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19 | <h3 style="line-height: 100%;">3.2 Example of a minimum configuration |
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20 | file</h3> |
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21 | <p style="line-height: 100%;">In this chapter a sample configuration |
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22 | file is described. It contains only instructions which are really |
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23 | necessary for the execution of a simple model run (configuration |
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24 | files can be much more complex). The example presented here is stored |
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25 | in an appropriate <a |
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26 | href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config">example |
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27 | file</a> (containing more than the configuration data presented here) |
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28 | and can be used, together with the <a |
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29 | href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">parameter |
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30 | file</a> presented in <a href="chapter_4.4.html">chapter |
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31 | 4.4</a>, for the execution of a simple model run. In chapter 4.4 the |
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32 | complete <b>mrun</b> options which are necessary for the appropriate |
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33 | parameter file are described. Furthermore not all details of the |
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34 | configuration file are described here. Therefore you should take a |
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35 | look at the <a |
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36 | href="http://www.muk.uni-hannover.de/%7Eraasch/Software/mrun_beschreibung.html">mrun</a> |
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37 | documentation (sorry: this is only available in German, so far. If you |
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38 | think that you |
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39 | would profit from an English version, please give a message to the PALM |
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40 | group). </p> |
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41 | <p style="line-height: 100%;">The following configuration data |
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42 | exclusively applies to model runs on the IBM Regatta hanni of the |
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43 | HLRN when using several processing elements (i.e. for the parallel |
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44 | version of the model). The proper installation of the model is |
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45 | presumed (see <a href="chapter_5.0.html">chapter |
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46 | 5.0</a>). Furthermore it is supposed that the user is located in the |
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47 | directory <tt><font style="font-size: 10pt;" size="2">$HOME/palm/current_version/SOURCE</font></tt> |
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48 | on its local computer. There are the FORTRAN source codes of the |
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49 | model (<tt><font style="font-size: 10pt;" size="2">*.f90</font></tt>) |
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50 | as |
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51 | well as the configuration file (name: <tt><font |
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52 | style="font-size: 10pt;" size="2">.mrun.config</font></tt>) |
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53 | and the make file (name: <tt><font style="font-size: 10pt;" size="2">Makefile</font></tt>). |
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54 | The configuration file has the following contents (among other things): |
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55 | <br> |
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56 | |
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57 | </p> |
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58 | <pre style="line-height: 100%;"><font style="font-size: 10pt;" size="2">% source_path <i>$HOME/palm/current_version/SOURCE</i></font><br><font |
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59 | style="font-size: 10pt;" size="2">% mainprog <i>palm.f90</i></font><br><font |
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60 | style="font-size: 10pt;" size="2">% use_makefile <i>true</i></font><br><font |
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61 | 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 |
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62 | 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 |
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63 | style="font-size: 10pt;" size="2">% lopts <span |
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64 | 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 |
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65 | style="font-size: 10pt;" size="2">#</font><br><font |
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66 | style="font-size: 10pt;" size="2">EC:[[ \$locat = execution]] & & <i>cat </i>RUN_CONTROL </font><br><font |
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67 | style="font-size: 10pt;" size="2">#</font><br><a |
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68 | href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN</font></a><font |
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69 | style="font-size: 10pt;" size="2"> in:job:npe d3# ~/palm/current_version/JOBS/$fname/INPUT _p3d</font><br><font |
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70 | style="font-size: 10pt;" size="2">#</font><br><a |
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71 | href="chapter_3.4.html#RUN_CONTROL"><font style="font-size: 10pt;" |
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72 | size="2">RUN_CONTROL</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr d3# ~/palm/current_version/JOBS/$fname/MONITORING _rc</font><br><a |
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73 | href="chapter_3.4.html#HEADER"><font style="font-size: 10pt;" size="2">HEADER</font></a><font |
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74 | style="font-size: 10pt;" size="2"> out:loc:tr d3# ~/palm/current_version/JOBS/$fname/MONITORING _header</font><br><a |
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75 | href="chapter_3.4.html#PLOT1D_PAR"><font style="font-size: 10pt;" |
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76 | size="2">PLOT1D_PAR</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr pr# ~/palm/current_version/JOBS/$fname/OUTPUT _pr_par</font><br><a |
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77 | href="chapter_3.4.html#PLOT1D_DATA"><font style="font-size: 10pt;" |
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78 | 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> |
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79 | <p style="line-height: 100%;"><font face="Thorndale, serif">The first |
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80 | five lines specify values of |
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81 | so-called environment variables. Such lines begin with a %- |
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82 | sign. After at least one blank the name of the variable</font> <font |
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83 | face="Thorndale, serif">(e.g. |
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84 | </font><tt><i><font face="Thorndale, serif">source_path</font></i></tt><font |
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85 | face="Thorndale, serif">) |
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86 | follows and then seperated by at least one blank the value of the |
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87 | variable. Again separated by blank t<font face="Thorndale, serif">he |
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88 | so-called validity domain</font> can be indicated (later more). |
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89 | With the first three variables <b>mrun</b> gets to know in which |
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90 | directory the source code lies (</font><tt><i><font |
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91 | face="Thorndale, serif">source_path</font></i></tt><font |
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92 | face="Thorndale, serif">), |
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93 | the file name of the main program (</font><tt><i><font |
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94 | face="Thorndale, serif">mainprog</font></i></tt><font |
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95 | face="Thorndale, serif">) |
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96 | and that the <font face="Thorndale, serif">make mechanism should be |
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97 | used </font>for compiling (</font><tt><font face="Thorndale, serif"><i>use_makefile |
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98 | =</i> <i>true</i></font></tt><font face="Thorndale, serif">). <b>mrun |
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99 | </b>needs these information, <font color="#000000">because for each |
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100 | model run the executable is created by compiling the source files.</font> |
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101 | Normally, only the main program (palm.f90) will be compiled while all |
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102 | other object files are just linked. These object files have already |
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103 | been created from the source code files during the installation of the |
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104 | model |
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105 | (see </font><a href="chapter_5.0.html"><font face="Thorndale, serif">chapter |
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106 | 5.0</font></a><font face="Thorndale, serif">). <b>mrun</b> uses |
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107 | certain standard options for the compilation process. Beyond that you |
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108 | can |
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109 | declare additional options with the environment variable </font><tt><i><font |
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110 | face="Thorndale, serif">fopts</font></i></tt><font |
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111 | face="Thorndale, serif">. |
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112 | Within the value assignment of an environment variable in the |
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113 | configuration file no blanks must be |
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114 | used. If blanks are necessary they must <font face="Thorndale, serif">be |
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115 | replaced </font>by colons (:). <b>mrun</b> will |
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116 | interpret these colons as blanks (2 colons written one behind the |
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117 | other will be interpreted as a colon). Thus in the example above </font><tt><font |
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118 | face="Thorndale, serif">fopts |
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119 | has the value </font></tt><font |
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120 | style="font-size: 10pt; font-family: monospace;" size="2"><i>-O3 -g |
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121 | -qrealsize=8 -Q -q64 -qmaxmem=-1 -qtune=pwr4 -qarch=pwr4 -qnosave |
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122 | -qnoescape</i></font><tt><i><font face="Thorndale, serif"><font |
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123 | color="#000000"></font></font></i></tt><font face="Thorndale, serif"><font |
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124 | color="#000000">. |
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125 | Thus a PALM executable is generated using high level optimization (</font></font><font |
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126 | color="#000000"><span |
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127 | style="font-style: italic; font-family: monospace;">-O3</span></font><font |
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128 | face="Thorndale, serif"><font color="#000000">).</font></font><font |
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129 | color="#000000"><font face="Thorndale, serif"> For all other options |
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130 | see the compiler manual on the IBM (</font><font size="2"><font |
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131 | face="Cumberland, monospace">man</font></font></font><tt><font |
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132 | color="#000000"> |
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133 | <font size="2"><font face="Cumberland, monospace">f90</font></font></font></tt><font |
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134 | face="Thorndale, serif"><font color="#000000">). Additional libraries |
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135 | which the compiler should use are described by |
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136 | the environment variable </font></font><tt><font size="2"><font |
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137 | face="Cumberland, monospace"><font color="#000000">lopts</font></font></font></tt><font |
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138 | color="#000000"> |
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139 | <font face="Thorndale, serif">(loader options).</font></font><font |
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140 | color="#800000"> |
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141 | </font><font face="Thorndale, serif"><font color="#000000">Here you |
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142 | have to indicate a special IBM library (ESSL, </font></font>Engineering |
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143 | and Scientific Subroutine Library)<font face="Thorndale, serif"><font |
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144 | color="#000000">.</font><font color="#800000"> </font>On the |
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145 | IBM-Regatta, all compiler options have also to be given to the linker.</font><font |
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146 | color="#000000"><font face="Thorndale, serif"> </font></font> |
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147 | </p> |
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148 | <p style="line-height: 100%;"><font color="#000000">Compiler and |
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149 | loader options usually differ from computer to computer. In the |
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150 | configuration file therefore several value assignments for the |
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151 | variables </font><tt><font style="font-size: 10pt;" size="2"><font |
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152 | color="#000000">fopts</font></font></tt><font color="#000000"> |
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153 | and </font><tt><font style="font-size: 10pt;" size="2"><font |
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154 | color="#000000">lopts</font></font></tt><font color="#000000"> |
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155 | exist which become active for different computers.</font><font |
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156 | color="#800000"> |
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157 | <font color="#000000">Which value assignment is used is described by |
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158 | the so-called validity domain which follows in the appropriate |
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159 | variable lines after the value of variables.</font></font><font |
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160 | color="#000000"> |
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161 | In the example above the entry </font><font color="#000000"><font |
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162 | style="font-size: 11pt; font-style: italic; font-family: monospace;" |
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163 | size="2">ibmh</font></font><tt><font color="#000000"><span |
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164 | style="font-style: italic; font-family: monospace;"> |
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165 | </span></font><font color="#000000"><i><font style="font-size: 11pt;" |
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166 | size="2">parallel</font></i></font></tt><font color="#000000"> |
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167 | stands for </font><tt><font style="font-size: 10pt;" size="2"><font |
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168 | color="#000000">fopts</font></font></tt><font color="#000000"> |
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169 | and </font><tt><font style="font-size: 10pt;" size="2"><font |
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170 | color="#000000">lopts</font></font></tt><font color="#000000">. |
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171 | These lines only become active if a run on the parallel computer of |
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172 | the HLRN (</font><tt><i><font style="font-size: 10pt;" size="2">ibmh</font></i></tt><font |
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173 | color="#000000">) |
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174 | on several <font color="#000000">(</font><tt><i><font |
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175 | style="font-size: 10pt;" size="2"><font color="#000000">parallel</font></font></i></tt><font |
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176 | color="#000000">) |
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177 | </font>processors is started. The activation takes place when you |
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178 | appropriately specify the <span style="font-weight: bold;">mrun</span> |
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179 | options </font><tt><font color="#000000">-h</font></tt><font |
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180 | color="#000000"> |
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181 | and </font><tt><font color="#000000">-K</font></tt><font |
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182 | color="#000000"> |
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183 | (see below). This way, the validity domain can be limited also for all |
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184 | other environment-variables. If no validity domain |
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185 | is indicated then the given values of variables are valid on all |
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186 | computers. </font> |
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187 | </p> |
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188 | <p style="line-height: 100%;">After the value assignment for the |
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189 | variables the so-called error commands follow which have to begin with <tt><font |
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190 | style="font-size: 11pt;" size="2">EC:</font></tt> |
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191 | in the first column (comment lines begin with <tt>#</tt>). Directly |
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192 | after the colon Unix commands follow (korn shell syntax) which are |
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193 | processed by <b>mrun</b> if errors arise during |
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194 | the model run. The command described in the example (<tt><font |
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195 | style="font-size: 10pt;" size="2">cat |
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196 | RUN_CONTROL</font></tt>) is executed thereby only on the |
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197 | condition that errors during the execution of the model (<tt><font |
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198 | style="font-size: 10pt;" size="2">execution</font></tt>) |
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199 | arise. An <b>mrun </b>internal environment variable which indicates |
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200 | the |
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201 | respective abort place in case of errors is <tt><a |
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202 | href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#locat">locat</a></tt>. |
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203 | In order to determine the actual value of this variable at the |
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204 | execution of <b>mrun</b> the <tt>$</tt> - prefix |
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205 | must be protected by a \ since the configuration file has been |
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206 | already interpreted once when reading in through <b>mrun</b> and the |
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207 | value from |
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208 | <tt>locat</tt> would then supply the empty character string. If |
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209 | errors arise during the model run this command |
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210 | copies the data written by the model up to then to the local file |
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211 | <a href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a> |
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212 | on the standard output where they can be checked after |
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213 | job end.<font color="#000000"> RUN_CONTROL is an output file of the |
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214 | model which has to be copied according to the default configuration |
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215 | file |
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216 | (see below) after the end of the model run to a permanent file of the |
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217 | user but this action would not be performed in case of errors |
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218 | in the model run, so that the file content would be lost.</font> With |
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219 | the help of the error command one can secure it nevertheless. </p> |
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220 | <p style="line-height: 100%;">Before and/or after |
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221 | the error commands in the example file you can find the so-called input |
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222 | and/or output commands which are implemented before and/or after the |
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223 | model run. </p> |
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224 | <p style="line-height: 100%;">After the output commands<font |
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225 | color="#000000"> |
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226 | <font color="#000000">in the example file t</font>he so-called file |
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227 | connection statements</font> <font color="#000000">follow </font>via |
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228 | which tell <span style="font-weight: bold;">mrun</span> how to connect |
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229 | the local files in the temporary working |
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230 | directory of the model with the respective permanent files of the user. |
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231 | <b>mrun</b> copies the input and output files in accordance with the |
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232 | data in these connection statements. The file connection statements are |
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233 | explained in detail in the <b>mrun</b> |
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234 | description (<a |
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235 | href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#chapter6.3">chapter |
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236 | 6.3</a>, in German) and are described here only as far as being |
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237 | necessary. A |
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238 | file connection statement usually consists of entries in 5 columns |
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239 | whereby all columns are separated from each other by one or more blanks |
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240 | (the blanks define the individual columns). In the |
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241 | first column the local file name (e.g. <tt><font size="2">PARIN</font></tt>) |
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242 | is given as it is addressed by the model. It must begin directly at |
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243 | the start of the line. In the second column the so-called file |
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244 | attributes |
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245 | are given. These determine whether the file is an input file (<tt><font |
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246 | style="font-size: 10pt;" size="2">in</font></tt>) |
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247 | or an output file (<tt><font size="2">out</font></tt>), whether output |
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248 | files are to be transferred to the local computer of the user (<tt><font |
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249 | style="font-size: 10pt;" size="2">tr</font></tt>) |
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250 | or whether they are to be archived (<font size="2"><font |
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251 | face="Cumberland, monospace">fl</font></font>). |
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252 | If a file has several attributes then they are separated by a <font |
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253 | color="#000000">colon |
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254 | in each case .</font> </p> |
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255 | <p style="line-height: 100%;">With the entries in the third column one |
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256 | specifies the conditions under which a file connection statement |
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257 | becomes active i.e. under |
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258 | which circumstances it is executed by <b>mrun</b>. Then <b>mrun</b> |
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259 | copies the appropriate in or output files only if at least one of the |
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260 | character strings registered in column 3 (again two or more character |
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261 | strings have to be separated from each other by a colon) is |
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262 | indicated within the mrun <b>call</b> by the option <a |
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263 | href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#Opt-r">-r</a>. |
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264 | Thus a call of the form </p> |
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265 | <ul> |
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266 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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267 | style="font-size: 10pt;" size="2">mrun - h ibmh -d abcde -r d3</font></pre> |
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268 | </ul> |
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269 | <p style="line-height: 100%;">would lead to the fact that the input |
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270 | file with the local name PARIN is made available and the output files |
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271 | RUN_CONTROL and HEADER are copied to permanent files. The output |
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272 | files PLOT1D_PAR and PLOT1D_DATA are not copied so that their |
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273 | contents are not available to the user after the end of the job. If |
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274 | these files are to be copied of <b>mrun</b> then the call must be</p> |
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275 | <ul> |
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276 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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277 | style="font-size: 10pt;" size="2">mrun -h ibmh -d abcde -r "d3 pr"</font></pre> |
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278 | </ul> |
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279 | <p style="line-height: 100%;">Instead of the option -r you can |
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280 | separately address the file connection statements for input and/or |
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281 | output files with the options -i and -o. If one likes to make sure with |
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282 | these two options that in the example configuration |
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283 | file all file connection statements are actually executed then |
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284 | the call must be: </p> |
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285 | <ul> |
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286 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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287 | style="font-size: 10pt;" size="2">mrun -h ibmh -d abcde -i d3 -o "d3 pr"</font></pre> |
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288 | </ul> |
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289 | <p style="line-height: 100%;"><font color="#000000">The names of the |
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290 | local files assigned permanent files are build from the entries in |
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291 | the 4th and 5th column of the file connection statements and the |
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292 | value of the <span style="font-weight: bold;">mrun</span> option </font><tt><font |
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293 | style="font-size: 10pt;" size="2"><font color="#000000">-d</font></font></tt><font |
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294 | color="#000000"> |
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295 | in the following way:</font><font color="#800000"> </font> |
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296 | </p> |
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297 | <ul> |
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298 | <p style="line-height: 100%;">File name (inclusive path) = value of |
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299 | the 4th column + value of the option <tt><font size="2">-d</font></tt> |
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300 | + value of the 5th column.</p> |
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301 | </ul> |
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302 | <p style="line-height: 100%;">The 4th column contains the path name |
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303 | whereby <tt><a |
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304 | href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#fname">$fname</a></tt> |
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305 | is replaced by the value indicated for the option <tt><font size="2">-d</font></tt>. |
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306 | The 5th column contains the so-called file name extension. The name |
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307 | of the permanent file which was copied by <b>mrun</b> to the local |
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308 | file <tt>PARIN</tt> thereby reads: </p> |
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309 | <ul> |
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310 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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311 | style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/abcde/INPUT/abcde_p3d.</font></pre> |
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312 | </ul> |
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313 | <p style="line-height: 100%;">In the same way the names of the |
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314 | permanent files of the remaining <font color="#000000">file |
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315 | connection statements </font>can be formed. </p> |
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316 | <p style="line-height: 100%;">With this example configuration file |
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317 | exactly one input file is copied into the temporary working directory |
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318 | of the model. This file has the local name <a |
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319 | href="chapter_3.4.html#PARIN">PARIN</a> |
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320 | and contains the steering parameters for the model and has to be |
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321 | provided by the user for each model run. </p> |
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322 | <p style="line-height: 100%;">The example configuration file also |
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323 | instructs <b>mrun</b> to copy four output files of the model to |
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324 | appropriate permanent files of the user at the end of the run. |
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325 | There are timestep information (local file name <tt><a |
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326 | href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a></tt>), |
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327 | the so-called header file, in which the values of the most selected |
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328 | parameters for this run (<tt><a href="chapter_3.4.html#HEADER">HEADER</a></tt>) |
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329 | are located, as well as a file with data of horizontally averaged |
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330 | vertical profiles |
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331 | (<tt><a href="chapter_3.4.html#PLOT1D_DATA">PLOT1D_DATA</a></tt>) |
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332 | and an associated parameter file (<tt><a |
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333 | href="chapter_3.4.html#PLOT1D_PAR">PLOT1D_PAR</a></tt>), |
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334 | which can be used as input files for the plot program <a |
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335 | href="http://www.muk.uni-hannover.de/institut/software/profil_beschreibung.html">profil</a>. |
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336 | A model run does not presuppose neither the file connection statements |
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337 | for |
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338 | output files nor their activation. But without declaring AND activating |
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339 | them usually the data produced by the model |
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340 | are lost after the end of the model run! </p> |
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341 | <p style="line-height: 100%;">As already mentioned the configuration |
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342 | file offers a variety of further possibilities to steer the |
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343 | execution of the model run. Some of them are described in the next |
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344 | chapter. Same applies to possible other options of the <b>mrun</b> |
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345 | call. For these please refer to the <a |
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346 | href="http://www.muk.uni-hannover.de/%7Eraasch/Software/mrun_beschreibung.html">mrun</a> |
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347 | documentation (in German). An <b>mrun </b>call for the execution of a |
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348 | model run |
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349 | on several processors on the IBM Regatta "hanni" of the HLRN must be |
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350 | supplemented by the following options in each case: </p> |
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351 | <ul> |
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352 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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353 | style="font-size: 10pt;" size="2">mrun - K parallel -X
-t
-m
</font></pre> |
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354 | </ul> |
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355 | <p style="line-height: 100%;">Only the indication of <tt><font |
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356 | style="font-size: 11pt;" size="2">-K |
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357 | parallel</font></tt> causes the parallel execution of the run on |
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358 | several processors (otherwise a scalar execution on one processor is |
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359 | accomplished). In addition to this the number of the |
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360 | processing elements which shall be used has to be pre-scribed with the |
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361 | option <tt><font style="font-size: 10pt;" size="2">-X</font> </tt><font |
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362 | size="2">(</font><font style="font-size: 10pt;" size="2">e.g. |
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363 | </font><tt><font style="font-size: 10pt;" size="2">-X 4</font></tt><font |
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364 | size="2">).</font> |
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365 | In each case the permitted CPU time in seconds and the required memory |
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366 | size in MB must be indicated by the options <tt><font |
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367 | style="font-size: 11pt;" size="2">-t</font></tt> |
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368 | and <tt><font style="font-size: 11pt;" size="2">-m</font></tt>, |
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369 | respectively<font face="Thorndale, serif">.</font> |
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370 | Alternatively, these can be set by the appropriate environment |
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371 | variables in the configuration file: </p> |
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372 | <blockquote style="line-height: 100%;"><tt><font |
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373 | style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">% |
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374 | memory <i>1630</i> ibmh parallel</font></font></tt><font |
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375 | style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><br> |
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376 | </font></font><tt><font style="font-size: 10pt;" size="2"><font |
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377 | face="Cumberland, monospace">% |
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378 | cputime <i>1000</i> ibmh parallel</font></font></tt></blockquote> |
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379 | <p style="line-height: 100%;">The values indicated there can be |
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380 | overridden with the values of the options <tt><font |
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381 | style="font-size: 10pt;" size="2">-t</font></tt> |
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382 | and/or <tt><font style="font-size: 10pt;" size="2">-m</font></tt>, |
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383 | respectivly. </p> |
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384 | <hr> |
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385 | <p style="line-height: 100%;"><br> |
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386 | <font color="#000080"><font color="#000080"><a href="chapter_3.1.html"><font |
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387 | color="#000080"><img src="left.gif" name="Grafik1" align="bottom" |
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388 | border="2" height="32" width="32"></font></a><a href="index.html"><font |
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389 | color="#000080"><img src="up.gif" name="Grafik2" align="bottom" |
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390 | border="2" height="32" width="32"></font></a><a href="chapter_3.3.html"><font |
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391 | color="#000080"><img src="right.gif" name="Grafik3" align="bottom" |
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392 | border="2" height="32" width="32"></font></a></font></font></p> |
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393 | <p style="line-height: 100%;"><i>Last change: </i> 14/04/05 (SR)</p> |
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394 | </body> |
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395 | </html> |
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