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Commit 4214af24 authored by Karl-Hermann Wieners's avatar Karl-Hermann Wieners
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Prepared for release 0.3.6

* Updated documentation version
* Updated package version
parent 74c5b55c
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Tags mkexp-0.3.6
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<?xml version="1.0" encoding="UTF-8"?> <?xml version="1.0" encoding="UTF-8"?>
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<text:p text:style-name="Footer"><text:page-number text:select-page="current">16</text:page-number><text:tab/><text:tab/><text:modification-date style:data-style-name="N84">2016-01-12</text:modification-date>, <text:modification-time style:data-style-name="N41">10:56:56</text:modification-time></text:p> <text:p text:style-name="Footer"><text:page-number text:select-page="current">2</text:page-number><text:tab/><text:tab/><text:modification-date style:data-style-name="N84">2016-01-14</text:modification-date>, <text:modification-time style:data-style-name="N41">09:09:29</text:modification-time></text:p>
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...@@ -1942,10 +1942,10 @@ ...@@ -1942,10 +1942,10 @@
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</text:sequence-decls> </text:sequence-decls>
<text:p text:style-name="P252">Make Experiments!</text:p> <text:p text:style-name="P256">Make Experiments!</text:p>
<text:p text:style-name="P245">Run-script generation for earth system models</text:p> <text:p text:style-name="P247">Run-script generation for earth system models</text:p>
<text:p text:style-name="P246">Release 0.3.<text:span text:style-name="T218">6dev</text:span></text:p> <text:p text:style-name="P248">Release 0.3.<text:span text:style-name="T218">6</text:span></text:p>
<text:p text:style-name="P223">Karl-Hermann Wieners<text:line-break/><text:span text:style-name="T208">Max-Planck-Institut für Meteorologie<text:line-break/>Hamburg</text:span></text:p> <text:p text:style-name="P225">Karl-Hermann Wieners<text:line-break/><text:span text:style-name="T208">Max-Planck-Institut für Meteorologie<text:line-break/>Hamburg</text:span></text:p>
<text:table-of-content text:style-name="Sect1" text:protected="true" text:name="Table of Contents1"> <text:table-of-content text:style-name="Sect1" text:protected="true" text:name="Table of Contents1">
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<text:index-title-template text:style-name="Contents_20_Heading">Table of Contents</text:index-title-template> <text:index-title-template text:style-name="Contents_20_Heading">Table of Contents</text:index-title-template>
...@@ -2032,58 +2032,58 @@ ...@@ -2032,58 +2032,58 @@
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</text:index-title> </text:index-title>
<text:p text:style-name="P226"><text:a xlink:type="simple" xlink:href="#__RefHeading__2518_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1 Introduction<text:tab/>3</text:a></text:p> <text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2518_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1 Introduction<text:tab/>3</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2520_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1 Example: ECHAM experiment setup<text:tab/>3</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2520_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1 Example: ECHAM experiment setup<text:tab/>3</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2522_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.1 Experiments are defined by custom and default settings<text:tab/>3</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2522_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.1 Experiments are defined by custom and default settings<text:tab/>3</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2524_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.2 Job templates are completed by settings to create scripts<text:tab/>4</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2524_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.2 Job templates are completed by settings to create scripts<text:tab/>4</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2526_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.3 Generating scripts only refers to the custom settings&apos; file<text:tab/>6</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2526_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.3 Generating scripts only refers to the custom settings&apos; file<text:tab/>6</text:a></text:p>
<text:p text:style-name="P226"><text:a xlink:type="simple" xlink:href="#__RefHeading__2528_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2 Details on experiment definition<text:tab/>6</text:a></text:p> <text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2528_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2 Details on experiment definition<text:tab/>6</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2530_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.1 Design<text:tab/>7</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2530_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.1 Design<text:tab/>7</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2532_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.2 Tools<text:tab/>7</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2532_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.2 Tools<text:tab/>7</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2534_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3 Format of .config files<text:tab/>8</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2534_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3 Format of .config files<text:tab/>8</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__1669_1438093122" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.1 Variables<text:tab/>8</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__1669_1438093122" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.1 Variables<text:tab/>8</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2536_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.2 Sections<text:tab/>9</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2536_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.2 Sections<text:tab/>9</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2538_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.3 Special variables and sections<text:tab/>9</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2538_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.3 Special variables and sections<text:tab/>9</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2540_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.4 Variable interpolation<text:tab/>11</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2540_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.4 Variable interpolation<text:tab/>11</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2542_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.5 Evaluation of interpolation<text:tab/>12</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2542_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.5 Evaluation of interpolation<text:tab/>12</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2544_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.6 Special expressions<text:tab/>13</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2544_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.6 Special expressions<text:tab/>13</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2546_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4 Format of .tmpl files<text:tab/>14</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2546_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4 Format of .tmpl files<text:tab/>14</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2548_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.1 Placeholders<text:tab/>14</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2548_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.1 Placeholders<text:tab/>14</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2550_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.2 Variables in sections<text:tab/>14</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2550_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.2 Variables in sections<text:tab/>14</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2552_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.3 Expressions<text:tab/>15</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2552_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.3 Expressions<text:tab/>15</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2554_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.4 Loops<text:tab/>15</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2554_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.4 Loops<text:tab/>15</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2556_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.5 Conditions<text:tab/>16</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2556_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.5 Conditions<text:tab/>16</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2558_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.6 Comments<text:tab/>16</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2558_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.6 Comments<text:tab/>16</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2560_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.5 Standard experiments<text:tab/>17</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2560_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.5 Standard experiments<text:tab/>17</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2562_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.6 Standard options<text:tab/>17</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2562_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.6 Standard options<text:tab/>17</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2564_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7 Standard environments<text:tab/>18</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2564_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7 Standard environments<text:tab/>18</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__1508_1711940803" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8 Generating jobs<text:tab/>18</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__1508_1711940803" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8 Generating jobs<text:tab/>18</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.1 Changing the model job list<text:tab/>19</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.1 Changing the model job list<text:tab/>19</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2568_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.2 Pre-defined job variables<text:tab/>19</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2568_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.2 Pre-defined job variables<text:tab/>19</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.3 Overriding namelist settings in derived jobs<text:tab/>20</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.3 Overriding namelist settings in derived jobs<text:tab/>20</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2572_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.4 Native script variables<text:tab/>20</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2572_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.4 Native script variables<text:tab/>20</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2574_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.5 Initializing native script variables<text:tab/>21</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2574_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.5 Initializing native script variables<text:tab/>21</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2576_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.6 Re-generation of scripts and backup<text:tab/>22</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2576_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.6 Re-generation of scripts and backup<text:tab/>22</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__1883_1672291846" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9 Defining namelists and other configuration files<text:tab/>22</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__1883_1672291846" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9 Defining namelists and other configuration files<text:tab/>22</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2578_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.1 Formatting the namelist information<text:tab/>23</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2578_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.1 Formatting the namelist information<text:tab/>23</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.2 Suppressing namelist groups or variables<text:tab/>23</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.2 Suppressing namelist groups or variables<text:tab/>23</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2714_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.3 Using the namelist text<text:tab/>24</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2714_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.3 Using the namelist text<text:tab/>24</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2584_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.4 Non-namelist configuration files<text:tab/>24</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2584_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.4 Non-namelist configuration files<text:tab/>24</text:a></text:p>
<text:p text:style-name="P227"><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10 Defining input files for an experiment<text:tab/>25</text:a></text:p> <text:p text:style-name="P229"><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10 Defining input files for an experiment<text:tab/>25</text:a></text:p>
<text:p text:style-name="P228"><text:a xlink:type="simple" xlink:href="#__RefHeading__2833_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10.1 Overriding input files for certain jobs<text:tab/>25</text:a></text:p> <text:p text:style-name="P230"><text:a xlink:type="simple" xlink:href="#__RefHeading__2833_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10.1 Overriding input files for certain jobs<text:tab/>25</text:a></text:p>
</text:index-body> </text:index-body>
</text:table-of-content> </text:table-of-content>
<text:p text:style-name="P81"/> <text:p text:style-name="P81"/>
<text:h text:style-name="P225" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2518_1114405012"/>Introduction<text:bookmark-end text:name="__RefHeading__2518_1114405012"/></text:h> <text:h text:style-name="P227" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2518_1114405012"/>Introduction<text:bookmark-end text:name="__RefHeading__2518_1114405012"/></text:h>
<text:p text:style-name="Text_20_body">Running a numerical earth system model experiment requires a number of preparatory and processing steps like staging input data files, providing namelists and other configuration data, housekeeping duties like model-time management, post-processing and storing <text:span text:style-name="T1">of </text:span>output data. These steps are usually put into scripts or another kind of job description that is finally executed on some high-performance computing system.</text:p> <text:p text:style-name="Text_20_body">Running a numerical earth system model experiment requires a number of preparatory and processing steps like staging input data files, providing namelists and other configuration data, housekeeping duties like model-time management, post-processing and storing <text:span text:style-name="T1">of </text:span>output data. These steps are usually put into scripts or another kind of job description that is finally executed on some high-performance computing system.</text:p>
<text:p text:style-name="P1">The <text:span text:style-name="T133">Make Experiments! (</text:span>mkexp<text:span text:style-name="T133">)</text:span> toolbox provides a generic interface to setting up such a<text:span text:style-name="T1">n experiment</text:span>. At the heart of this <text:span text:style-name="T1">lies</text:span> the so-called .config file. This is a simple <text:span text:style-name="T1">text </text:span>file that contains the model settings for your experiment in a way that is <text:span text:style-name="T1">largely </text:span>independent of the job description that is later used to run it.</text:p> <text:p text:style-name="P1">The <text:span text:style-name="T133">Make Experiments! (</text:span>mkexp<text:span text:style-name="T133">)</text:span> toolbox provides a generic interface to setting up such a<text:span text:style-name="T1">n experiment</text:span>. At the heart of this <text:span text:style-name="T1">lies</text:span> the so-called .config file. This is a simple <text:span text:style-name="T1">text </text:span>file that contains the model settings for your experiment in a way that is <text:span text:style-name="T1">largely </text:span>independent of the job description that is later used to run it.</text:p>
<text:p text:style-name="P4">To make this an easy task, MPI-M&apos;s models are delivered with a number of standard experiment types. Your own .config file will chose one of these, thus inheriting their settings for use in your experiment. Typically, it will also override or amend these settings for the purpose of your experiment.</text:p> <text:p text:style-name="P4">To make this an easy task, MPI-M&apos;s models are delivered with a number of standard experiment types. Your own .config file will chose one of these, thus inheriting their settings for use in your experiment. Typically, it will also override or amend these settings for the purpose of your experiment.</text:p>
<text:p text:style-name="P2">While the .config fil<text:span text:style-name="T2">e contains all necessary settings, there is much more to the actual job description. Therefore, the standard experiment types also provide templates (.tmpl files) for the jobs to run, that are then converted to the final job step descriptions, using the .config file settings. Besides, the .config file contains a &apos;jobs&apos; section, where the job control flow and parameters of the job description itself may be adjusted, e.g. requiring more resources or disabling certain job steps.</text:span></text:p> <text:p text:style-name="P2">While the .config fil<text:span text:style-name="T2">e contains all necessary settings, there is much more to the actual job description. Therefore, the standard experiment types also provide templates (.tmpl files) for the jobs to run, that are then converted to the final job step descriptions, using the .config file settings. Besides, the .config file contains a &apos;jobs&apos; section, where the job control flow and parameters of the job description itself may be adjusted, e.g. requiring more resources or disabling certain job steps.</text:span></text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2520_1114405012"/>Example: <text:span text:style-name="T3">ECHAM experiment setup</text:span><text:bookmark-end text:name="__RefHeading__2520_1114405012"/></text:h> <text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2520_1114405012"/>Example: <text:span text:style-name="T3">ECHAM experiment setup</text:span><text:bookmark-end text:name="__RefHeading__2520_1114405012"/></text:h>
<text:p text:style-name="P32">To illustrate the way <text:span text:style-name="T9">mkexp</text:span> works, let us look at the way that experiments with ECHAM, MPI-M&apos;s atmospheric circulation model, are set up.</text:p> <text:p text:style-name="P32">To illustrate the way <text:span text:style-name="T9">mkexp</text:span> works, let us look at the way that experiments with ECHAM, MPI-M&apos;s atmospheric circulation model, are set up.</text:p>
<text:h text:style-name="P232" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2522_1114405012"/>Experiments are defined by custom and default settings<text:bookmark-end text:name="__RefHeading__2522_1114405012"/></text:h> <text:h text:style-name="P234" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2522_1114405012"/>Experiments are defined by custom and default settings<text:bookmark-end text:name="__RefHeading__2522_1114405012"/></text:h>
<text:p text:style-name="P3">ECHAM comes with five <text:span text:style-name="T178">pre-defined </text:span>experiment types, amip-LR, amip-MR, amip-HR, sstClim-LR and sstClim-MR. <text:span text:style-name="T3">To set up an experiment based on one of these, like amip-LR, all you have to do is create your own experiment configuration file within ECHAM&apos;s run subdirectory, e.g. &apos;joe1234.config&apos;, setting amip-LR as experiment type and providing an experiment description with the header comment:</text:span></text:p> <text:p text:style-name="P3">ECHAM comes with five <text:span text:style-name="T178">pre-defined </text:span>experiment types, amip-LR, amip-MR, amip-HR, sstClim-LR and sstClim-MR. <text:span text:style-name="T3">To set up an experiment based on one of these, like amip-LR, all you have to do is create your own experiment configuration file within ECHAM&apos;s run subdirectory, e.g. &apos;joe1234.config&apos;, setting amip-LR as experiment type and providing an experiment description with the header comment:</text:span></text:p>
<text:p text:style-name="P93"><text:soft-page-break/># Standard AMIP experiment as baseline for further experiments (LR)</text:p> <text:p text:style-name="P93"><text:soft-page-break/># Standard AMIP experiment as baseline for further experiments (LR)</text:p>
<text:p text:style-name="P93"/> <text:p text:style-name="P93"/>
...@@ -2109,7 +2109,7 @@ ...@@ -2109,7 +2109,7 @@
<text:p text:style-name="P98">ATMO_INPUT_ROOT = /pool/data/ECHAM6/input/r0004 </text:p> <text:p text:style-name="P98">ATMO_INPUT_ROOT = /pool/data/ECHAM6/input/r0004 </text:p>
<text:p text:style-name="P98">LAND_INPUT_ROOT = /pool/data/JSBACH/input/r0004 </text:p> <text:p text:style-name="P98">LAND_INPUT_ROOT = /pool/data/JSBACH/input/r0004 </text:p>
<text:p text:style-name="P6">The final configuration is then merged from all of these three sources, where the experiment configuration may override <text:span text:style-name="T40">or amend </text:span>settings from the experiment type, and the type config may in turn change the model defaults.</text:p> <text:p text:style-name="P6">The final configuration is then merged from all of these three sources, where the experiment configuration may override <text:span text:style-name="T40">or amend </text:span>settings from the experiment type, and the type config may in turn change the model defaults.</text:p>
<text:h text:style-name="P233" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2524_1114405012"/>Job templates are completed by settings to create scripts<text:bookmark-end text:name="__RefHeading__2524_1114405012"/></text:h> <text:h text:style-name="P235" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2524_1114405012"/>Job templates are completed by settings to create scripts<text:bookmark-end text:name="__RefHeading__2524_1114405012"/></text:h>
<text:p text:style-name="P6"><text:span text:style-name="T177">Now the experiment configuration is finalized, the </text:span>settings are used to fill in <text:span text:style-name="T177">a kind of job description forms, so called </text:span><text:span text:style-name="T9">templates</text:span><text:span text:style-name="T177">, </text:span>from which eventually the <text:span text:style-name="T177">actual </text:span>job description files are created. As the structure of<text:span text:style-name="T177"> </text:span>jobs is largely independent of the model resolution, all amip- experiment types share the same set of template files. One of them is <text:span text:style-name="T198">&apos;</text:span>amip.run.tmpl<text:span text:style-name="T198">&apos;</text:span>, also within the run/standard_experiments subdirectory. <text:span text:style-name="T6">The excerpt below shows that t</text:span>his looks mostly like a shell script, but contains <text:span text:style-name="T132">placeholders</text:span> that are filled using the .config file information:</text:p> <text:p text:style-name="P6"><text:span text:style-name="T177">Now the experiment configuration is finalized, the </text:span>settings are used to fill in <text:span text:style-name="T177">a kind of job description forms, so called </text:span><text:span text:style-name="T9">templates</text:span><text:span text:style-name="T177">, </text:span>from which eventually the <text:span text:style-name="T177">actual </text:span>job description files are created. As the structure of<text:span text:style-name="T177"> </text:span>jobs is largely independent of the model resolution, all amip- experiment types share the same set of template files. One of them is <text:span text:style-name="T198">&apos;</text:span>amip.run.tmpl<text:span text:style-name="T198">&apos;</text:span>, also within the run/standard_experiments subdirectory. <text:span text:style-name="T6">The excerpt below shows that t</text:span>his looks mostly like a shell script, but contains <text:span text:style-name="T132">placeholders</text:span> that are filled using the .config file information:</text:p>
<text:p text:style-name="P98"><text:soft-page-break/>#! /bin/bash</text:p> <text:p text:style-name="P98"><text:soft-page-break/>#! /bin/bash</text:p>
<text:p text:style-name="P98"/> <text:p text:style-name="P98"/>
...@@ -2176,15 +2176,15 @@ ...@@ -2176,15 +2176,15 @@
<text:p text:style-name="P13"><text:span text:style-name="T177">So, as soon as</text:span> <text:span text:style-name="T177">you have set up &apos;</text:span>joe1234.config<text:span text:style-name="T177">&apos;</text:span>, you may create the job scripts that are needed to run your experiment. Still within ECHAM&apos;s <text:span text:style-name="T179">&apos;</text:span>run<text:span text:style-name="T179">&apos;</text:span> subdirectory, type the following into your terminal:</text:p> <text:p text:style-name="P13"><text:span text:style-name="T177">So, as soon as</text:span> <text:span text:style-name="T177">you have set up &apos;</text:span>joe1234.config<text:span text:style-name="T177">&apos;</text:span>, you may create the job scripts that are needed to run your experiment. Still within ECHAM&apos;s <text:span text:style-name="T179">&apos;</text:span>run<text:span text:style-name="T179">&apos;</text:span> subdirectory, type the following into your terminal:</text:p>
<text:p text:style-name="Preformatted_20_Text">../util/mkexp/mkexp joe1234.config</text:p> <text:p text:style-name="Preformatted_20_Text">../util/mkexp/mkexp joe1234.config</text:p>
<text:p text:style-name="P14">This will <text:span text:style-name="T133">read all configuration information and </text:span>create all job scripts that are defined within your experiment&apos;s setup, <text:span text:style-name="T133">using their respective templates as shown in the previous section</text:span>. <text:span text:style-name="T9">mkexp</text:span> will put these <text:span text:style-name="T133">scripts </text:span>in <text:span text:style-name="T133">a common</text:span> directory defined by the .config variable <text:span text:style-name="T179">&apos;</text:span>SCRIPT_DIR<text:span text:style-name="T179">&apos;</text:span>, and <text:span text:style-name="T179">print</text:span> the name of this directory on your terminal.</text:p> <text:p text:style-name="P14">This will <text:span text:style-name="T133">read all configuration information and </text:span>create all job scripts that are defined within your experiment&apos;s setup, <text:span text:style-name="T133">using their respective templates as shown in the previous section</text:span>. <text:span text:style-name="T9">mkexp</text:span> will put these <text:span text:style-name="T133">scripts </text:span>in <text:span text:style-name="T133">a common</text:span> directory defined by the .config variable <text:span text:style-name="T179">&apos;</text:span>SCRIPT_DIR<text:span text:style-name="T179">&apos;</text:span>, and <text:span text:style-name="T179">print</text:span> the name of this directory on your terminal.</text:p>
<text:h text:style-name="P229" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2528_1114405012"/>Details on <text:span text:style-name="T197">experiment</text:span> <text:span text:style-name="T197">definition</text:span><text:bookmark-end text:name="__RefHeading__2528_1114405012"/></text:h> <text:h text:style-name="P231" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2528_1114405012"/>Details on <text:span text:style-name="T197">experiment</text:span> <text:span text:style-name="T197">definition</text:span><text:bookmark-end text:name="__RefHeading__2528_1114405012"/></text:h>
<text:p text:style-name="P15">With the introductory example of the previous section in mind, this section will give some more detailed information on specific aspects of <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T43">.</text:span></text:p> <text:p text:style-name="P15">With the introductory example of the previous section in mind, this section will give some more detailed information on specific aspects of <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T43">.</text:span></text:p>
<text:h text:style-name="P247" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2530_1114405012"/><text:soft-page-break/>Design<text:bookmark-end text:name="__RefHeading__2530_1114405012"/></text:h> <text:h text:style-name="P249" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2530_1114405012"/><text:soft-page-break/>Design<text:bookmark-end text:name="__RefHeading__2530_1114405012"/></text:h>
<text:p text:style-name="P34">Experiment definition with <text:span text:style-name="T9">mkexp</text:span> <text:span text:style-name="T159">is organized</text:span> <text:span text:style-name="T159">in</text:span> three levels.</text:p> <text:p text:style-name="P34">Experiment definition with <text:span text:style-name="T9">mkexp</text:span> <text:span text:style-name="T159">is organized</text:span> <text:span text:style-name="T159">in</text:span> three levels.</text:p>
<text:p text:style-name="P34">The first level is the <text:span text:style-name="T9">mkexp</text:span> toolbox. It provides the front end to create an executable job description from a generic experiment configuration, <text:span text:style-name="T158">but does not contain any model specific information. Instead a basic set of conventions is defined that should be applicable to a very large range of model systems. When this document uses the term </text:span><text:span text:style-name="T18">mkexp</text:span><text:span text:style-name="T49">, it refers to this system level.</text:span></text:p> <text:p text:style-name="P34">The first level is the <text:span text:style-name="T9">mkexp</text:span> toolbox. It provides the front end to create an executable job description from a generic experiment configuration, <text:span text:style-name="T158">but does not contain any model specific information. Instead a basic set of conventions is defined that should be applicable to a very large range of model systems. When this document uses the term </text:span><text:span text:style-name="T18">mkexp</text:span><text:span text:style-name="T49">, it refers to this system level.</text:span></text:p>
<text:p text:style-name="P34"><text:span text:style-name="T158">At a second level, a model needs to provide a number of files containing the information needed by </text:span><text:span text:style-name="T17">mkexp</text:span><text:span text:style-name="T158">: the required job steps and their interaction, the basic contents of job scripts, model specific information, and building blocks that may be combined to define a specific experiment. This is called the </text:span><text:span text:style-name="T17">model setup</text:span><text:span text:style-name="T48">. The files must maintain the naming conventions prescribed by </text:span><text:span text:style-name="T17">mkexp</text:span><text:span text:style-name="T48">.</text:span></text:p> <text:p text:style-name="P34"><text:span text:style-name="T158">At a second level, a model needs to provide a number of files containing the information needed by </text:span><text:span text:style-name="T17">mkexp</text:span><text:span text:style-name="T158">: the required job steps and their interaction, the basic contents of job scripts, model specific information, and building blocks that may be combined to define a specific experiment. This is called the </text:span><text:span text:style-name="T17">model setup</text:span><text:span text:style-name="T48">. The files must maintain the naming conventions prescribed by </text:span><text:span text:style-name="T17">mkexp</text:span><text:span text:style-name="T48">.</text:span></text:p>
<text:p text:style-name="P35"><text:span text:style-name="T43">Finally, the third level is the actual experiment definition. Here the user decides which of the building blocks from the previous level are needed, and </text:span><text:span text:style-name="T80">defines</text:span><text:span text:style-name="T43"> experiment specific settings that override or amend the information from the model setup. It is also essential to supply an experiment description and a – possibly unique – experiment identifier. All this is called the </text:span><text:span text:style-name="T9">user setup</text:span><text:span text:style-name="T43">.</text:span></text:p> <text:p text:style-name="P35"><text:span text:style-name="T43">Finally, the third level is the actual experiment definition. Here the user decides which of the building blocks from the previous level are needed, and </text:span><text:span text:style-name="T80">defines</text:span><text:span text:style-name="T43"> experiment specific settings that override or amend the information from the model setup. It is also essential to supply an experiment description and a – possibly unique – experiment identifier. All this is called the </text:span><text:span text:style-name="T9">user setup</text:span><text:span text:style-name="T43">.</text:span></text:p>
<text:p text:style-name="P36"><text:span text:style-name="T43">All levels should make a clear distinction </text:span><text:span text:style-name="T50">between </text:span><text:span text:style-name="T43">the .config files, containing the experiment&apos;s configuration information, </text:span><text:span text:style-name="T50">and </text:span><text:span text:style-name="T43">the .tmpl files, containing the actual job description and job control syntax.</text:span></text:p> <text:p text:style-name="P36"><text:span text:style-name="T43">All levels should make a clear distinction </text:span><text:span text:style-name="T50">between </text:span><text:span text:style-name="T43">the .config files, containing the experiment&apos;s configuration information, </text:span><text:span text:style-name="T50">and </text:span><text:span text:style-name="T43">the .tmpl files, containing the actual job description and job control syntax.</text:span></text:p>
<text:h text:style-name="P248" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2532_1114405012"/>Tools<text:bookmark-end text:name="__RefHeading__2532_1114405012"/></text:h> <text:h text:style-name="P250" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2532_1114405012"/>Tools<text:bookmark-end text:name="__RefHeading__2532_1114405012"/></text:h>
<text:p text:style-name="P82"><text:span text:style-name="T133">The </text:span><text:span text:style-name="T32">mkexp</text:span><text:span text:style-name="T133"> package provides a number of tools for working with script configurations and setups.</text:span></text:p> <text:p text:style-name="P82"><text:span text:style-name="T133">The </text:span><text:span text:style-name="T32">mkexp</text:span><text:span text:style-name="T133"> package provides a number of tools for working with script configurations and setups.</text:span></text:p>
<text:p text:style-name="Preformatted_20_List_20_Heading">mkexp <text:span text:style-name="T23">file</text:span><text:span text:style-name="T61">.</text:span><text:span text:style-name="T43">config</text:span> [<text:span text:style-name="T9">name</text:span>=<text:span text:style-name="T9">value</text:span> ...]</text:p> <text:p text:style-name="Preformatted_20_List_20_Heading">mkexp <text:span text:style-name="T23">file</text:span><text:span text:style-name="T61">.</text:span><text:span text:style-name="T43">config</text:span> [<text:span text:style-name="T9">name</text:span>=<text:span text:style-name="T9">value</text:span> ...]</text:p>
<text:p text:style-name="P190"><text:span text:style-name="T133">This is the main tool for generating an experiment setup. It </text:span>takes <text:span text:style-name="T180">the given</text:span> <text:span text:style-name="T180">user setup</text:span> and <text:span text:style-name="T199">the model setup that is referenced by the user setup </text:span>to generate <text:span text:style-name="T180">the</text:span> <text:span text:style-name="T180">job description files or</text:span> scripts that <text:span text:style-name="T199">are required to run a model experiment as specified in </text:span><text:span text:style-name="T21">file.</text:span><text:span text:style-name="T61">config</text:span><text:span text:style-name="T180">.</text:span></text:p> <text:p text:style-name="P190"><text:span text:style-name="T133">This is the main tool for generating an experiment setup. It </text:span>takes <text:span text:style-name="T180">the given</text:span> <text:span text:style-name="T180">user setup</text:span> and <text:span text:style-name="T199">the model setup that is referenced by the user setup </text:span>to generate <text:span text:style-name="T180">the</text:span> <text:span text:style-name="T180">job description files or</text:span> scripts that <text:span text:style-name="T199">are required to run a model experiment as specified in </text:span><text:span text:style-name="T21">file.</text:span><text:span text:style-name="T61">config</text:span><text:span text:style-name="T180">.</text:span></text:p>
...@@ -2197,7 +2197,7 @@ ...@@ -2197,7 +2197,7 @@
<text:p text:style-name="P182">For an easy comparison of the whole set of generated scripts for two different experiments, this tool takes the directories defined in each configuration, locates the job scripts corresponding to each other (e.g. exp0001.run and exp0002.run), equalizes all occurrences of the experiment name in the scripts and then uses the diff tool to show differences. The environment variable &apos;DIFF&apos; may be set to an alternative tool to be called instead.</text:p> <text:p text:style-name="P182">For an easy comparison of the whole set of generated scripts for two different experiments, this tool takes the directories defined in each configuration, locates the job scripts corresponding to each other (e.g. exp0001.run and exp0002.run), equalizes all occurrences of the experiment name in the scripts and then uses the diff tool to show differences. The environment variable &apos;DIFF&apos; may be set to an alternative tool to be called instead.</text:p>
<text:p text:style-name="P208">rmexp <text:span text:style-name="T24">file</text:span><text:span text:style-name="T183">.config</text:span><text:span text:style-name="T62"> [</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T62">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T62">]</text:span></text:p> <text:p text:style-name="P208">rmexp <text:span text:style-name="T24">file</text:span><text:span text:style-name="T183">.config</text:span><text:span text:style-name="T62"> [</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T62">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T62">]</text:span></text:p>
<text:p text:style-name="P196">This allows <text:span text:style-name="T186">interactive </text:span>remov<text:span text:style-name="T186">al for </text:span>all scripting and run-time data of an experiment without having to deal with path names, as these are read from the configuration.</text:p> <text:p text:style-name="P196">This allows <text:span text:style-name="T186">interactive </text:span>remov<text:span text:style-name="T186">al for </text:span>all scripting and run-time data of an experiment without having to deal with path names, as these are read from the configuration.</text:p>
<text:h text:style-name="P249" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2534_1114405012"/><text:span text:style-name="T139">F</text:span>ormat of .config files<text:bookmark-end text:name="__RefHeading__2534_1114405012"/></text:h> <text:h text:style-name="P251" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2534_1114405012"/><text:span text:style-name="T139">F</text:span>ormat of .config files<text:bookmark-end text:name="__RefHeading__2534_1114405012"/></text:h>
<text:p text:style-name="P15">The .config files are simple text files containing a dictionary of variables with their respective values. They may be structured using sections and comments. <text:span text:style-name="T134">For reading these files, </text:span><text:span text:style-name="T12">mkexp</text:span><text:span text:style-name="T134"> uses the </text:span><text:span text:style-name="T12">configobj</text:span><text:span text:style-name="T134"> Python library. All settings found in the .config files are handled as Python variables internally.</text:span></text:p> <text:p text:style-name="P15">The .config files are simple text files containing a dictionary of variables with their respective values. They may be structured using sections and comments. <text:span text:style-name="T134">For reading these files, </text:span><text:span text:style-name="T12">mkexp</text:span><text:span text:style-name="T134"> uses the </text:span><text:span text:style-name="T12">configobj</text:span><text:span text:style-name="T134"> Python library. All settings found in the .config files are handled as Python variables internally.</text:span></text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__1669_1438093122"/>Variables<text:bookmark-end text:name="__RefHeading__1669_1438093122"/></text:h> <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__1669_1438093122"/>Variables<text:bookmark-end text:name="__RefHeading__1669_1438093122"/></text:h>
<text:p text:style-name="P18">A <text:span text:style-name="T135">configuration variable is set by simply assigning a text value to a name, as in</text:span></text:p> <text:p text:style-name="P18">A <text:span text:style-name="T135">configuration variable is set by simply assigning a text value to a name, as in</text:span></text:p>
...@@ -2348,25 +2348,25 @@ ...@@ -2348,25 +2348,25 @@
<text:p text:style-name="P215">split<text:span text:style-name="T150">(</text:span><text:span text:style-name="T38">s</text:span><text:span text:style-name="T117">, </text:span><text:span text:style-name="T38">m</text:span><text:span text:style-name="T117">=-1)</text:span></text:p> <text:p text:style-name="P215">split<text:span text:style-name="T150">(</text:span><text:span text:style-name="T38">s</text:span><text:span text:style-name="T117">, </text:span><text:span text:style-name="T38">m</text:span><text:span text:style-name="T117">=-1)</text:span></text:p>
<text:p text:style-name="P186">cuts <text:span text:style-name="T220">the input </text:span>string <text:span text:style-name="T220">at all occurrences of </text:span><text:span text:style-name="T34">s</text:span><text:span text:style-name="T220">, returning</text:span> a list of substrings. <text:span text:style-name="T219">If </text:span><text:span text:style-name="T33">m</text:span><text:span text:style-name="T219"> is positive or zero, it cuts only at the first </text:span><text:span text:style-name="T33">m</text:span><text:span text:style-name="T219"> occurrences; the last element contains the remaining substring:</text:span></text:p> <text:p text:style-name="P186">cuts <text:span text:style-name="T220">the input </text:span>string <text:span text:style-name="T220">at all occurrences of </text:span><text:span text:style-name="T34">s</text:span><text:span text:style-name="T220">, returning</text:span> a list of substrings. <text:span text:style-name="T219">If </text:span><text:span text:style-name="T33">m</text:span><text:span text:style-name="T219"> is positive or zero, it cuts only at the first </text:span><text:span text:style-name="T33">m</text:span><text:span text:style-name="T219"> occurrences; the last element contains the remaining substring:</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text_20_Indented">%{ &apos;A B C&apos; | <text:span text:style-name="T120">split</text:span><text:span text:style-name="T150">(&apos; &apos;) }<text:tab/><text:tab/></text:span><text:span text:style-name="T153"> </text:span><text:span text:style-name="T152">[&apos;A&apos;, &apos;B&apos;, &apos;C&apos;]</text:span></text:p> <text:p text:style-name="Preformatted_20_Text_20_Indented">%{ &apos;A B C&apos; | <text:span text:style-name="T120">split</text:span><text:span text:style-name="T150">(&apos; &apos;) }<text:tab/><text:tab/></text:span><text:span text:style-name="T153"> </text:span><text:span text:style-name="T152">[&apos;A&apos;, &apos;B&apos;, &apos;C&apos;]</text:span></text:p>
<text:p text:style-name="P220"><text:span text:style-name="T152">%{ &apos;A B C&apos; | split(&apos; &apos;, </text:span><text:span text:style-name="T130">1</text:span><text:span text:style-name="T152">) } <text:tab/></text:span><text:span text:style-name="T153"></text:span><text:span text:style-name="T152">[&apos;A&apos;, </text:span><text:span text:style-name="T130">&apos;B C&apos;</text:span><text:span text:style-name="T152">]</text:span></text:p> <text:p text:style-name="P222"><text:span text:style-name="T152">%{ &apos;A B C&apos; | split(&apos; &apos;, </text:span><text:span text:style-name="T130">1</text:span><text:span text:style-name="T152">) } <text:tab/></text:span><text:span text:style-name="T153"></text:span><text:span text:style-name="T152">[&apos;A&apos;, </text:span><text:span text:style-name="T130">&apos;B C&apos;</text:span><text:span text:style-name="T152">]</text:span></text:p>
<text:p text:style-name="P202"/> <text:p text:style-name="P202"/>
<text:p text:style-name="P111">filter<text:span text:style-name="T150">()</text:span></text:p> <text:p text:style-name="P111">filter<text:span text:style-name="T150">()</text:span></text:p>
<text:p text:style-name="P203">removes empty elements from <text:span text:style-name="T220">the input</text:span> list:</text:p> <text:p text:style-name="P203">removes empty elements from <text:span text:style-name="T220">the input</text:span> list:</text:p>
<text:p text:style-name="P221"><text:span text:style-name="T152">%{ [&apos;A&apos;, &apos;&apos;, &apos;C&apos;] | </text:span><text:span text:style-name="T130">filter</text:span><text:span text:style-name="T152">() }<text:tab/></text:span><text:span text:style-name="T150"> [&apos;A&apos;, &apos;C&apos;]</text:span></text:p> <text:p text:style-name="P223"><text:span text:style-name="T152">%{ [&apos;A&apos;, &apos;&apos;, &apos;C&apos;] | </text:span><text:span text:style-name="T130">filter</text:span><text:span text:style-name="T152">() }<text:tab/></text:span><text:span text:style-name="T150"> [&apos;A&apos;, &apos;C&apos;]</text:span></text:p>
<text:p text:style-name="P216">match<text:span text:style-name="T150">(</text:span><text:span text:style-name="T38">regexp</text:span><text:span text:style-name="T150">, </text:span><text:span text:style-name="T38">default</text:span><text:span text:style-name="T150">=&apos;&apos;)</text:span></text:p> <text:p text:style-name="P216">match<text:span text:style-name="T150">(</text:span><text:span text:style-name="T38">regexp</text:span><text:span text:style-name="T150">, </text:span><text:span text:style-name="T38">default</text:span><text:span text:style-name="T150">=&apos;&apos;)</text:span></text:p>
<text:p text:style-name="P204"><text:span text:style-name="T150">returns the input string</text:span><text:span text:style-name="T117">, if </text:span><text:span text:style-name="T38">regexp</text:span><text:span text:style-name="T117"> matches somewhere in it. If </text:span><text:span text:style-name="T38">regexp</text:span><text:span text:style-name="T117"> contains matching groups (parentheses), the substring matching the first group is returned. If no match is found, the </text:span><text:span text:style-name="T38">default</text:span><text:span text:style-name="T117"> string is returned:</text:span></text:p> <text:p text:style-name="P204"><text:span text:style-name="T150">returns the input string</text:span><text:span text:style-name="T117">, if </text:span><text:span text:style-name="T38">regexp</text:span><text:span text:style-name="T117"> matches somewhere in it. If </text:span><text:span text:style-name="T38">regexp</text:span><text:span text:style-name="T117"> contains matching groups (parentheses), the substring matching the first group is returned. If no match is found, the </text:span><text:span text:style-name="T38">default</text:span><text:span text:style-name="T117"> string is returned:</text:span></text:p>
<text:p text:style-name="P221"><text:span text:style-name="T117">%{ &apos;Douglas Adams&apos; | </text:span><text:span text:style-name="T114">match</text:span><text:span text:style-name="T117">(&apos;Adam&apos;) }<text:tab/><text:tab/>&apos;Douglas Adams&apos;</text:span></text:p> <text:p text:style-name="P223"><text:span text:style-name="T117">%{ &apos;Douglas Adams&apos; | </text:span><text:span text:style-name="T114">match</text:span><text:span text:style-name="T117">(&apos;Adam&apos;) }<text:tab/><text:tab/>&apos;Douglas Adams&apos;</text:span></text:p>
<text:p text:style-name="P221"><text:span text:style-name="T117">%{ &apos;Douglas Adams&apos; | match(</text:span><text:span text:style-name="T114">&apos;Eve&apos;</text:span><text:span text:style-name="T117">) }<text:tab/><text:tab/>&apos;&apos;</text:span></text:p> <text:p text:style-name="P223"><text:span text:style-name="T117">%{ &apos;Douglas Adams&apos; | match(</text:span><text:span text:style-name="T114">&apos;Eve&apos;</text:span><text:span text:style-name="T117">) }<text:tab/><text:tab/>&apos;&apos;</text:span></text:p>
<text:p text:style-name="P221"><text:span text:style-name="T117">%{ &apos;Douglas Adams&apos; | match(&apos;Abel&apos;, </text:span><text:span text:style-name="T114">&apos;Cain&apos;</text:span><text:span text:style-name="T117">) }<text:tab/>&apos;Cain&apos;</text:span></text:p> <text:p text:style-name="P223"><text:span text:style-name="T117">%{ &apos;Douglas Adams&apos; | match(&apos;Abel&apos;, </text:span><text:span text:style-name="T114">&apos;Cain&apos;</text:span><text:span text:style-name="T117">) }<text:tab/>&apos;Cain&apos;</text:span></text:p>
<text:p text:style-name="P221"><text:span text:style-name="T117">%{ &apos;Douglas Adams&apos; | match(&apos;l</text:span><text:span text:style-name="T114">(.*)</text:span><text:span text:style-name="T117">m&apos;) }<text:tab/><text:tab/>&apos;as Ada&apos;</text:span></text:p> <text:p text:style-name="P223"><text:span text:style-name="T117">%{ &apos;Douglas Adams&apos; | match(&apos;l</text:span><text:span text:style-name="T114">(.*)</text:span><text:span text:style-name="T117">m&apos;) }<text:tab/><text:tab/>&apos;as Ada&apos;</text:span></text:p>
<text:p text:style-name="P217"><text:span text:style-name="T114">wordwrap</text:span><text:span text:style-name="T117">(width=79, break_long_words=true, break_on_hyphens=true, <text:s text:c="2"/><text:line-break/> <text:s text:c="8"/>wrapstring=none)</text:span></text:p> <text:p text:style-name="P217"><text:span text:style-name="T114">wordwrap</text:span><text:span text:style-name="T117">(width=79, break_long_words=true, break_on_hyphens=true, <text:s text:c="2"/><text:line-break/> <text:s text:c="8"/>wrapstring=none)</text:span></text:p>
<text:p text:style-name="P205"><text:span text:style-name="T117">replaces the </text:span><text:span text:style-name="T118">builtin </text:span><text:span text:style-name="T39">Jinja </text:span><text:span text:style-name="T118">filter &apos;wordwrap&apos; <text:s/>by a private version that allows to suppress breaks on hyphens:</text:span></text:p> <text:p text:style-name="P205"><text:span text:style-name="T117">replaces the </text:span><text:span text:style-name="T118">builtin </text:span><text:span text:style-name="T39">Jinja </text:span><text:span text:style-name="T118">filter &apos;wordwrap&apos; <text:s/>by a private version that allows to suppress breaks on hyphens:</text:span></text:p>
<text:p text:style-name="P271"><text:soft-page-break/>%{&apos;long-hyphenated-text&apos;|<text:span text:style-name="T120">wordwrap</text:span>(15, false)}</text:p> <text:p text:style-name="P220"><text:soft-page-break/>%{&apos;long-hyphenated-text&apos;|<text:span text:style-name="T120">wordwrap</text:span>(15, false)}</text:p>
<text:p text:style-name="P222"><text:span text:style-name="T118"></text:span><text:span text:style-name="T117"> &apos;long- </text:span></text:p> <text:p text:style-name="P224"><text:span text:style-name="T118"></text:span><text:span text:style-name="T117"> &apos;long- </text:span></text:p>
<text:p text:style-name="P272"><text:s text:c="3"/>hyphenated-text&apos;</text:p> <text:p text:style-name="P221"><text:s text:c="3"/>hyphenated-text&apos;</text:p>
<text:p text:style-name="P222"/> <text:p text:style-name="P224"/>
<text:p text:style-name="P271">%{&apos;long-hyphenated-text&apos;|wordwrap(15, false, <text:span text:style-name="T120">false</text:span>)} </text:p> <text:p text:style-name="P220">%{&apos;long-hyphenated-text&apos;|wordwrap(15, false, <text:span text:style-name="T120">false</text:span>)} </text:p>
<text:p text:style-name="P222"><text:span text:style-name="T118"></text:span><text:span text:style-name="T117"> &apos;long-</text:span><text:span text:style-name="T118">hyphenated-text&apos;</text:span></text:p> <text:p text:style-name="P224"><text:span text:style-name="T118"></text:span><text:span text:style-name="T117"> &apos;long-</text:span><text:span text:style-name="T118">hyphenated-text&apos;</text:span></text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2554_1114405012"/>Loops<text:bookmark-end text:name="__RefHeading__2554_1114405012"/></text:h> <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2554_1114405012"/>Loops<text:bookmark-end text:name="__RefHeading__2554_1114405012"/></text:h>
<text:p text:style-name="P28">Text in a template may be used repeatedly, like a classical &apos;for&apos; loop. Loops are defined by structured comments <text:span text:style-name="T204">i.e. lines </text:span>beginning with &apos;#%&apos;. <text:span text:style-name="T204">They </text:span>start with &apos;#% for … <text:span text:style-name="T147">in …:</text:span>&apos; and end in &apos;#% endfor&apos;:</text:p> <text:p text:style-name="P28">Text in a template may be used repeatedly, like a classical &apos;for&apos; loop. Loops are defined by structured comments <text:span text:style-name="T204">i.e. lines </text:span>beginning with &apos;#%&apos;. <text:span text:style-name="T204">They </text:span>start with &apos;#% for … <text:span text:style-name="T147">in …:</text:span>&apos; and end in &apos;#% endfor&apos;:</text:p>
<text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T120">#% for</text:span> countdown <text:span text:style-name="T120">in</text:span> [3, 2, 1, &apos;<text:span text:style-name="T204">liftoff</text:span>&apos;]<text:span text:style-name="T120">:</text:span></text:p> <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T120">#% for</text:span> countdown <text:span text:style-name="T120">in</text:span> [3, 2, 1, &apos;<text:span text:style-name="T204">liftoff</text:span>&apos;]<text:span text:style-name="T120">:</text:span></text:p>
...@@ -2410,7 +2410,7 @@ ...@@ -2410,7 +2410,7 @@
<text:p text:style-name="P11">Besides the standard experiment types, <text:span text:style-name="T9">mkexp</text:span> also supports option sets that are independent of the experiment type chosen.</text:p> <text:p text:style-name="P11">Besides the standard experiment types, <text:span text:style-name="T9">mkexp</text:span> also supports option sets that are independent of the experiment type chosen.</text:p>
<text:p text:style-name="P11">Usually these option sets contain a number of settings needed for a certain technical aspect, e.g. for changing the output interval or aggregation method for output data, or providing resolution dependent model settings. They reside in a subdirectory &apos;standard_options&apos; of the current working directory, each in their respective <text:span text:style-name="T9">optionname</text:span>.config file.</text:p> <text:p text:style-name="P11">Usually these option sets contain a number of settings needed for a certain technical aspect, e.g. for changing the output interval or aggregation method for output data, or providing resolution dependent model settings. They reside in a subdirectory &apos;standard_options&apos; of the current working directory, each in their respective <text:span text:style-name="T9">optionname</text:span>.config file.</text:p>
<text:p text:style-name="P11">Within the experiment&apos;s .config file, options are selected by setting the variable EXP_OPTIONS to the list of required option names. These settings are loaded after the experiment type configuration but before the user defined experiment configuration.</text:p> <text:p text:style-name="P11">Within the experiment&apos;s .config file, options are selected by setting the variable EXP_OPTIONS to the list of required option names. These settings are loaded after the experiment type configuration but before the user defined experiment configuration.</text:p>
<text:h text:style-name="P250" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1508_1711940803"/>Generating <text:span text:style-name="T172">j</text:span>obs<text:bookmark-end text:name="__RefHeading__1508_1711940803"/></text:h> <text:h text:style-name="P252" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1508_1711940803"/>Generating <text:span text:style-name="T172">j</text:span>obs<text:bookmark-end text:name="__RefHeading__1508_1711940803"/></text:h>
<text:p text:style-name="P42">When<text:span text:style-name="T160"> </text:span>running <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T92">, </text:span><text:span text:style-name="T93">the special configuration section [jobs]</text:span><text:span text:style-name="T37"> </text:span><text:span text:style-name="T93">is read and evaluated. Each of its subsections, e.g. [[run]], defines a job definition file or job script to be created.</text:span></text:p> <text:p text:style-name="P42">When<text:span text:style-name="T160"> </text:span>running <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T92">, </text:span><text:span text:style-name="T93">the special configuration section [jobs]</text:span><text:span text:style-name="T37"> </text:span><text:span text:style-name="T93">is read and evaluated. Each of its subsections, e.g. [[run]], defines a job definition file or job script to be created.</text:span></text:p>
<text:p text:style-name="P133"># <text:span text:style-name="T161">model setup: experiment type &apos;control&apos;</text:span></text:p> <text:p text:style-name="P133"># <text:span text:style-name="T161">model setup: experiment type &apos;control&apos;</text:span></text:p>
<text:p text:style-name="P120">[jobs]</text:p> <text:p text:style-name="P120">[jobs]</text:p>
...@@ -2434,7 +2434,7 @@ ...@@ -2434,7 +2434,7 @@
<text:p text:style-name="P134"><text:span text:style-name="T92"><text:s text:c="4"/>.</text:span><text:span text:style-name="T96">extends</text:span><text:span text:style-name="T92"> = p</text:span><text:span text:style-name="T97">ost</text:span></text:p> <text:p text:style-name="P134"><text:span text:style-name="T92"><text:s text:c="4"/>.</text:span><text:span text:style-name="T96">extends</text:span><text:span text:style-name="T92"> = p</text:span><text:span text:style-name="T97">ost</text:span></text:p>
<text:p text:style-name="P121"><text:s text:c="4"/>command = $HOME/bin/my_special_command</text:p> <text:p text:style-name="P121"><text:s text:c="4"/>command = $HOME/bin/my_special_command</text:p>
<text:p text:style-name="P50">With this configuration, an additional &apos;joe1234.my_post&apos; is created based on the existing &apos;post&apos; template. A dedicated &apos;joe1234.my_post.tmpl&apos; file is not needed here. The &apos;command&apos; setting is <text:span text:style-name="T163">made available </text:span>to <text:span text:style-name="T163">the template via the</text:span> &apos;JOB&apos; dictionary.</text:p> <text:p text:style-name="P50">With this configuration, an additional &apos;joe1234.my_post&apos; is created based on the existing &apos;post&apos; template. A dedicated &apos;joe1234.my_post.tmpl&apos; file is not needed here. The &apos;command&apos; setting is <text:span text:style-name="T163">made available </text:span>to <text:span text:style-name="T163">the template via the</text:span> &apos;JOB&apos; dictionary.</text:p>
<text:h text:style-name="P235" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2568_1114405012"/>Pre-defined job variables<text:bookmark-end text:name="__RefHeading__2568_1114405012"/></text:h> <text:h text:style-name="P237" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2568_1114405012"/>Pre-defined job variables<text:bookmark-end text:name="__RefHeading__2568_1114405012"/></text:h>
<text:p text:style-name="P55">While <text:span text:style-name="T9">mkexp</text:span> in general does not impose any naming convention on the variable names used in the job sections and leaves the details to the respective model setup, there are a few exceptions.</text:p> <text:p text:style-name="P55">While <text:span text:style-name="T9">mkexp</text:span> in general does not impose any naming convention on the variable names used in the job sections and leaves the details to the respective model setup, there are a few exceptions.</text:p>
<text:p text:style-name="P168">tasks</text:p> <text:p text:style-name="P168">tasks</text:p>
<text:p text:style-name="P187">The total number of parallel (MPI) tasks that will be started when running the model. If a job section does not define &apos;tasks&apos;, its value defaults to &apos;nodes&apos; times &apos;tasks_per_node&apos;. Some models require that &apos;tasks&apos; may explicitly be set to some artificial value to trigger the testing mode.</text:p> <text:p text:style-name="P187">The total number of parallel (MPI) tasks that will be started when running the model. If a job section does not define &apos;tasks&apos;, its value defaults to &apos;nodes&apos; times &apos;tasks_per_node&apos;. Some models require that &apos;tasks&apos; may explicitly be set to some artificial value to trigger the testing mode.</text:p>
...@@ -2442,7 +2442,7 @@ ...@@ -2442,7 +2442,7 @@
<text:p text:style-name="P187">Number of computing nodes required on the computing system. Needed if &apos;tasks&apos; is not set.</text:p> <text:p text:style-name="P187">Number of computing nodes required on the computing system. Needed if &apos;tasks&apos; is not set.</text:p>
<text:p text:style-name="P169">tasks_per_node</text:p> <text:p text:style-name="P169">tasks_per_node</text:p>
<text:p text:style-name="P187">Number of parallel (MPI) tasks on a single node. Needed if &apos;tasks&apos; is not set.</text:p> <text:p text:style-name="P187">Number of parallel (MPI) tasks on a single node. Needed if &apos;tasks&apos; is not set.</text:p>
<text:h text:style-name="P234" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2570_1114405012"/>Overriding namelist settings in derived jobs<text:bookmark-end text:name="__RefHeading__2570_1114405012"/></text:h> <text:h text:style-name="P236" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2570_1114405012"/>Overriding namelist settings in derived jobs<text:bookmark-end text:name="__RefHeading__2570_1114405012"/></text:h>
<text:p text:style-name="P50">There is special provision to change namelist files settings for a specific job. Consider this setting from the introductory example.</text:p> <text:p text:style-name="P50">There is special provision to change namelist files settings for a specific job. Consider this setting from the introductory example.</text:p>
<text:p text:style-name="P135"><text:soft-page-break/>[namelists]</text:p> <text:p text:style-name="P135"><text:soft-page-break/>[namelists]</text:p>
<text:p text:style-name="P95"><text:s text:c="2"/>[[namelist.jsbach]]</text:p> <text:p text:style-name="P95"><text:s text:c="2"/>[[namelist.jsbach]]</text:p>
...@@ -2457,7 +2457,7 @@ ...@@ -2457,7 +2457,7 @@
<text:p text:style-name="P95"><text:s text:c="8"/><text:span text:style-name="T162">[[</text:span>[[[jsbach_ctl]]]<text:span text:style-name="T162">]]</text:span></text:p> <text:p text:style-name="P95"><text:s text:c="8"/><text:span text:style-name="T162">[[</text:span>[[[jsbach_ctl]]]<text:span text:style-name="T162">]]</text:span></text:p>
<text:p text:style-name="P95"><text:span text:style-name="T92"><text:s text:c="10"/>use_dynveg = </text:span><text:span text:style-name="T97">true</text:span></text:p> <text:p text:style-name="P95"><text:span text:style-name="T92"><text:s text:c="10"/>use_dynveg = </text:span><text:span text:style-name="T97">true</text:span></text:p>
<text:p text:style-name="P46"><text:span text:style-name="T98">This</text:span><text:span text:style-name="T92"> will result in a &apos;joe1234.run_first&apos; file that is identical to &apos;joe1234.run&apos; except for the &apos;use_dynveg&apos; setting.</text:span></text:p> <text:p text:style-name="P46"><text:span text:style-name="T98">This</text:span><text:span text:style-name="T92"> will result in a &apos;joe1234.run_first&apos; file that is identical to &apos;joe1234.run&apos; except for the &apos;use_dynveg&apos; setting.</text:span></text:p>
<text:h text:style-name="P234" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2572_1114405012"/>Native script variables<text:bookmark-end text:name="__RefHeading__2572_1114405012"/></text:h> <text:h text:style-name="P236" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2572_1114405012"/>Native script variables<text:bookmark-end text:name="__RefHeading__2572_1114405012"/></text:h>
<text:p text:style-name="P48"><text:span text:style-name="T92">While the definition of .config variables may use</text:span><text:span text:style-name="T99"> variable references like</text:span><text:span text:style-name="T92"> $NAME or ${NAME} to include the </text:span><text:span text:style-name="T99">verbatim </text:span><text:span text:style-name="T92">value of other .config variables, this may not always be what you want. If you want to create a job </text:span><text:span text:style-name="T99">script</text:span><text:span text:style-name="T92"> that is supposed to be &apos;user-serviceable&apos; for certain applications, the users will not appreciate having to change the same value several times in the same script. </text:span><text:span text:style-name="T99">Instead they will want to have a single, native script variable that is used throughout the job script, and that may be re-defined on a single line.</text:span></text:p> <text:p text:style-name="P48"><text:span text:style-name="T92">While the definition of .config variables may use</text:span><text:span text:style-name="T99"> variable references like</text:span><text:span text:style-name="T92"> $NAME or ${NAME} to include the </text:span><text:span text:style-name="T99">verbatim </text:span><text:span text:style-name="T92">value of other .config variables, this may not always be what you want. If you want to create a job </text:span><text:span text:style-name="T99">script</text:span><text:span text:style-name="T92"> that is supposed to be &apos;user-serviceable&apos; for certain applications, the users will not appreciate having to change the same value several times in the same script. </text:span><text:span text:style-name="T99">Instead they will want to have a single, native script variable that is used throughout the job script, and that may be re-defined on a single line.</text:span></text:p>
<text:p text:style-name="P52">To allow this, <text:span text:style-name="T9">mkexp</text:span> locates all expressions like $${NAME} in the configuration values, and re-formats them to the syntax of the current job script:</text:p> <text:p text:style-name="P52">To allow this, <text:span text:style-name="T9">mkexp</text:span> locates all expressions like $${NAME} in the configuration values, and re-formats them to the syntax of the current job script:</text:p>
<text:p text:style-name="P120"># joe1234.config</text:p> <text:p text:style-name="P120"># joe1234.config</text:p>
...@@ -2486,7 +2486,7 @@ ...@@ -2486,7 +2486,7 @@
<text:p text:style-name="P138">#! /usr/bin/env python </text:p> <text:p text:style-name="P138">#! /usr/bin/env python </text:p>
<text:p text:style-name="P138">NAME = &apos;<text:span text:style-name="T169">Joe User</text:span>&apos; </text:p> <text:p text:style-name="P138">NAME = &apos;<text:span text:style-name="T169">Joe User</text:span>&apos; </text:p>
<text:p text:style-name="P139">print<text:span text:style-name="T206">(</text:span>&apos;<text:span text:style-name="T92">This experiment was generated by </text:span><text:span text:style-name="T101">&apos; + str(</text:span><text:span text:style-name="T92">NAME) </text:span><text:span text:style-name="T101">+ &apos;</text:span>&apos;<text:span text:style-name="T206">)</text:span></text:p> <text:p text:style-name="P139">print<text:span text:style-name="T206">(</text:span>&apos;<text:span text:style-name="T92">This experiment was generated by </text:span><text:span text:style-name="T101">&apos; + str(</text:span><text:span text:style-name="T92">NAME) </text:span><text:span text:style-name="T101">+ &apos;</text:span>&apos;<text:span text:style-name="T206">)</text:span></text:p>
<text:h text:style-name="P241" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2574_1114405012"/>Initializing native script variables<text:bookmark-end text:name="__RefHeading__2574_1114405012"/></text:h> <text:h text:style-name="P243" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2574_1114405012"/>Initializing native script variables<text:bookmark-end text:name="__RefHeading__2574_1114405012"/></text:h>
<text:p text:style-name="P61">In the previous section, the native variables were initialized by an addition<text:span text:style-name="T173">al script line. While this is sufficient for a small number of variables, it may be difficult to maintain these initialization lines for a more complex setup with changing requirements.</text:span></text:p> <text:p text:style-name="P61">In the previous section, the native variables were initialized by an addition<text:span text:style-name="T173">al script line. While this is sufficient for a small number of variables, it may be difficult to maintain these initialization lines for a more complex setup with changing requirements.</text:span></text:p>
<text:p text:style-name="P61"><text:span text:style-name="T174">To allow a self-maintaining variable list based on the current configuration, </text:span><text:span text:style-name="T20">mkexp</text:span><text:span text:style-name="T174"> maintains the special variable VARIABLES_. When generating output for</text:span></text:p> <text:p text:style-name="P61"><text:span text:style-name="T174">To allow a self-maintaining variable list based on the current configuration, </text:span><text:span text:style-name="T20">mkexp</text:span><text:span text:style-name="T174"> maintains the special variable VARIABLES_. When generating output for</text:span></text:p>
<text:p text:style-name="P127">NAME = Joe User</text:p> <text:p text:style-name="P127">NAME = Joe User</text:p>
...@@ -2511,12 +2511,12 @@ ...@@ -2511,12 +2511,12 @@
<text:p text:style-name="P85">may be used to regenerate scripts with a new final date. Note that these settings are also recorded, i.e. running just &apos;./update&apos; the next time will again set FINAL_DATE.</text:p> <text:p text:style-name="P85">may be used to regenerate scripts with a new final date. Note that these settings are also recorded, i.e. running just &apos;./update&apos; the next time will again set FINAL_DATE.</text:p>
<text:p text:style-name="P60"><text:span text:style-name="T43">Of course, there is also the possibility to </text:span><text:span text:style-name="T53">change</text:span><text:span text:style-name="T43"> the </text:span><text:span text:style-name="T19">generated</text:span><text:span text:style-name="T52"> </text:span><text:span text:style-name="T43">job scripts directly, and then go on. This is fine as long as the required setting is using a native variable or is otherwise easily editable. On the other hand, </text:span><text:span text:style-name="T54">facing</text:span><text:span text:style-name="T43"> the next </text:span><text:span text:style-name="T54">change,</text:span><text:span text:style-name="T43"> this might not be the case, so eventually you </text:span><text:span text:style-name="T52">may</text:span><text:span text:style-name="T43"> need to re-generate the whole thing. What now about those manual changes to the job scripts?</text:span></text:p> <text:p text:style-name="P60"><text:span text:style-name="T43">Of course, there is also the possibility to </text:span><text:span text:style-name="T53">change</text:span><text:span text:style-name="T43"> the </text:span><text:span text:style-name="T19">generated</text:span><text:span text:style-name="T52"> </text:span><text:span text:style-name="T43">job scripts directly, and then go on. This is fine as long as the required setting is using a native variable or is otherwise easily editable. On the other hand, </text:span><text:span text:style-name="T54">facing</text:span><text:span text:style-name="T43"> the next </text:span><text:span text:style-name="T54">change,</text:span><text:span text:style-name="T43"> this might not be the case, so eventually you </text:span><text:span text:style-name="T52">may</text:span><text:span text:style-name="T43"> need to re-generate the whole thing. What now about those manual changes to the job scripts?</text:span></text:p>
<text:p text:style-name="P60"><text:span text:style-name="T43">Whenever </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T43"> sees existing job scripts while trying to generate the new description, it will automatically create backup files. They are placed in a subdirectory of SCRIPT_DIR, named &apos;backup&apos;. </text:span><text:span text:style-name="T52">Also, the scripts for each regeneration are bundled in their own subdirectory, named after the current date-time stamp. </text:span><text:span text:style-name="T53">This way you may easily compare old and new scripts to evaluate and possibly transfer any manual changes </text:span><text:span text:style-name="T88">after a necessary regeneration</text:span><text:span text:style-name="T53">.</text:span></text:p> <text:p text:style-name="P60"><text:span text:style-name="T43">Whenever </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T43"> sees existing job scripts while trying to generate the new description, it will automatically create backup files. They are placed in a subdirectory of SCRIPT_DIR, named &apos;backup&apos;. </text:span><text:span text:style-name="T52">Also, the scripts for each regeneration are bundled in their own subdirectory, named after the current date-time stamp. </text:span><text:span text:style-name="T53">This way you may easily compare old and new scripts to evaluate and possibly transfer any manual changes </text:span><text:span text:style-name="T88">after a necessary regeneration</text:span><text:span text:style-name="T53">.</text:span></text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2564_1114405012"/><text:soft-page-break/>Standard environments<text:bookmark-end text:name="__RefHeading__2564_1114405012"/></text:h> <text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2564_1114405012"/>Standard environments<text:bookmark-end text:name="__RefHeading__2564_1114405012"/></text:h>
<text:p text:style-name="P12">The above examples neglect an important feature <text:span text:style-name="T119">of job descriptions, namely the system or machine dependent set up. Different computing centers use different job control software and naming conventions, might provide different versions of the same software at differing locations. This needs to be handled in a way that is independent of the other configuration as far as possible.</text:span></text:p> <text:p text:style-name="P12">The above examples neglect an important feature <text:span text:style-name="T119">of job descriptions, namely the system or machine dependent set up. Different computing centers use different job control software and naming conventions, might provide different versions of the same software at differing locations. This needs to be handled in a way that is independent </text:span><text:soft-page-break/><text:span text:style-name="T119">of the other configuration as far as possible.</text:span></text:p>
<text:p text:style-name="P13">For this, a standard environment, like a standard experiment, consists of a .config file and a corresponding template. The <text:span text:style-name="T9">environmentname</text:span>.config file contains settings like directory paths or a description of machine capacities for job control</text:p> <text:p text:style-name="P13">For this, a standard environment, like a standard experiment, consists of a .config file and a corresponding template. The <text:span text:style-name="T9">environmentname</text:span>.config file contains settings like directory paths or a description of machine capacities for job control</text:p>
<text:p text:style-name="P13">The actual job control headers needed to run a certain job step are saved as <text:span text:style-name="T9">environmentname</text:span>.tmpl. This template will be filled using configuration information from both experiment, options, and environment. <text:span text:style-name="T133">The resulting job header</text:span> is usually included at the beginning of the experiment&apos;s job script templates.</text:p> <text:p text:style-name="P13">The actual job control headers needed to run a certain job step are saved as <text:span text:style-name="T9">environmentname</text:span>.tmpl. This template will be filled using configuration information from both experiment, options, and environment. <text:span text:style-name="T133">The resulting job header</text:span> is usually included at the beginning of the experiment&apos;s job script templates.</text:p>
<text:p text:style-name="P9">An experiment configuration <text:span text:style-name="T175">may</text:span> <text:span text:style-name="T175">set</text:span> the special variable E<text:span text:style-name="T175">NVIRONMENT</text:span> to the name of <text:span text:style-name="T175">the host </text:span>e<text:span text:style-name="T175">nvironment</text:span> to use. <text:span text:style-name="T175">If it is not set, or empty, the &apos;DEFAULT&apos; environment settings will be used.</text:span></text:p> <text:p text:style-name="P9">An experiment configuration <text:span text:style-name="T175">may</text:span> <text:span text:style-name="T175">set</text:span> the special variable E<text:span text:style-name="T175">NVIRONMENT</text:span> to the name of <text:span text:style-name="T175">the host </text:span>e<text:span text:style-name="T175">nvironment</text:span> to use. <text:span text:style-name="T175">If it is not set, or empty, the &apos;DEFAULT&apos; environment settings will be used.</text:span></text:p>
<text:h text:style-name="P251" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1883_1672291846"/>Defining namelists and other configuration files<text:bookmark-end text:name="__RefHeading__1883_1672291846"/></text:h> <text:h text:style-name="P253" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1883_1672291846"/>Defining namelists and other configuration files<text:bookmark-end text:name="__RefHeading__1883_1672291846"/></text:h>
<text:p text:style-name="P68"><text:span text:style-name="T65">Most models need at least one Fortran namelist file or another form of configuration file to run. </text:span><text:span text:style-name="T66">The special section [namelists] </text:span><text:span text:style-name="T65">is designed to </text:span><text:span text:style-name="T66">contain all information that goes into </text:span><text:span text:style-name="T65">these</text:span><text:span text:style-name="T66"> files. Each </text:span><text:span text:style-name="T63">immediate </text:span><text:span text:style-name="T66">subsection defines settings for a single file that will </text:span><text:span text:style-name="T65">by default be </text:span><text:span text:style-name="T66">formatted as a Fortran namelist. </text:span><text:span text:style-name="T65">For </text:span><text:span text:style-name="T66">example,</text:span></text:p> <text:p text:style-name="P68"><text:span text:style-name="T65">Most models need at least one Fortran namelist file or another form of configuration file to run. </text:span><text:span text:style-name="T66">The special section [namelists] </text:span><text:span text:style-name="T65">is designed to </text:span><text:span text:style-name="T66">contain all information that goes into </text:span><text:span text:style-name="T65">these</text:span><text:span text:style-name="T66"> files. Each </text:span><text:span text:style-name="T63">immediate </text:span><text:span text:style-name="T66">subsection defines settings for a single file that will </text:span><text:span text:style-name="T65">by default be </text:span><text:span text:style-name="T66">formatted as a Fortran namelist. </text:span><text:span text:style-name="T65">For </text:span><text:span text:style-name="T66">example,</text:span></text:p>
<text:p text:style-name="P141">[namelists]</text:p> <text:p text:style-name="P141">[namelists]</text:p>
<text:p text:style-name="P151"/> <text:p text:style-name="P151"/>
...@@ -2528,9 +2528,9 @@ ...@@ -2528,9 +2528,9 @@
<text:p text:style-name="P143"><text:s text:c="6"/>out_expname = joe1234</text:p> <text:p text:style-name="P143"><text:s text:c="6"/>out_expname = joe1234</text:p>
<text:p text:style-name="P143"><text:s text:c="6"/><text:span text:style-name="T188">dt_stop = 2009, 1, 1, 0, 0, 0</text:span></text:p> <text:p text:style-name="P143"><text:s text:c="6"/><text:span text:style-name="T188">dt_stop = 2009, 1, 1, 0, 0, 0</text:span></text:p>
<text:p text:style-name="P65"><text:span text:style-name="T43">defines </text:span><text:span text:style-name="T64">a single </text:span><text:span text:style-name="T43">namelist file, </text:span><text:span text:style-name="T67">&apos;namelist.echam&apos;</text:span><text:span text:style-name="T43">, </text:span><text:span text:style-name="T65">containing a single namelist group with four variables of different types. Note </text:span><text:span text:style-name="T84">that you do not </text:span><text:span text:style-name="T65">need to use quotes for strings nor periods for logical values.</text:span></text:p> <text:p text:style-name="P65"><text:span text:style-name="T43">defines </text:span><text:span text:style-name="T64">a single </text:span><text:span text:style-name="T43">namelist file, </text:span><text:span text:style-name="T67">&apos;namelist.echam&apos;</text:span><text:span text:style-name="T43">, </text:span><text:span text:style-name="T65">containing a single namelist group with four variables of different types. Note </text:span><text:span text:style-name="T84">that you do not </text:span><text:span text:style-name="T65">need to use quotes for strings nor periods for logical values.</text:span></text:p>
<text:h text:style-name="P237" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2578_1114405012"/>Formatting the namelist information<text:bookmark-end text:name="__RefHeading__2578_1114405012"/></text:h> <text:h text:style-name="P239" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2578_1114405012"/>Formatting the namelist information<text:bookmark-end text:name="__RefHeading__2578_1114405012"/></text:h>
<text:p text:style-name="P70"><text:span text:style-name="T63">The </text:span><text:span text:style-name="T64">names of the </text:span><text:span text:style-name="T63">subsections of each namelist file entry, i.e. the second level subsections under the immediate subsections of [namelists], are taken as namelist group </text:span><text:span text:style-name="T64">name</text:span><text:span text:style-name="T63">s, and their variables are formatted as fields of this namelist </text:span><text:span text:style-name="T64">group</text:span><text:span text:style-name="T63">. </text:span><text:span text:style-name="T64">In the </text:span><text:soft-page-break/><text:span text:style-name="T64">example above, there is a single namelist group &apos;runctl&apos;, which will be converted to the Fortran namelist convention. </text:span><text:span text:style-name="T187">The values of the group&apos;s fields are checked to determine whether they are numerical, logical, or string values. Logical and string values will then be formatted using periods or quotes, respectively.</text:span></text:p> <text:p text:style-name="P70"><text:span text:style-name="T63">The </text:span><text:span text:style-name="T64">names of the </text:span><text:span text:style-name="T63">subsections of each namelist file entry, i.e. the second level subsections under the immediate subsections of [namelists], are taken as namelist group </text:span><text:span text:style-name="T64">name</text:span><text:span text:style-name="T63">s, and their variables are formatted as fields of this namelist </text:span><text:span text:style-name="T64">group</text:span><text:span text:style-name="T63">. </text:span><text:span text:style-name="T64">In the example above, there is a single namelist group &apos;runctl&apos;, which will be converted to the Fortran namelist convention. </text:span><text:span text:style-name="T187">The values of the group&apos;s fields are checked to determine whether they are numerical, logical, or string values. Logical and string values will then be formatted using periods or quotes, respectively.</text:span></text:p>
<text:p text:style-name="P70"><text:span text:style-name="T207">In the example above, the first four fields are single values of logical, integer, floating point, and string type.</text:span><text:span text:style-name="T67"> The fifth is a list of integer values, that will be passed as such to the namelist file:</text:span></text:p> <text:p text:style-name="P70"><text:span text:style-name="T207">In the example above, the first four fields are single values of logical, integer, floating </text:span><text:soft-page-break/><text:span text:style-name="T207">point, and string type.</text:span><text:span text:style-name="T67"> The fifth is a list of integer values, that will be passed as such to the namelist file:</text:span></text:p>
<text:p text:style-name="P110">&amp;runctl</text:p> <text:p text:style-name="P110">&amp;runctl</text:p>
<text:p text:style-name="P145"><text:s text:c="4"/>lamip = <text:span text:style-name="T120">.true.</text:span></text:p> <text:p text:style-name="P145"><text:s text:c="4"/>lamip = <text:span text:style-name="T120">.true.</text:span></text:p>
<text:p text:style-name="P145"><text:s text:c="4"/><text:span text:style-name="T187">nproma = </text:span><text:span text:style-name="T125">48</text:span></text:p> <text:p text:style-name="P145"><text:s text:c="4"/><text:span text:style-name="T187">nproma = </text:span><text:span text:style-name="T125">48</text:span></text:p>
...@@ -2538,11 +2538,11 @@ ...@@ -2538,11 +2538,11 @@
<text:p text:style-name="P144"><text:s text:c="4"/>out_expname = <text:span text:style-name="T126">&apos;</text:span><text:span text:style-name="T120">joe1234</text:span><text:span text:style-name="T126">&apos;</text:span></text:p> <text:p text:style-name="P144"><text:s text:c="4"/>out_expname = <text:span text:style-name="T126">&apos;</text:span><text:span text:style-name="T120">joe1234</text:span><text:span text:style-name="T126">&apos;</text:span></text:p>
<text:p text:style-name="P144"><text:span text:style-name="T67"><text:s text:c="4"/>dt_stop = </text:span><text:span text:style-name="T115">2009, 1, 1, 0, 0, 0</text:span></text:p> <text:p text:style-name="P144"><text:span text:style-name="T67"><text:s text:c="4"/>dt_stop = </text:span><text:span text:style-name="T115">2009, 1, 1, 0, 0, 0</text:span></text:p>
<text:p text:style-name="P129">/</text:p> <text:p text:style-name="P129">/</text:p>
<text:h text:style-name="P242" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2580_1114405012"/><text:span text:style-name="T65">S</text:span><text:span text:style-name="T43">uppressing namelist groups or variables</text:span><text:bookmark-end text:name="__RefHeading__2580_1114405012"/></text:h> <text:h text:style-name="P244" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2580_1114405012"/><text:span text:style-name="T65">S</text:span><text:span text:style-name="T43">uppressing namelist groups or variables</text:span><text:bookmark-end text:name="__RefHeading__2580_1114405012"/></text:h>
<text:p text:style-name="P56">Both the namelist file sections and the namelist group section honor the special variable &apos;.remove&apos; which may be set to a list of names. Any namelist groups listed in the file&apos;s &apos;.remove&apos; variable, and any variables listed in the group&apos;s &apos;.remove&apos; variable will be deleted from the namelist definition.</text:p> <text:p text:style-name="P56">Both the namelist file sections and the namelist group section honor the special variable &apos;.remove&apos; which may be set to a list of names. Any namelist groups listed in the file&apos;s &apos;.remove&apos; variable, and any variables listed in the group&apos;s &apos;.remove&apos; variable will be deleted from the namelist definition.</text:p>
<text:p text:style-name="P56">The names may contain the usual file wildcards, &apos;*&apos; and &apos;?&apos; to remove a whole range of groups or variables.</text:p> <text:p text:style-name="P56">The names may contain the usual file wildcards, &apos;*&apos; and &apos;?&apos; to remove a whole range of groups or variables.</text:p>
<text:p text:style-name="P79"><text:span text:style-name="T43">While &apos;.remove&apos; is useful to </text:span><text:span text:style-name="T74">suppress</text:span><text:span text:style-name="T43"> default settings that must not be present for the experiment setup, currently there is no way to resurrect a removed setting in a later setup level. </text:span><text:span text:style-name="T75">Therefore, its use in model setups is strongly discouraged.</text:span></text:p> <text:p text:style-name="P79"><text:span text:style-name="T43">While &apos;.remove&apos; is useful to </text:span><text:span text:style-name="T74">suppress</text:span><text:span text:style-name="T43"> default settings that must not be present for the experiment setup, currently there is no way to resurrect a removed setting in a later setup level. </text:span><text:span text:style-name="T75">Therefore, its use in model setups is strongly discouraged.</text:span></text:p>
<text:h text:style-name="P238" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2714_1114405012"/>Using the namelist text<text:bookmark-end text:name="__RefHeading__2714_1114405012"/></text:h> <text:h text:style-name="P240" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2714_1114405012"/>Using the namelist text<text:bookmark-end text:name="__RefHeading__2714_1114405012"/></text:h>
<text:p text:style-name="P66"><text:span text:style-name="T65">T</text:span><text:span text:style-name="T67">he </text:span><text:span text:style-name="T56">formatted namelist text </text:span><text:span text:style-name="T43">is </text:span><text:span text:style-name="T67">stor</text:span><text:span text:style-name="T43">ed </text:span><text:span text:style-name="T67">in</text:span><text:span text:style-name="T43"> a global variable </text:span><text:span text:style-name="T67">that may be used by a template placeholder</text:span><text:span text:style-name="T43">. </text:span><text:span text:style-name="T65">This way, </text:span><text:span text:style-name="T43">all job information </text:span><text:span text:style-name="T67">available </text:span><text:span text:style-name="T65">is written to</text:span><text:span text:style-name="T43"> a single script or description file, </text:span><text:span text:style-name="T65">and </text:span><text:span text:style-name="T43">native script variables </text:span><text:span text:style-name="T65">may be used</text:span><text:span text:style-name="T43"> in the namelist definitions.</text:span></text:p> <text:p text:style-name="P66"><text:span text:style-name="T65">T</text:span><text:span text:style-name="T67">he </text:span><text:span text:style-name="T56">formatted namelist text </text:span><text:span text:style-name="T43">is </text:span><text:span text:style-name="T67">stor</text:span><text:span text:style-name="T43">ed </text:span><text:span text:style-name="T67">in</text:span><text:span text:style-name="T43"> a global variable </text:span><text:span text:style-name="T67">that may be used by a template placeholder</text:span><text:span text:style-name="T43">. </text:span><text:span text:style-name="T65">This way, </text:span><text:span text:style-name="T43">all job information </text:span><text:span text:style-name="T67">available </text:span><text:span text:style-name="T65">is written to</text:span><text:span text:style-name="T43"> a single script or description file, </text:span><text:span text:style-name="T65">and </text:span><text:span text:style-name="T43">native script variables </text:span><text:span text:style-name="T65">may be used</text:span><text:span text:style-name="T43"> in the namelist definitions.</text:span></text:p>
<text:p text:style-name="P68"><text:span text:style-name="T56">The name of </text:span><text:span text:style-name="T67">this </text:span><text:span text:style-name="T56">variable</text:span><text:span text:style-name="T57"> </text:span><text:span text:style-name="T67">is</text:span><text:span text:style-name="T56"> generated from </text:span><text:span text:style-name="T67">its</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T57">respective</text:span><text:span text:style-name="T56"> file name, </text:span><text:span text:style-name="T67">like</text:span><text:span text:style-name="T56"> &apos;namelist.echam&apos;, by </text:span><text:span text:style-name="T66">converting all letters to upper case </text:span><text:span text:style-name="T56">(</text:span><text:span text:style-name="T66">namelist.echam →</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T66">NAMELIST.ECHAM</text:span><text:span text:style-name="T56">) </text:span><text:span text:style-name="T57">and </text:span><text:span text:style-name="T56">replacing non-word characters by an underscore (NAMELIST.ECHAM → NAMELIST_ECHAM).</text:span></text:p> <text:p text:style-name="P68"><text:span text:style-name="T56">The name of </text:span><text:span text:style-name="T67">this </text:span><text:span text:style-name="T56">variable</text:span><text:span text:style-name="T57"> </text:span><text:span text:style-name="T67">is</text:span><text:span text:style-name="T56"> generated from </text:span><text:span text:style-name="T67">its</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T57">respective</text:span><text:span text:style-name="T56"> file name, </text:span><text:span text:style-name="T67">like</text:span><text:span text:style-name="T56"> &apos;namelist.echam&apos;, by </text:span><text:span text:style-name="T66">converting all letters to upper case </text:span><text:span text:style-name="T56">(</text:span><text:span text:style-name="T66">namelist.echam →</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T66">NAMELIST.ECHAM</text:span><text:span text:style-name="T56">) </text:span><text:span text:style-name="T57">and </text:span><text:span text:style-name="T56">replacing non-word characters by an underscore (NAMELIST.ECHAM → NAMELIST_ECHAM).</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text"># joe1234.config</text:p> <text:p text:style-name="Preformatted_20_Text"># joe1234.config</text:p>
...@@ -2565,7 +2565,7 @@ ...@@ -2565,7 +2565,7 @@
<text:p text:style-name="P100">EOF</text:p> <text:p text:style-name="P100">EOF</text:p>
<text:p text:style-name="P69"><text:span text:style-name="T67">Note how this setup uses the native script variable &apos;EXP_ID&apos; to set the </text:span><text:span text:style-name="T63">namelist contents.</text:span></text:p> <text:p text:style-name="P69"><text:span text:style-name="T67">Note how this setup uses the native script variable &apos;EXP_ID&apos; to set the </text:span><text:span text:style-name="T63">namelist contents.</text:span></text:p>
<text:p text:style-name="P69"><text:span text:style-name="T68">As in the example above, the script template is responsible for writing the namelist text to an actual file. </text:span><text:span text:style-name="T67">While in general the namelist file takes the same name as the .config subsection defining it, </text:span><text:span text:style-name="T25">mkexp</text:span><text:span text:style-name="T67"> </text:span><text:span text:style-name="T68">ha</text:span><text:span text:style-name="T67">s currently no way to enforce this. The template needs to be set up accordingly.</text:span></text:p> <text:p text:style-name="P69"><text:span text:style-name="T68">As in the example above, the script template is responsible for writing the namelist text to an actual file. </text:span><text:span text:style-name="T67">While in general the namelist file takes the same name as the .config subsection defining it, </text:span><text:span text:style-name="T25">mkexp</text:span><text:span text:style-name="T67"> </text:span><text:span text:style-name="T68">ha</text:span><text:span text:style-name="T67">s currently no way to enforce this. The template needs to be set up accordingly.</text:span></text:p>
<text:h text:style-name="P243" text:outline-level="3">Using native script variables in namelists</text:h> <text:h text:style-name="P245" text:outline-level="3">Using native script variables in namelists</text:h>
<text:p text:style-name="P86">When using native script variables in a namelist, it may be necessary to suppress the conversion of values to namelist conventions. Consider</text:p> <text:p text:style-name="P86">When using native script variables in a namelist, it may be necessary to suppress the conversion of values to namelist conventions. Consider</text:p>
<text:p text:style-name="P154">[namelists]</text:p> <text:p text:style-name="P154">[namelists]</text:p>
<text:p text:style-name="P154"><text:s text:c="2"/><text:span text:style-name="T212">[[namelist.echam]]</text:span></text:p> <text:p text:style-name="P154"><text:s text:c="2"/><text:span text:style-name="T212">[[namelist.echam]]</text:span></text:p>
...@@ -2578,11 +2578,11 @@ ...@@ -2578,11 +2578,11 @@
<text:p text:style-name="P86">When the text for NAMELIST_ECHAM is generated, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T43"> converts the value of &apos;dt_stop&apos; to a string surrounded by single quotes (see &apos;EXP_ID&apos; in the previous example), as &apos;$$final_date&apos; cannot be </text:span><text:span text:style-name="T90">recognized</text:span><text:span text:style-name="T43"> as a numer</text:span><text:span text:style-name="T90">ic</text:span><text:span text:style-name="T43"> or logical value. In the namelist context however it is </text:span><text:span text:style-name="T90">needed</text:span><text:span text:style-name="T43"> as a</text:span><text:span text:style-name="T90">n unquoted</text:span><text:span text:style-name="T43"> list of integers. </text:span><text:span text:style-name="T89">To fix this, simply use the special syntax &apos;raw(…)&apos; </text:span><text:span text:style-name="T90">around the value:</text:span></text:p> <text:p text:style-name="P86">When the text for NAMELIST_ECHAM is generated, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T43"> converts the value of &apos;dt_stop&apos; to a string surrounded by single quotes (see &apos;EXP_ID&apos; in the previous example), as &apos;$$final_date&apos; cannot be </text:span><text:span text:style-name="T90">recognized</text:span><text:span text:style-name="T43"> as a numer</text:span><text:span text:style-name="T90">ic</text:span><text:span text:style-name="T43"> or logical value. In the namelist context however it is </text:span><text:span text:style-name="T90">needed</text:span><text:span text:style-name="T43"> as a</text:span><text:span text:style-name="T90">n unquoted</text:span><text:span text:style-name="T43"> list of integers. </text:span><text:span text:style-name="T89">To fix this, simply use the special syntax &apos;raw(…)&apos; </text:span><text:span text:style-name="T90">around the value:</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T90"><text:s text:c="6"/></text:span><text:span text:style-name="T88">dt_stop = </text:span><text:span text:style-name="T90">raw(</text:span><text:span text:style-name="T88">$$final_date</text:span><text:span text:style-name="T90">)</text:span></text:p> <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T90"><text:s text:c="6"/></text:span><text:span text:style-name="T88">dt_stop = </text:span><text:span text:style-name="T90">raw(</text:span><text:span text:style-name="T88">$$final_date</text:span><text:span text:style-name="T90">)</text:span></text:p>
<text:p text:style-name="P57">which disables the conversion to a valid namelist value, leaving the correct formatting of the native variable to the script.</text:p> <text:p text:style-name="P57">which disables the conversion to a valid namelist value, leaving the correct formatting of the native variable to the script.</text:p>
<text:h text:style-name="P240" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2584_1114405012"/><text:soft-page-break/>Non-namelist configuration files<text:bookmark-end text:name="__RefHeading__2584_1114405012"/></text:h> <text:h text:style-name="P242" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2584_1114405012"/><text:soft-page-break/>Non-namelist configuration files<text:bookmark-end text:name="__RefHeading__2584_1114405012"/></text:h>
<text:p text:style-name="P80"><text:span text:style-name="T78">A [namelists] subsection may not only define a Fortran namelist file but also a custom format configuration file. </text:span><text:span text:style-name="T76">F</text:span><text:span text:style-name="T43">or any </text:span><text:span text:style-name="T78">of these</text:span><text:span text:style-name="T77"> files, the special section variable &apos;.use_template&apos; m</text:span><text:span text:style-name="T91">ay</text:span><text:span text:style-name="T77"> be set to &apos;true&apos;, </text:span><text:span text:style-name="T91">if </text:span><text:span text:style-name="T78">the model setup provid</text:span><text:span text:style-name="T91">es</text:span><text:span text:style-name="T78"> a template &apos;</text:span><text:span text:style-name="T29">subsection</text:span><text:span text:style-name="T78">.tmpl&apos;, </text:span><text:span text:style-name="T91">or to an arbitrary template name, replacing </text:span><text:span text:style-name="T35">subsection,</text:span><text:span text:style-name="T91"> if a template is applicable to more than one section</text:span><text:span text:style-name="T78">. This template is expanded using the subsection&apos;s variables to create a suitably formatted text. </text:span><text:span text:style-name="T79">As for genuine namelists, the result is stored in a global variable.</text:span></text:p> <text:p text:style-name="P80"><text:span text:style-name="T78">A [namelists] subsection may not only define a Fortran namelist file but also a custom format configuration file. </text:span><text:span text:style-name="T76">F</text:span><text:span text:style-name="T43">or any </text:span><text:span text:style-name="T78">of these</text:span><text:span text:style-name="T77"> files, the special section variable &apos;.use_template&apos; m</text:span><text:span text:style-name="T91">ay</text:span><text:span text:style-name="T77"> be set to &apos;true&apos;, </text:span><text:span text:style-name="T91">if </text:span><text:span text:style-name="T78">the model setup provid</text:span><text:span text:style-name="T91">es</text:span><text:span text:style-name="T78"> a template &apos;</text:span><text:span text:style-name="T29">subsection</text:span><text:span text:style-name="T78">.tmpl&apos;, </text:span><text:span text:style-name="T91">or to an arbitrary template name, replacing </text:span><text:span text:style-name="T35">subsection,</text:span><text:span text:style-name="T91"> if a template is applicable to more than one section</text:span><text:span text:style-name="T78">. This template is expanded using the subsection&apos;s variables to create a suitably formatted text. </text:span><text:span text:style-name="T79">As for genuine namelists, the result is stored in a global variable.</text:span></text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2831_1132221942"/><text:span text:style-name="T79">D</text:span><text:span text:style-name="T43">efining input files for an experiment</text:span><text:bookmark-end text:name="__RefHeading__2831_1132221942"/></text:h> <text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2831_1132221942"/><text:span text:style-name="T79">D</text:span><text:span text:style-name="T43">efining input files for an experiment</text:span><text:bookmark-end text:name="__RefHeading__2831_1132221942"/></text:h>
<text:p text:style-name="P83"><text:span text:style-name="T43">While the namelist files determine the model properties, the model state </text:span><text:span text:style-name="T87">also </text:span><text:span text:style-name="T43">depends on input files for initial and boundary conditions or assimilation data. These files are defined in the [files] special section. </text:span><text:span text:style-name="T87">There are no restrictions on the content structure of this section, and the job script templates are responsible for converting this content into a suitable script text.</text:span></text:p> <text:p text:style-name="P83"><text:span text:style-name="T43">While the namelist files determine the model properties, the model state </text:span><text:span text:style-name="T87">also </text:span><text:span text:style-name="T43">depends on input files for initial and boundary conditions or assimilation data. These files are defined in the [files] special section. </text:span><text:span text:style-name="T87">There are no restrictions on the content structure of this section, and the job script templates are responsible for converting this content into a suitable script text.</text:span></text:p>
<text:h text:style-name="P236" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2833_1132221942"/>Overriding <text:span text:style-name="T210">input file</text:span>s <text:span text:style-name="T210">for certain</text:span> jobs<text:bookmark-end text:name="__RefHeading__2833_1132221942"/></text:h> <text:h text:style-name="P238" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2833_1132221942"/>Overriding <text:span text:style-name="T210">input file</text:span>s <text:span text:style-name="T210">for certain</text:span> jobs<text:bookmark-end text:name="__RefHeading__2833_1132221942"/></text:h>
<text:p text:style-name="P51"><text:span text:style-name="T211">As for namelists, t</text:span>here is special provision to change <text:span text:style-name="T210">the [</text:span>files<text:span text:style-name="T210">]</text:span> settings for a specific job. <text:span text:style-name="T210">Let us assume</text:span> <text:span text:style-name="T210">that a model run continues a previous run and reads that run&apos;s state from a restart file that may be defined like this:</text:span></text:p> <text:p text:style-name="P51"><text:span text:style-name="T211">As for namelists, t</text:span>here is special provision to change <text:span text:style-name="T210">the [</text:span>files<text:span text:style-name="T210">]</text:span> settings for a specific job. <text:span text:style-name="T210">Let us assume</text:span> <text:span text:style-name="T210">that a model run continues a previous run and reads that run&apos;s state from a restart file that may be defined like this:</text:span></text:p>
<text:p text:style-name="P136">[<text:span text:style-name="T210">files</text:span>]</text:p> <text:p text:style-name="P136">[<text:span text:style-name="T210">files</text:span>]</text:p>
<text:p text:style-name="P96"><text:s text:c="2"/>[[<text:span text:style-name="T210">echam</text:span>]]</text:p> <text:p text:style-name="P96"><text:s text:c="2"/>[[<text:span text:style-name="T210">echam</text:span>]]</text:p>
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from distutils.core import setup from distutils.core import setup
name = 'mkexp' name = 'mkexp'
version = '0.3.6dev' version = '0.3.6'
setup( setup(
name = name, name = name,
......
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