b>internal environment variable which |
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| 123 | indicates |
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| 124 | the |
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| 125 | respective abort place in case of errors is <tt><a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#locat">locat</a></tt>. |
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| 126 | In order to determine the actual value of this variable at the |
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| 127 | execution of <b>mrun</b> the “<tt>$</tt>” |
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| 128 | - prefix |
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| 129 | must be protected by a “\” since the configuration |
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| 130 | file has been |
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| 131 | already interpreted once when reading in through <b>mrun</b> |
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| 132 | and the |
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| 133 | value from |
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| 134 | <tt>locat</tt> would then supply the empty character |
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| 135 | string. If |
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| 136 | errors arise during the model run this command |
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| 137 | copies the data written by the model up to then to the local file |
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| 138 | <a href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a> |
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| 139 | on the standard output where they can be checked after |
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| 140 | job end.<font color="#000000"> RUN_CONTROL is an output |
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| 141 | file of the |
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| 142 | model which has to be copied according to the default configuration |
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| 143 | file |
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| 144 | (see below) after the end of the model run to a permanent file of the |
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| 145 | user but this action would not be performed in case of errors |
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| 146 | in the model run, so that the file content would be lost.</font> |
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| 147 | With |
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| 148 | the help of the error command one can secure it nevertheless. </p> |
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| 149 | <p style="line-height: 100%;">Before and/or after |
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| 150 | the error commands in the example file you can find the so-called input |
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| 151 | and/or output commands which are implemented before and/or after the |
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| 152 | model run. </p> |
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| 153 | <p style="line-height: 100%;">After the output commands<font color="#000000"> |
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| 154 | <font color="#000000">in the example file t</font>he |
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| 155 | so-called file |
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| 156 | connection statements</font> <font color="#000000">follow |
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| 157 | </font>via |
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| 158 | which tell <span style="font-weight: bold;">mrun</span> |
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| 159 | how to connect |
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| 160 | the local files in the temporary working |
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| 161 | directory of the model with the respective permanent files of the user. |
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| 162 | <b>mrun</b> copies the input and output files in accordance |
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| 163 | with the |
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| 164 | data in these connection statements. The file connection statements are |
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| 165 | explained in detail in the <b>mrun</b> |
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| 166 | description (<a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#chapter6.3">chapter |
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| 167 | 6.3</a>, in German) and are described here only as far as |
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| 168 | necessary. A |
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| 169 | file connection statement usually consists of entries in 5 columns |
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| 170 | whereby all columns are separated from each other by one or more blanks |
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| 171 | (the blanks define the individual columns). In the |
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| 172 | first column the local file name (e.g. <tt><font size="2">PARIN</font></tt>) |
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| 173 | is given as it is addressed by the model. It must begin directly at |
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| 174 | the start of the line. In the second column the so-called file |
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| 175 | attributes |
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| 176 | are given. These determine whether the file is an input file (<tt><font style="font-size: 10pt;" size="2">in</font></tt>) |
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| 177 | or an output file (<tt><font size="2">out</font></tt>), |
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| 178 | whether output |
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| 179 | files are to be transferred to the local computer of the user (<tt><font style="font-size: 10pt;" size="2">tr</font></tt>) |
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| 180 | or whether they are to be archived (<font size="2"><font face="Cumberland, monospace">fl</font></font>). |
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| 181 | If a file has several attributes then they are separated by a <font color="#000000">colon |
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| 182 | in each case .</font> </p> |
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| 183 | <p style="line-height: 100%;">With the entries in the |
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| 184 | third column one |
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| 185 | specifies the conditions under which a file connection statement |
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| 186 | becomes active i.e. under |
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| 187 | which circumstances it is executed by <b>mrun</b>. Then <b>mrun</b> |
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| 188 | copies the appropriate in or output files only if at least one of the |
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| 189 | character strings registered in column 3 (again two or more character |
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| 190 | strings have to be separated from each other by a colon) is |
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| 191 | indicated within the mrun <b>call</b> by the option <a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#Opt-r">-r</a>. |
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| 192 | Thus a call of the form </p> |
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| 193 | <ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun - h lcsgih -d abcde -r "d3#"</font></pre></ul> |
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| 194 | <p style="line-height: 100%;">would lead to the fact that |
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| 195 | the input |
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| 196 | file with the local name PARIN is made available and the output files |
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| 197 | RUN_CONTROL and HEADER are copied to permanent files. The output |
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| 198 | files PLOT1D_PAR and PLOT1D_DATA are not copied so that their |
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| 199 | contents are not available to the user after the end of the job. If |
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| 200 | these files are to be copied of <b>mrun</b> then the call |
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| 201 | must be</p> |
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| 202 | <ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h lcsgih -d abcde -r "d3# pr#"</font></pre></ul> |
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| 203 | <p style="line-height: 100%;">Instead of the option -r you |
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| 204 | can |
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| 205 | separately address the file connection statements for input and/or |
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| 206 | output files with the options -i and -o. If one likes to make sure with |
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| 207 | these two options that in the example configuration |
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| 208 | file all file connection statements are actually executed then |
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| 209 | the call must be: </p> |
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| 210 | <ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h lcsgih -d abcde -i "d3#" -o "d3# pr#"</font></pre></ul> |
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| 211 | <p style="line-height: 100%;"><font color="#000000">The |
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| 212 | names of the |
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| 213 | local files assigned permanent files are build from the entries in |
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| 214 | the 4th and 5th column of the file connection statements and the |
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| 215 | value of the <span style="font-weight: bold;">mrun</span> |
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| 216 | option </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">-d</font></font></tt><font color="#000000"> |
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| 217 | in the following way:</font><font color="#800000"> </font> |
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| 218 | </p><ul> <p style="line-height: 100%;">File |
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| 219 | name (inclusive path) = “value of |
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| 220 | the 4th column” + “value of the option <tt><font size="2">-d</font></tt>” |
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| 221 | + “value of the 5th column”.</p> |
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| 222 | </ul><p style="line-height: 100%;">The 4th column |
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| 223 | contains the path name |
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| 224 | whereby <tt><a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#fname">$fname</a></tt> |
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| 225 | is replaced by the value indicated for the option <tt><font size="2">-d</font></tt>. |
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| 226 | The 5th column contains the so-called file name extension. The name |
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| 227 | of the permanent file which was copied by <b>mrun</b> to |
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| 228 | the local |
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| 229 | file <tt>PARIN</tt> thereby reads: </p> |
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| 230 | <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> |
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| 231 | <p style="line-height: 100%;">In the same way the names of |
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| 232 | the |
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| 233 | permanent files of the remaining <font color="#000000">file |
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| 234 | connection statements </font>can be formed. </p> |
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| 235 | <p style="line-height: 100%;">With this example |
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| 236 | configuration file |
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| 237 | exactly one input file is copied into the temporary working directory |
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| 238 | of the model. This file has the local name <a href="chapter_3.4.html#PARIN">PARIN</a> |
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| 239 | and contains the steering parameters for the model and has to be |
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| 240 | provided by the user for each model run. </p> |
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| 241 | <p style="line-height: 100%;">The example configuration |
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| 242 | file also |
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| 243 | instructs <b>mrun</b> to copy three output files of the |
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| 244 | model to |
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| 245 | appropriate permanent files of the user at the end of the run. |
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| 246 | There are timestep information (local file name <tt><a href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a></tt>), |
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| 247 | the so-called header file, in which the values of the most selected |
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| 248 | parameters for this run (<tt><a href="chapter_3.4.html#HEADER">HEADER</a></tt>) |
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| 249 | are located, as well as a file with data of horizontally averaged |
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| 250 | vertical profiles |
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| 251 | (<tt><a href="chapter_3.4.html#DATA_1D_PR_NETCDF">DATA_1D_PR_NETCDF</a></tt>). |
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| 252 | A model run does not presuppose neither the file connection statements |
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| 253 | for |
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| 254 | output files nor their activation. But without declaring AND activating |
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| 255 | them usually the data produced by the model |
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| 256 | are lost after the end of the model run! </p> |
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| 257 | <p style="line-height: 100%;">As already mentioned the |
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| 258 | configuration |
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| 259 | file offers a variety of further possibilities to steer the |
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| 260 | execution of the model run. Some of them are described in the next |
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| 261 | chapter. Same applies to possible other options of the <b>mrun</b> |
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| 262 | call. For these please refer to the <a href="http://www.muk.uni-hannover.de/%7Eraasch/Software/mrun_beschreibung.html">mrun</a> |
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| 263 | documentation (in German). An <b>mrun </b>call for the |
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| 264 | execution of a |
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| 265 | model run |
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| 266 | on several processors on the SGI ICE of the HLRN must be |
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| 267 | supplemented by the following options in each case: </p> |
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| 268 | <ul style="font-family: monospace;"> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun - K parallel -X ... -T ... -t ... -m ---</font></pre></ul> |
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| 269 | <p style="line-height: 100%;">Only the indication of <tt><font style="font-size: 11pt;" size="2">-K |
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| 270 | parallel</font></tt> causes the parallel execution of the |
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| 271 | run on |
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| 272 | several processors (otherwise a scalar execution on one processor is |
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| 273 | accomplished). In addition to this the number of the |
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| 274 | processing elements which shall be used has to be pre-scribed with the |
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| 275 | option <tt><font style="font-size: 10pt;" size="2">-X</font> |
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| 276 | </tt><font size="2">(</font><font style="font-size: 10pt;" size="2">e.g. |
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| 277 | </font><tt><font style="font-size: 10pt;" size="2">-X 32</font></tt><font size="2">) and the number of tasks (processors) on onde node have to be given by option -T.</font> |
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| 278 | In each case the permitted CPU time in seconds and the required memory |
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| 279 | size in MB must be indicated by the options <tt><font style="font-size: 11pt;" size="2">-t</font></tt> |
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| 280 | and <tt><font style="font-size: 11pt;" size="2">-m</font></tt>, |
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| 281 | respectively<font face="Thorndale, serif">.</font> |
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| 282 | Alternatively, memory and cpu-time demands can be set by the appropriate environment |
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| 283 | variables in the configuration file: </p> |
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| 284 | <blockquote style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">%memory <i>1500</i> lcsgih 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">%cputime <i>1000</i> lcsgih parallel</font></font></tt></blockquote> |
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| 285 | <p style="line-height: 100%;">The values indicated there |
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| 286 | can be |
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| 287 | overridden with the values of the options <tt><font style="font-size: 10pt;" size="2">-t</font></tt> |
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| 288 | and/or <tt><font style="font-size: 10pt;" size="2">-m</font></tt>, |
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| 289 | respectivly.</p><p style="line-height: 100%;"><span style="font-weight: bold;">Warning: When changing the coniguration file, please never use the TAB key!</span> </p> |
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| 290 | <hr><p style="line-height: 100%;"><br> |
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| 291 | <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: </i> |
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| 292 | $Id: chapter_3.2.html 336 2009-06-10 11:19:35Z franke $</p> |
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| 293 | </body></html> |
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