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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 heinze $</p> |
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293 | </body></html> |
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