diff --git a/doc/mkexp.fodt b/doc/mkexp.fodt
index a88c4ab2d4864a7d063b50dadd24fae5cc17512c..0bec88fb0c06775c3aef80bc28a8ecac5371deb9 100644
--- a/doc/mkexp.fodt
+++ b/doc/mkexp.fodt
@@ -1,24 +1,24 @@
<?xml version="1.0" encoding="UTF-8"?>
<office:document xmlns:officeooo="http://openoffice.org/2009/office" xmlns:css3t="http://www.w3.org/TR/css3-text/" xmlns:grddl="http://www.w3.org/2003/g/data-view#" xmlns:xhtml="http://www.w3.org/1999/xhtml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:chart="urn:oasis:names:tc:opendocument:xmlns:chart:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xmlns:draw="urn:oasis:names:tc:opendocument:xmlns:drawing:1.0" xmlns:rpt="http://openoffice.org/2005/report" xmlns:text="urn:oasis:names:tc:opendocument:xmlns:text:1.0" xmlns:style="urn:oasis:names:tc:opendocument:xmlns:style:1.0" xmlns:meta="urn:oasis:names:tc:opendocument:xmlns:meta:1.0" xmlns:config="urn:oasis:names:tc:opendocument:xmlns:config:1.0" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:fo="urn:oasis:names:tc:opendocument:xmlns:xsl-fo-compatible:1.0" xmlns:of="urn:oasis:names:tc:opendocument:xmlns:of:1.2" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:ooo="http://openoffice.org/2004/office" xmlns:dr3d="urn:oasis:names:tc:opendocument:xmlns:dr3d:1.0" xmlns:formx="urn:openoffice:names:experimental:ooxml-odf-interop:xmlns:form:1.0" xmlns:calcext="urn:org:documentfoundation:names:experimental:calc:xmlns:calcext:1.0" xmlns:drawooo="http://openoffice.org/2010/draw" xmlns:field="urn:openoffice:names:experimental:ooo-ms-interop:xmlns:field:1.0" xmlns:office="urn:oasis:names:tc:opendocument:xmlns:office:1.0" xmlns:table="urn:oasis:names:tc:opendocument:xmlns:table:1.0" xmlns:number="urn:oasis:names:tc:opendocument:xmlns:datastyle:1.0" xmlns:ooow="http://openoffice.org/2004/writer" xmlns:oooc="http://openoffice.org/2004/calc" xmlns:tableooo="http://openoffice.org/2009/table" xmlns:loext="urn:org:documentfoundation:names:experimental:office:xmlns:loext:1.0" xmlns:math="http://www.w3.org/1998/Math/MathML" xmlns:form="urn:oasis:names:tc:opendocument:xmlns:form:1.0" xmlns:script="urn:oasis:names:tc:opendocument:xmlns:script:1.0" xmlns:dom="http://www.w3.org/2001/xml-events" xmlns:xforms="http://www.w3.org/2002/xforms" office:version="1.2" office:mimetype="application/vnd.oasis.opendocument.text">
- <office:meta><meta:creation-date>2015-01-05T17:44:27.618344249</meta:creation-date><dc:title>Make Experiments!</dc:title><meta:editing-duration>P12DT4H50M16S</meta:editing-duration><meta:editing-cycles>189</meta:editing-cycles><meta:generator>LibreOffice/6.4.7.2$Linux_X86_64 LibreOffice_project/40$Build-2</meta:generator><meta:initial-creator>Karl-Hermann Wieners</meta:initial-creator><dc:date>2022-03-22T18:34:45.339000446</dc:date><dc:creator>Karl-Hermann Wieners</dc:creator><meta:printed-by>Karl-Hermann Wieners</meta:printed-by><meta:print-date>2015-01-20T10:55:48.576690105</meta:print-date><dc:subject>Run-script generation for earth system models</dc:subject><meta:document-statistic meta:table-count="0" meta:image-count="0" meta:object-count="0" meta:page-count="30" meta:paragraph-count="645" meta:word-count="9069" meta:character-count="57713" meta:non-whitespace-character-count="48801"/><meta:template xlink:type="simple" xlink:actuate="onRequest" xlink:title="A4" xlink:href="../../../../../run/user/1001/gvfs/sftp:host=levante.dkrz.de/home/m221078/.config/libreoffice/4/user/template/A4.ott" meta:date="2015-01-05T17:44:27.463210655"/></office:meta>
+ <office:meta><meta:creation-date>2015-01-05T17:44:27.618344249</meta:creation-date><dc:title>Make Experiments!</dc:title><meta:editing-duration>P12DT4H53M16S</meta:editing-duration><meta:editing-cycles>190</meta:editing-cycles><meta:generator>LibreOffice/6.4.7.2$Linux_X86_64 LibreOffice_project/40$Build-2</meta:generator><meta:initial-creator>Karl-Hermann Wieners</meta:initial-creator><dc:date>2022-03-23T17:38:54.212697910</dc:date><dc:creator>Karl-Hermann Wieners</dc:creator><meta:printed-by>Karl-Hermann Wieners</meta:printed-by><meta:print-date>2015-01-20T10:55:48.576690105</meta:print-date><dc:subject>Run-script generation for earth system models</dc:subject><meta:document-statistic meta:table-count="0" meta:image-count="0" meta:object-count="0" meta:page-count="29" meta:paragraph-count="651" meta:word-count="9129" meta:character-count="58113" meta:non-whitespace-character-count="49147"/><meta:template xlink:type="simple" xlink:actuate="onRequest" xlink:title="A4" xlink:href="../../../run/user/1001/gvfs/sftp:host=levante.dkrz.de/home/m221078/.config/libreoffice/4/user/template/A4.ott" meta:date="2015-01-05T17:44:27.463210655"/></office:meta>
<office:settings>
<config:config-item-set config:name="ooo:view-settings">
- <config:config-item config:name="ViewAreaTop" config:type="long">177181</config:config-item>
+ <config:config-item config:name="ViewAreaTop" config:type="long">231114</config:config-item>
<config:config-item config:name="ViewAreaLeft" config:type="long">0</config:config-item>
<config:config-item config:name="ViewAreaWidth" config:type="long">22050</config:config-item>
- <config:config-item config:name="ViewAreaHeight" config:type="long">18237</config:config-item>
+ <config:config-item config:name="ViewAreaHeight" config:type="long">19166</config:config-item>
<config:config-item config:name="ShowRedlineChanges" config:type="boolean">false</config:config-item>
<config:config-item config:name="InBrowseMode" config:type="boolean">false</config:config-item>
<config:config-item-map-indexed config:name="Views">
<config:config-item-map-entry>
<config:config-item config:name="ViewId" config:type="string">view2</config:config-item>
- <config:config-item config:name="ViewLeft" config:type="long">2524</config:config-item>
- <config:config-item config:name="ViewTop" config:type="long">183709</config:config-item>
+ <config:config-item config:name="ViewLeft" config:type="long">6556</config:config-item>
+ <config:config-item config:name="ViewTop" config:type="long">245525</config:config-item>
<config:config-item config:name="VisibleLeft" config:type="long">0</config:config-item>
- <config:config-item config:name="VisibleTop" config:type="long">177181</config:config-item>
+ <config:config-item config:name="VisibleTop" config:type="long">231114</config:config-item>
<config:config-item config:name="VisibleRight" config:type="long">22049</config:config-item>
- <config:config-item config:name="VisibleBottom" config:type="long">195416</config:config-item>
+ <config:config-item config:name="VisibleBottom" config:type="long">250278</config:config-item>
<config:config-item config:name="ZoomType" config:type="short">3</config:config-item>
<config:config-item config:name="ViewLayoutColumns" config:type="short">0</config:config-item>
<config:config-item config:name="ViewLayoutBookMode" config:type="boolean">false</config:config-item>
@@ -81,9 +81,9 @@
<config:config-item config:name="AddParaTableSpacing" config:type="boolean">true</config:config-item>
<config:config-item config:name="StylesNoDefault" config:type="boolean">false</config:config-item>
<config:config-item config:name="ChartAutoUpdate" config:type="boolean">true</config:config-item>
- <config:config-item config:name="PrinterSetup" config:type="base64Binary">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</config:config-item>
+ <config:config-item config:name="PrinterSetup" config:type="base64Binary">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</config:config-item>
<config:config-item config:name="AddParaTableSpacingAtStart" config:type="boolean">true</config:config-item>
- <config:config-item config:name="Rsid" config:type="int">20938951</config:config-item>
+ <config:config-item config:name="Rsid" config:type="int">21016999</config:config-item>
<config:config-item config:name="EmbeddedDatabaseName" config:type="string"/>
<config:config-item config:name="FieldAutoUpdate" config:type="boolean">true</config:config-item>
<config:config-item config:name="OutlineLevelYieldsNumbering" config:type="boolean">false</config:config-item>
@@ -148,7 +148,7 @@
<office:styles>
<style:default-style style:family="graphic">
<style:graphic-properties svg:stroke-color="#3465a4" draw:fill-color="#729fcf" fo:wrap-option="no-wrap" draw:shadow-offset-x="0.3cm" draw:shadow-offset-y="0.3cm" draw:start-line-spacing-horizontal="0.283cm" draw:start-line-spacing-vertical="0.283cm" draw:end-line-spacing-horizontal="0.283cm" draw:end-line-spacing-vertical="0.283cm" style:flow-with-text="false"/>
- <style:paragraph-properties style:text-autospace="ideograph-alpha" style:line-break="strict" style:writing-mode="lr-tb" style:font-independent-line-spacing="false">
+ <style:paragraph-properties style:text-autospace="ideograph-alpha" style:line-break="strict" style:font-independent-line-spacing="false">
<style:tab-stops/>
</style:paragraph-properties>
<style:text-properties style:use-window-font-color="true" style:font-name="Liberation Serif" fo:font-size="12pt" fo:language="en" fo:country="US" style:letter-kerning="true" style:font-name-asian="Droid Sans Fallback" style:font-size-asian="10.5pt" style:language-asian="zh" style:country-asian="CN" style:font-name-complex="FreeSans" style:font-size-complex="12pt" style:language-complex="hi" style:country-complex="IN"/>
@@ -1515,97 +1515,79 @@
<style:paragraph-properties style:page-number="auto"/>
<style:text-properties officeooo:rsid="00cef9a3" officeooo:paragraph-rsid="00cef9a3"/>
</style:style>
- <style:style style:name="P358" style:family="paragraph" style:parent-style-name="Contents_20_1">
- <style:paragraph-properties>
- <style:tab-stops>
- <style:tab-stop style:position="17cm" style:type="right" style:leader-style="dotted" style:leader-text="."/>
- </style:tab-stops>
- </style:paragraph-properties>
- </style:style>
- <style:style style:name="P359" style:family="paragraph" style:parent-style-name="Contents_20_2">
- <style:paragraph-properties>
- <style:tab-stops>
- <style:tab-stop style:position="16.501cm" style:type="right" style:leader-style="dotted" style:leader-text="."/>
- </style:tab-stops>
- </style:paragraph-properties>
- </style:style>
- <style:style style:name="P360" style:family="paragraph" style:parent-style-name="Contents_20_3">
- <style:paragraph-properties>
- <style:tab-stops>
- <style:tab-stop style:position="16.002cm" style:type="right" style:leader-style="dotted" style:leader-text="."/>
- </style:tab-stops>
- </style:paragraph-properties>
- </style:style>
- <style:style style:name="P361" style:family="paragraph" style:parent-style-name="Contents_20_Heading">
- <style:paragraph-properties fo:break-before="page"/>
- </style:style>
- <style:style style:name="P362" style:family="paragraph" style:parent-style-name="Heading_20_1">
+ <style:style style:name="P358" style:family="paragraph" style:parent-style-name="Heading_20_1">
<style:text-properties officeooo:rsid="001888a2" officeooo:paragraph-rsid="009eea28"/>
</style:style>
- <style:style style:name="P363" style:family="paragraph" style:parent-style-name="Heading_20_1">
+ <style:style style:name="P359" style:family="paragraph" style:parent-style-name="Heading_20_1">
<style:paragraph-properties fo:break-before="page"/>
<style:text-properties officeooo:rsid="000a3505" officeooo:paragraph-rsid="000a3505"/>
</style:style>
- <style:style style:name="P364" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P360" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="00b17591"/>
</style:style>
- <style:style style:name="P365" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P361" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:rsid="00288fc1" officeooo:paragraph-rsid="00423119"/>
</style:style>
- <style:style style:name="P366" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P362" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="012dcfed"/>
</style:style>
- <style:style style:name="P367" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P363" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="00f3a79a"/>
</style:style>
- <style:style style:name="P368" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P364" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="0063d022"/>
</style:style>
- <style:style style:name="P369" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P365" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties fo:font-style="normal" officeooo:paragraph-rsid="0086f697" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P370" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P366" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties officeooo:rsid="00750ebf" officeooo:paragraph-rsid="0074d148"/>
</style:style>
- <style:style style:name="P371" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P367" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties officeooo:rsid="00750ebf" officeooo:paragraph-rsid="00750ebf"/>
</style:style>
- <style:style style:name="P372" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P368" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties officeooo:rsid="00f3a79a" officeooo:paragraph-rsid="00f3a79a"/>
</style:style>
- <style:style style:name="P373" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P369" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties officeooo:rsid="00d7bd9c" officeooo:paragraph-rsid="00d7bd9c"/>
</style:style>
- <style:style style:name="P374" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P370" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties fo:font-style="normal" style:text-underline-style="none" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P375" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P371" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties fo:font-style="normal" style:text-underline-style="none" officeooo:rsid="009beecc" officeooo:paragraph-rsid="009beecc" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P376" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P372" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties fo:font-style="normal" style:text-underline-style="none" officeooo:paragraph-rsid="00c2926f" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P377" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P373" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties fo:font-style="normal" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P378" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P374" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties fo:font-style="normal" officeooo:paragraph-rsid="00931d47" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P379" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P375" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties fo:font-style="normal" officeooo:rsid="009715be" officeooo:paragraph-rsid="00c6886f" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P380" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P376" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties officeooo:rsid="0063d022" officeooo:paragraph-rsid="0063d022"/>
</style:style>
- <style:style style:name="P381" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P377" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties officeooo:paragraph-rsid="00fb6b92"/>
</style:style>
- <style:style style:name="P382" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P378" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties officeooo:rsid="011bfd3c" officeooo:paragraph-rsid="011bfd3c"/>
</style:style>
- <style:style style:name="P383" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P379" style:family="paragraph" style:parent-style-name="Heading_20_3">
<style:text-properties officeooo:rsid="00c6886f" officeooo:paragraph-rsid="00c6886f"/>
</style:style>
+ <style:style style:name="P380" style:family="paragraph" style:parent-style-name="List_20_Contents">
+ <style:text-properties officeooo:paragraph-rsid="0140b1a7"/>
+ </style:style>
+ <style:style style:name="P381" style:family="paragraph" style:parent-style-name="Preformatted_20_List_20_Heading">
+ <style:text-properties officeooo:paragraph-rsid="0140b1a7"/>
+ </style:style>
<style:style style:name="T1" style:family="text">
<style:text-properties officeooo:rsid="000be205"/>
</style:style>
@@ -2808,7 +2790,7 @@
<office:master-styles>
<style:master-page style:name="Standard" style:page-layout-name="pm1">
<style:footer>
- <text:p text:style-name="Footer"><text:page-number text:select-page="current">7</text:page-number><text:tab/><text:tab/><text:modification-date style:data-style-name="N84">2022-03-22</text:modification-date>, <text:modification-time style:data-style-name="N41">18:34:45</text:modification-time></text:p>
+ <text:p text:style-name="Footer"><text:page-number text:select-page="current">9</text:page-number><text:tab/><text:tab/><text:modification-date style:data-style-name="N84">2022-03-23</text:modification-date>, <text:modification-time style:data-style-name="N41">17:38:54</text:modification-time></text:p>
</style:footer>
</style:master-page>
<style:master-page style:name="First_20_Page" style:display-name="First Page" style:page-layout-name="pm2" style:next-style-name="Standard"/>
@@ -3101,11 +3083,17 @@
<text:p text:style-name="P270"><text:span text:style-name="T329">Filter tool to alter configuration files via command line. Reads </text:span><text:span text:style-name="Variable"><text:span text:style-name="T329">file</text:span></text:span><text:span text:style-name="T329">.config (standard input by default or if </text:span><text:span text:style-name="Variable"><text:span text:style-name="T329">file</text:span></text:span><text:span text:style-name="T329">.config = '-') and prints the filtered configuration to standard output. Add or alter variables by </text:span><text:span text:style-name="T43">name</text:span><text:span text:style-name="T329">=</text:span><text:span text:style-name="T43">value </text:span><text:span text:style-name="T329">as described before. With '-d' or '--delete', the variable </text:span><text:span text:style-name="Variable"><text:span text:style-name="T329">key</text:span></text:span><text:span text:style-name="T329"> is removed from the configuration. </text:span><text:span text:style-name="T125">With '-H' or '--header', </text:span><text:span text:style-name="Variable"><text:span text:style-name="T330">text</text:span></text:span> <text:span text:style-name="T330">is appended to the configuration's header comment. For files given with '-a' or '--add', all settings are merged with </text:span><text:span text:style-name="Variable"><text:span text:style-name="T329">file</text:span></text:span><text:span text:style-name="T329">.config.</text:span></text:p>
<text:p text:style-name="P305"><text:span text:style-name="T329">se</text:span><text:span text:style-name="T365">l</text:span><text:span text:style-name="T329">config</text:span><text:span text:style-name="T330"> [-</text:span><text:span text:style-name="T233">t</text:span><text:span text:style-name="T330">]</text:span> <text:span text:style-name="T330">[-</text:span><text:span text:style-name="T365">c</text:span><text:span text:style-name="T330">] </text:span><text:span text:style-name="Variable">section</text:span> <text:span text:style-name="T331">[</text:span><text:span text:style-name="Variable">file</text:span>.<text:span text:style-name="T331">config</text:span><text:span text:style-name="T126">]</text:span></text:p>
<text:p text:style-name="P274"><text:span text:style-name="T329">Filter tool to </text:span><text:span text:style-name="T354">extract</text:span><text:span text:style-name="T365"> sections from </text:span><text:span text:style-name="T329">configuration files via command line. Reads </text:span><text:span text:style-name="Variable"><text:span text:style-name="T329">file</text:span></text:span><text:span text:style-name="T329">.config (standard input by default or if </text:span><text:span text:style-name="Variable"><text:span text:style-name="T329">file</text:span></text:span><text:span text:style-name="T329">.config = '-') and prints the filtered configuration to standard output. </text:span><text:span text:style-name="Variable"><text:span text:style-name="T365">section</text:span></text:span><text:span text:style-name="T365"> is specified as described for </text:span><text:span text:style-name="T45">mkexp. </text:span><text:span text:style-name="T329">With '-</text:span><text:span text:style-name="T365">t</text:span><text:span text:style-name="T329">' or '--trailing-space', t</text:span><text:span text:style-name="T365">railing space is </text:span><text:span text:style-name="T329">removed from the </text:span><text:span text:style-name="T365">output lines</text:span><text:span text:style-name="T329">. </text:span><text:span text:style-name="T125">With '-</text:span><text:span text:style-name="T132">c</text:span><text:span text:style-name="T125">' or '--</text:span><text:span text:style-name="T344">inline-comments</text:span><text:span text:style-name="T125">', </text:span><text:span text:style-name="T132">multiple spaces between a variable value and an inline comment are reduced to a single space.</text:span></text:p>
- <text:p text:style-name="P309"><text:span text:style-name="T383">diff</text:span><text:span text:style-name="T329">config</text:span><text:span text:style-name="T330"> [-</text:span><text:span text:style-name="T233">t</text:span><text:span text:style-name="T330">]</text:span> <text:span text:style-name="T330">[-</text:span><text:span text:style-name="T365">c</text:span><text:span text:style-name="T330">] </text:span><text:span text:style-name="Variable">file</text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">1</text:span></text:span>.<text:span text:style-name="T331">config</text:span><text:span text:style-name="T126"> </text:span><text:span text:style-name="Variable"><text:span text:style-name="T331">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">2</text:span></text:span><text:span text:style-name="T126">.config</text:span></text:p>
- <text:p text:style-name="P280"><text:span text:style-name="T124">Filter tool to </text:span><text:span text:style-name="T348">remove all settings from </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T358">1</text:span></text:span><text:span text:style-name="T349">.config </text:span><text:span text:style-name="T348">that are duplicated in </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T358">2</text:span></text:span><text:span text:style-name="T349">.config. </text:span><text:span text:style-name="T348">Useful to check new experiment type configs against the default config. Takes the same options as </text:span><text:span text:style-name="T362">selconfig</text:span><text:span text:style-name="T348">.</text:span></text:p>
- <text:p text:style-name="P310"><text:span text:style-name="T384">comp</text:span><text:span text:style-name="T329">config</text:span><text:span text:style-name="T330"> [-</text:span><text:span text:style-name="T384">t]</text:span> <text:span text:style-name="T330">[-</text:span><text:span text:style-name="T365">c</text:span><text:span text:style-name="T330">] </text:span><text:span text:style-name="Variable">file</text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">1</text:span></text:span>.<text:span text:style-name="T331">config</text:span><text:span text:style-name="T126"> </text:span><text:span text:style-name="Variable"><text:span text:style-name="T331">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">2</text:span></text:span><text:span text:style-name="T126">.config [</text:span><text:span text:style-name="Variable"><text:span text:style-name="T331">file</text:span></text:span><text:span text:style-name="T126">.config ...]</text:span></text:p>
- <text:p text:style-name="P281"><text:span text:style-name="T349">Filter tool to </text:span><text:span text:style-name="T350">select</text:span><text:span text:style-name="T348"> all settings from </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T358">1</text:span></text:span><text:span text:style-name="T349">.config </text:span><text:span text:style-name="T348">that are </text:span><text:span text:style-name="T350">common to</text:span><text:span text:style-name="T348"> </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T358">2</text:span></text:span><text:span text:style-name="T349">.config </text:span><text:span text:style-name="T350">and every </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="T349">.config. </text:span><text:span text:style-name="T348">Useful to </text:span><text:span text:style-name="T350">extract a default config for a number of experiment </text:span><text:soft-page-break/><text:span text:style-name="T350">type configs. </text:span><text:span text:style-name="T348">Takes the same options as </text:span><text:span text:style-name="T362">selconfig</text:span><text:span text:style-name="T348">.</text:span></text:p>
- <text:p text:style-name="P308"><text:span text:style-name="T381">importexp</text:span><text:span text:style-name="T364"> </text:span><text:span text:style-name="T381">[</text:span><text:span text:style-name="Variable"><text:span text:style-name="T381">option</text:span></text:span><text:span text:style-name="T381"> ...] </text:span><text:span text:style-name="Variable"><text:span text:style-name="T381">run_script</text:span></text:span><text:span text:style-name="T381"> [</text:span><text:span text:style-name="Variable"><text:span text:style-name="T235">run_script</text:span></text:span><text:span text:style-name="T381"> ...]</text:span></text:p>
+ <text:p text:style-name="P381"><text:span text:style-name="T384">comp</text:span><text:span text:style-name="T329">config</text:span><text:span text:style-name="T330"> [-</text:span><text:span text:style-name="T384">t]</text:span> <text:span text:style-name="T330">[-</text:span><text:span text:style-name="T365">c</text:span><text:span text:style-name="T330">] </text:span><text:span text:style-name="Variable">file</text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">1</text:span></text:span>.<text:span text:style-name="T331">config</text:span><text:span text:style-name="T126"> </text:span><text:span text:style-name="Variable"><text:span text:style-name="T331">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">2</text:span></text:span><text:span text:style-name="T126">.config [</text:span><text:span text:style-name="Variable"><text:span text:style-name="T331">file</text:span></text:span><text:span text:style-name="T126">.config ...]</text:span></text:p>
+ <text:p text:style-name="P380"><text:span text:style-name="T349">Filter tool to </text:span><text:span text:style-name="T350">select</text:span><text:span text:style-name="T348"> all settings from </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T358">1</text:span></text:span><text:span text:style-name="T349">.config </text:span><text:span text:style-name="T348">that are </text:span><text:span text:style-name="T350">common to</text:span><text:span text:style-name="T348"> </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T358">2</text:span></text:span><text:span text:style-name="T349">.config </text:span><text:span text:style-name="T350">and every </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="T349">.config. </text:span><text:span text:style-name="T348">Useful to </text:span><text:span text:style-name="T350">extract a default config for a number of experiment type configs. </text:span><text:span text:style-name="T348">Takes the same options as </text:span><text:span text:style-name="T362">selconfig</text:span><text:span text:style-name="T348">.</text:span></text:p>
+ <text:p text:style-name="P381"><text:span text:style-name="T383">diff</text:span><text:span text:style-name="T329">config</text:span><text:span text:style-name="T330"> [-</text:span><text:span text:style-name="T233">t</text:span><text:span text:style-name="T330">]</text:span> <text:span text:style-name="T330">[-</text:span><text:span text:style-name="T365">c</text:span><text:span text:style-name="T330">] </text:span><text:span text:style-name="Variable">file</text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">1</text:span></text:span>.<text:span text:style-name="T331">config</text:span><text:span text:style-name="T126"> </text:span><text:span text:style-name="Variable"><text:span text:style-name="T331">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">2</text:span></text:span><text:span text:style-name="T126">.config</text:span></text:p>
+ <text:p text:style-name="P280"><text:span text:style-name="T124">Filter tool to </text:span><text:span text:style-name="T348">remove all settings from </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T358">1</text:span></text:span><text:span text:style-name="T349">.config </text:span><text:span text:style-name="T348">that are duplicated in </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T358">2</text:span></text:span><text:span text:style-name="T349">.config. </text:span><text:span text:style-name="T348">Useful to check new experiment type configs against the default </text:span><text:soft-page-break/><text:span text:style-name="T348">config. Takes the same options as </text:span><text:span text:style-name="T362">selconfig</text:span><text:span text:style-name="T348">.</text:span></text:p>
+ <text:p text:style-name="P381"><text:span text:style-name="T330">unmergeconfig [-</text:span><text:span text:style-name="T384">t]</text:span> <text:span text:style-name="T330">[-</text:span><text:span text:style-name="T365">c</text:span><text:span text:style-name="T330">] </text:span><text:span text:style-name="Variable">file</text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">1</text:span></text:span>.<text:span text:style-name="T331">config</text:span><text:span text:style-name="T126"> </text:span><text:span text:style-name="Variable"><text:span text:style-name="T331">file</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T383">2</text:span></text:span><text:span text:style-name="T126">.config</text:span></text:p>
+ <text:p text:style-name="List_20_Contents">Filter tool to substitute literal settings in <text:span text:style-name="Variable">file1</text:span>.config by the corresponding</text:p>
+ <text:p text:style-name="List_20_Contents">variable references as defined in <text:span text:style-name="Variable">file2</text:span>.config. From <text:span text:style-name="Variable">file2</text:span>.config, only settings like</text:p>
+ <text:p text:style-name="List_20_Contents"><text:span text:style-name="Variable">var1 = $var2</text:span> or <text:span text:style-name="Variable">var1 = ${var2}</text:span> are considered. Useful to create a new experiment</text:p>
+ <text:p text:style-name="List_20_Contents">type config from <text:span text:style-name="T9">importexp</text:span> output by running it against the default config. Takes</text:p>
+ <text:p text:style-name="List_20_Contents">the same options as <text:span text:style-name="T9">selconfig</text:span>.</text:p>
+ <text:p text:style-name="P381"><text:span text:style-name="T381">importexp</text:span><text:span text:style-name="T364"> </text:span><text:span text:style-name="T381">[</text:span><text:span text:style-name="Variable"><text:span text:style-name="T381">option</text:span></text:span><text:span text:style-name="T381"> ...] </text:span><text:span text:style-name="Variable"><text:span text:style-name="T381">run_script</text:span></text:span><text:span text:style-name="T381"> [</text:span><text:span text:style-name="Variable"><text:span text:style-name="T235">run_script</text:span></text:span><text:span text:style-name="T381"> ...]</text:span></text:p>
<text:p text:style-name="P280"><text:span text:style-name="T136">Runs the given runscripts in a sandbox and </text:span><text:span text:style-name="T139">tries to </text:span><text:span text:style-name="T136">extract namelists and files from the resulting log file by use of </text:span><text:span text:style-name="T46">namelist2config</text:span><text:span text:style-name="T136"> </text:span><text:span text:style-name="T137">and </text:span><text:span text:style-name="T47">files2config</text:span><text:span text:style-name="T137">. The resulting config is written to standard output. </text:span><text:span text:style-name="T138">Note that this </text:span><text:span text:style-name="T139">is tailored to ICON scripts, and </text:span><text:span text:style-name="T138">must be </text:span><text:span text:style-name="T139">called from the 'run' </text:span><text:span text:style-name="T138">directory. For out-of-source builds, this must be located </text:span><text:span text:style-name="T139">under</text:span><text:span text:style-name="T138"> the build directory and the '-b' option is mandatory. </text:span><text:span text:style-name="T137">Options are<text:line-break/>-b </text:span><text:span text:style-name="Variable"><text:span text:style-name="T382">build_subdir</text:span></text:span><text:span text:style-name="T137">: set name of build subdirectory [</text:span><text:span text:style-name="Variable"><text:span text:style-name="T382">none</text:span></text:span><text:span text:style-name="T137">]<text:line-break/>-</text:span>d <text:span text:style-name="Variable"><text:span text:style-name="T356">data_base_dir</text:span></text:span><text:span text:style-name="T356">: change base </text:span><text:span text:style-name="T357">of</text:span><text:span text:style-name="T356"> data directory [derived from </text:span><text:span text:style-name="Variable"><text:span text:style-name="T356">run_script</text:span></text:span><text:span text:style-name="T356">]<text:line-break/>-</text:span><text:span text:style-name="T137">D data_dir: </text:span><text:span text:style-name="T138">change</text:span><text:span text:style-name="T137"> data directory </text:span><text:span text:style-name="T138">explicitly [</text:span><text:span text:style-name="T346">derived from </text:span><text:span text:style-name="Variable"><text:span text:style-name="T356">run_script</text:span></text:span><text:span text:style-name="T346">]<text:line-break/>-</text:span><text:span text:style-name="T137">e </text:span><text:span text:style-name="T138">environment:</text:span><text:span text:style-name="T137"> </text:span><text:span text:style-name="T138">set ENVIRONMENT for </text:span><text:span text:style-name="T139">the </text:span><text:span text:style-name="T138">resulting config [levante]<text:line-break/>-</text:span><text:span text:style-name="T137">i: </text:span><text:span text:style-name="T139">in the </text:span><text:span text:style-name="T348">resulting config</text:span><text:span text:style-name="T139">, create an 'intake' job only, ignore the standard jobs</text:span><text:span text:style-name="T138"><text:line-break/>-</text:span><text:span text:style-name="T137">s </text:span><text:span text:style-name="T347">custom_subdir: needed </text:span><text:span text:style-name="T348">if scripts were moved from the run directory<text:line-break/>-</text:span><text:span text:style-name="T137">t </text:span><text:span text:style-name="T139">exp_type: </text:span><text:span text:style-name="T138">set </text:span><text:span text:style-name="T139">EXP_TYPE</text:span><text:span text:style-name="T138"> for </text:span><text:span text:style-name="T139">the </text:span><text:span text:style-name="T138">resulting config [</text:span><text:span text:style-name="T348">DEFAULT</text:span><text:span text:style-name="T138">]<text:line-break/>-</text:span><text:span text:style-name="T137">c </text:span><text:span text:style-name="T139">cpus_per_node</text:span><text:span text:style-name="T137">: </text:span><text:span text:style-name="T139">set alleged number of cpus per node [256]<text:line-break/>-x: debug mode, do not remove temporary files, nor the sandbox directory</text:span></text:p>
<text:p text:style-name="P304">namelist2config [-d <text:span text:style-name="T338">[-c]</text:span> [-v]<text:span text:style-name="T340">]</text:span></text:p>
<text:p text:style-name="P272">Tries to extract namelist settings from shell scripts or log files and converts them to <text:span text:style-name="T339">the </text:span>.config format. <text:span text:style-name="T339">By default, comments are ignored and names of namelist groups and variables sorted to allow easier comparisons. With '-d', namelists are </text:span><text:span text:style-name="T340">printed directly, in original order</text:span><text:span text:style-name="T339">. </text:span><text:span text:style-name="T340">In this mode, </text:span><text:span text:style-name="T339">'-c' enables comments, '-v' will output non-namelist lines from input files as comments, prefixed with '###'.</text:span></text:p>
@@ -3115,9 +3103,9 @@
<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="T192">For reading these files, </text:span><text:span text:style-name="T12">mkexp</text:span><text:span text:style-name="T192"> uses the </text:span><text:span text:style-name="T12">configobj</text:span><text:span text:style-name="T192"> 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:p text:style-name="P18">A <text:span text:style-name="T193">configuration variable is set by simply assigning a text value to a name, as in</text:span></text:p>
- <text:p text:style-name="Preformatted_20_Text">NAME = Joe User</text:p>
+ <text:p text:style-name="Preformatted_20_Text"><text:soft-page-break/>NAME = Joe User</text:p>
<text:p text:style-name="P19">Note that <text:span text:style-name="T194">spaces before and after the 'equals' sign are always ignored. The value starts with the first non-space character. Spaces and additional equals after this are part of the value. In the case above, the variable NAME is set to 'Joe User'. To include leading spaces, you may enclose the actual value in single or double quote characters as in</text:span></text:p>
- <text:p text:style-name="Preformatted_20_Text"><text:soft-page-break/>SEPARATOR = ' <text:s text:c="7"/>'</text:p>
+ <text:p text:style-name="Preformatted_20_Text">SEPARATOR = ' <text:s text:c="7"/>'</text:p>
<text:p text:style-name="P20">Comma separated values are taken to be a list of string values. Thus</text:p>
<text:p text:style-name="Preformatted_20_Text">PATH = /bin, /usr/bin, /usr/local/bin</text:p>
<text:p text:style-name="P21">will set PATH to ['/bin', '/usr/bin', '/usr/local/bin'].</text:p>
@@ -3137,12 +3125,12 @@
<text:p text:style-name="P140"><text:s text:c="4"/>description = This is the second section </text:p>
<text:p text:style-name="P23"><text:span text:style-name="T257">A s</text:span>ection <text:span text:style-name="T257">is</text:span> closed by the beginning of a new section of the same level, by a section <text:span text:style-name="T257">of </text:span>l<text:span text:style-name="T257">ower</text:span> <text:span text:style-name="T257">nesting </text:span>depth, <text:span text:style-name="T257">or the end of the .config file</text:span>. Thus, section1 will contain 'description' and two dictionaries 'subsection1' and 'subsection2', each of those containing their own 'description'. 'section2' then is a top-level dictionary, again with its own 'description' variable.</text:p>
<text:p text:style-name="P23">Note that indentation may be used to make the file more legible but is completely ignored when the file is loaded. The number of brackets is the only way to define the level of a section. This means that all variables in a section must be defined before any subsections. Otherwise, the variable <text:s/>would be<text:span text:style-name="T196">long</text:span> to the respective subsection.</text:p>
- <text:p text:style-name="P22">Fortran scholars will also want to note that names are case-sensitive, i.e. the variable 'NAME' is quite different from 'name'. Usually, setups use upper-case names for global variables and lower-case names for sections and their variables.</text:p>
- <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2538_1114405012"/><text:soft-page-break/>Special <text:span text:style-name="T249">v</text:span>ariables <text:span text:style-name="T249">and sections</text:span><text:bookmark-end text:name="__RefHeading__2538_1114405012"/></text:h>
+ <text:p text:style-name="P22"><text:soft-page-break/>Fortran scholars will also want to note that names are case-sensitive, i.e. the variable 'NAME' is quite different from 'name'. Usually, setups use upper-case names for global variables and lower-case names for sections and their variables.</text:p>
+ <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2538_1114405012"/>Special <text:span text:style-name="T249">v</text:span>ariables <text:span text:style-name="T249">and sections</text:span><text:bookmark-end text:name="__RefHeading__2538_1114405012"/></text:h>
<text:p text:style-name="P39"><text:span text:style-name="T58">There are a number of special variables that influence the way </text:span>mkexp<text:span text:style-name="T58"> works. They must be present in one of the .config files, unless noted otherwise below. </text:span><text:span text:style-name="T62">They are listed here for a first overview. Their exact meaning is explained in more detail in the upcoming sections.</text:span></text:p>
<text:p text:style-name="P40"><text:span text:style-name="T62">T</text:span><text:span text:style-name="T58">he first set of variables is usually defined in the model setup:</text:span></text:p>
<text:p text:style-name="P204">SCRIPT_DIR</text:p>
- <text:p text:style-name="P219"><text:span text:style-name="T61">D</text:span><text:span text:style-name="T58">irectory where the generated job descriptions are stored. This directory and its </text:span><text:span text:style-name="T58">parents are created by </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T58"> if they do not exist.</text:span></text:p>
+ <text:p text:style-name="P219"><text:span text:style-name="T61">D</text:span><text:span text:style-name="T58">irectory where the generated job descriptions are stored. This directory and its parents are created by </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T58"> if they do not exist.</text:span></text:p>
<text:p text:style-name="P205">WORK_DIR</text:p>
<text:p text:style-name="P222">Directory where the experiment is run. The jobs will use this for providing input data and configuration files needed for model execution. This directory and its parents are created if they do not exist.</text:p>
<text:p text:style-name="P206">DATA_DIR</text:p>
@@ -3161,8 +3149,8 @@
<text:p text:style-name="P215">EXP_ID (<text:span text:style-name="T9">optional</text:span>)</text:p>
<text:p text:style-name="P238">Name of the experiment to be created. If not set, this will be set to the base name of the user's .config file, e.g. 'joe1234' in the introductory example. All job description files will carry this as the first part of their name. For almost all model setups, this will be used in the definitions of SCRIPT_DIR, WORK_DIR, and DATA_DIR.</text:p>
<text:p text:style-name="P203">EXP_DESCRIPTION <text:span text:style-name="T221">(</text:span><text:span text:style-name="T16">optional</text:span><text:span text:style-name="T221">)</text:span></text:p>
- <text:p text:style-name="P223">Extensive description of the experiment to be created. If not set, this will contain all text in the header comment of the user's .config file. The leading comment characters, <text:span text:style-name="T316">as well as </text:span>leading and trailing empty lines <text:span text:style-name="T316">or comment boilerplate </text:span>are removed. Note that <text:span text:style-name="T273">both header comment and </text:span>EXP_DESCRIPTION may reference any other global variable defined in the experiment configuration <text:span text:style-name="T273">(see section </text:span><text:span text:style-name="T273"><text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__2540_1114405012">2.3.4</text:bookmark-ref></text:span><text:span text:style-name="T273">)</text:span>.</text:p>
- <text:p text:style-name="P223"><text:soft-page-break/>The contents of this variable is written to a 'README' file in SCRIPT_DIR.</text:p>
+ <text:p text:style-name="P223">Extensive description of the experiment to be created. If not set, this will contain all text in the header comment of the user's .config file. The leading comment <text:soft-page-break/>characters, <text:span text:style-name="T316">as well as </text:span>leading and trailing empty lines <text:span text:style-name="T316">or comment boilerplate </text:span>are removed. Note that <text:span text:style-name="T273">both header comment and </text:span>EXP_DESCRIPTION may reference any other global variable defined in the experiment configuration <text:span text:style-name="T273">(see section </text:span><text:span text:style-name="T273"><text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__2540_1114405012">2.3.4</text:bookmark-ref></text:span><text:span text:style-name="T273">)</text:span>.</text:p>
+ <text:p text:style-name="P223">The contents of this variable is written to a 'README' file in SCRIPT_DIR.</text:p>
<text:p text:style-name="P38"><text:span text:style-name="T58">Another set of variables is automatically added to the job specific experiment configuration. </text:span><text:span text:style-name="T73">These are considered read-only</text:span><text:span text:style-name="T58"> </text:span><text:span text:style-name="T66">and may not be altered</text:span><text:span text:style-name="T58">.</text:span></text:p>
<text:p text:style-name="P202">JOB</text:p>
<text:p text:style-name="P220">A dictionary of system settings pertaining to the current job.</text:p>
@@ -3190,9 +3178,9 @@
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="2"/>size = 42 </text:p>
<text:p text:style-name="Preformatted_20_Text">[jobs] </text:p>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="2"/>ensemble_size = $size </text:p>
- <text:p text:style-name="P77">will fail with</text:p>
+ <text:p text:style-name="P77"><text:soft-page-break/>will fail with</text:p>
<text:p text:style-name="P201">Oops: missing option "size" in interpolation while reading key 'ensemble_size'</text:p>
- <text:p text:style-name="P77"><text:soft-page-break/>because 'size' is not defined in 'jobs', nor on the global level.</text:p>
+ <text:p text:style-name="P77">because 'size' is not defined in 'jobs', nor on the global level.</text:p>
<text:p text:style-name="P79">As in shell scripts, the variable name must be enclosed in braces if the interpolation continues with a word character (alphanumerical or underscore), or if the variable name contains a space (which is perfectly legal):</text:p>
<text:p text:style-name="Preformatted_20_Text">WORK_DIR = /tmp/$EXP_ID_test <text:s text:c="3"/><text:span text:style-name="T264"># ERROR: missing option "EXP_ID_test"</text:span></text:p>
<text:p text:style-name="P179"><text:span text:style-name="T264">WORK_DIR = /tmp/</text:span><text:span text:style-name="T181">${EXP_ID}_test</text:span><text:span text:style-name="T264"> <text:s/># OK</text:span></text:p>
@@ -3213,8 +3201,8 @@
<text:p text:style-name="P81">The disadvantage is that there may be no incremental adding of values to a given variable because this would cause circular dependencies. Imagine</text:p>
<text:p text:style-name="Preformatted_20_Text">SUBMODELS = $SUBMODELS jsbach</text:p>
<text:p text:style-name="P82">When <text:span text:style-name="T9">mkexp</text:span> tries to evaluate 'SUBMODELS', it sees that it needs to do an interpolation; but to do this interpolation, 'SUBMODELS' would need to have been evaluated already! So this results in</text:p>
- <text:p text:style-name="P201">Oops: interpolation loop detected in value "SUBMODELS" while reading key 'SUBMODELS'</text:p>
- <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2544_1114405012"/><text:soft-page-break/>Special expressions<text:bookmark-end text:name="__RefHeading__2544_1114405012"/></text:h>
+ <text:p text:style-name="P201"><text:soft-page-break/>Oops: interpolation loop detected in value "SUBMODELS" while reading key 'SUBMODELS'</text:p>
+ <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2544_1114405012"/>Special expressions<text:bookmark-end text:name="__RefHeading__2544_1114405012"/></text:h>
<text:p text:style-name="P83">For some applications, simply including some other variable is not enough. You might want to compute a time limit from a given constant divided by the number of computing nodes, or convert a time stamp to a list of values. For these purposes, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T58"> includes some special expressions, that are evaluated when interpolation occurs.</text:span></text:p>
<text:p text:style-name="P285"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T58"> = </text:span><text:span text:style-name="T164">eval(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T164">)</text:span><text:span text:style-name="T58"><text:line-break/></text:span><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T58"> = </text:span><text:span text:style-name="T164">evals(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T164">)</text:span></text:p>
<text:p text:style-name="P278"><text:span text:style-name="T88">I</text:span><text:span text:style-name="T117">nterpret </text:span><text:span text:style-name="T41">expression</text:span><text:span text:style-name="T117"> as a valid Python expression and assign the result to </text:span><text:span text:style-name="T41">variable</text:span><text:span text:style-name="T117"> as a string. </text:span><text:span text:style-name="T116">The modules </text:span><text:span text:style-name="T316">'</text:span>os<text:span text:style-name="T316">'</text:span>, <text:span text:style-name="T316">'</text:span>re<text:span text:style-name="T316">'</text:span> and <text:span text:style-name="T316">'</text:span>time<text:span text:style-name="T316">'</text:span> <text:span text:style-name="T116">may be used in </text:span><text:span text:style-name="T40">expression</text:span><text:span text:style-name="T116">. </text:span><text:span text:style-name="T133">Besides, a </text:span><text:span text:style-name="T345">predicate</text:span><text:span text:style-name="T133"> 'is_set' is available to </text:span><text:span text:style-name="T170">test if a string evaluates to</text:span><text:span text:style-name="T53"> true</text:span><text:span text:style-name="T170"> when used as namelist </text:span><text:span text:style-name="T351">logical, </text:span><text:span text:style-name="T352">r</text:span><text:span text:style-name="T351">eturn</text:span><text:span text:style-name="T352">ing</text:span><text:span text:style-name="T360"> false</text:span><text:span text:style-name="T351"> when used on </text:span><text:span text:style-name="T352">'None'.</text:span></text:p>
@@ -3231,8 +3219,8 @@
<text:p text:style-name="P289"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T174">add_years</text:span>(<text:span text:style-name="T9">datestamp</text:span>, <text:span text:style-name="T9">offset</text:span>)'</text:p>
<text:p text:style-name="P251">Take integer <text:span text:style-name="T9">offset</text:span><text:span text:style-name="T58"> (may be negative), add it to the year portion of </text:span><text:span text:style-name="T9">datestamp</text:span><text:span text:style-name="T58"> and return the resulting date string.</text:span></text:p>
<text:p text:style-name="P290"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T174">add_</text:span><text:span text:style-name="T182">days</text:span>(<text:span text:style-name="T9">datestamp</text:span>, <text:span text:style-name="T9">offset</text:span>)'</text:p>
- <text:p text:style-name="P252"><text:span text:style-name="T58">Take integer </text:span><text:span text:style-name="T9">offset</text:span><text:span text:style-name="T58"> (may be negative), add it to the </text:span><text:span text:style-name="T101">day</text:span><text:span text:style-name="T58"> portion of </text:span><text:span text:style-name="T9">datestamp</text:span><text:span text:style-name="T58"> and return the resulting date string. </text:span><text:span text:style-name="T101">Year and month portions will be set as appropriate, assuming a Proleptic Gregorian calendar with year 0.</text:span></text:p>
- <text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2546_1114405012"/><text:soft-page-break/>Format of .tmpl files<text:bookmark-end text:name="__RefHeading__2546_1114405012"/></text:h>
+ <text:p text:style-name="P252"><text:span text:style-name="T58">Take integer </text:span><text:span text:style-name="T9">offset</text:span><text:span text:style-name="T58"> (may be negative), add it to the </text:span><text:span text:style-name="T101">day</text:span><text:span text:style-name="T58"> portion of </text:span><text:span text:style-name="T9">datestamp</text:span><text:span text:style-name="T58"> and return the resulting date string. </text:span><text:span text:style-name="T101">Year and month portions will be set as </text:span><text:soft-page-break/><text:span text:style-name="T101">appropriate, assuming a Proleptic Gregorian calendar with year 0.</text:span></text:p>
+ <text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2546_1114405012"/>Format of .tmpl files<text:bookmark-end text:name="__RefHeading__2546_1114405012"/></text:h>
<text:p text:style-name="P24">The .tmpl files are also text files mostly written in the syntax of the job description that <text:span text:style-name="T9">mkexp</text:span> is meant to create. Currently this is usually the ksh or bash shell script syntax, but may also be any other interpreted language, like Perl or Python, or even a configuration or namelist file. The main difference are placeholders and structured comments that are embedded in the program text. These are evaluated or expanded using the information that comes with the .config files, to create the final text files, defining the jobs to be run on the target system.</text:p>
<text:p text:style-name="P24">The expansion of .tmpl files into the job description uses the <text:span text:style-name="T9">Jinja</text:span> Python library. It provides a default set of facilities that can be used to expand any textual template. The proposed default syntax was slightly customized to fit the needs of <text:span text:style-name="T9">mkexp</text:span>.</text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2548_1114405012"/>Placeholders<text:bookmark-end text:name="__RefHeading__2548_1114405012"/></text:h>
@@ -3388,8 +3376,8 @@
<text:p text:style-name="P118"><text:s text:c="8"/><text:span text:style-name="T226">[[</text:span>[[[jsbach_ctl]]]<text:span text:style-name="T226">]]</text:span></text:p>
<text:p text:style-name="P118"><text:span text:style-name="T140"><text:s text:c="10"/>use_dynveg = </text:span><text:span text:style-name="T145">true</text:span></text:p>
<text:p text:style-name="P46"><text:span text:style-name="T146">This</text:span><text:span text:style-name="T140"> will result in a 'joe1234.run_first' file that is identical to 'joe1234.run' except for the 'use_dynveg' setting.</text:span></text:p>
- <text:h text:style-name="P331" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2572_1114405012"/><text:soft-page-break/>Native script variables<text:bookmark-end text:name="__RefHeading__2572_1114405012"/></text:h>
- <text:p text:style-name="P48"><text:span text:style-name="T140">While the definition of .config variables may use</text:span><text:span text:style-name="T147"> variable references like</text:span><text:span text:style-name="T140"> $NAME or ${NAME} to include the </text:span><text:span text:style-name="T147">verbatim </text:span><text:span text:style-name="T140">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="T147">script</text:span><text:span text:style-name="T140"> that is supposed to be 'user-serviceable' 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="T147">Instead they will want to have a single, native script variable that is used throughout the job script, and that may be re-</text:span><text:span text:style-name="T147">defined on a single line.</text:span></text:p>
+ <text:h text:style-name="P331" 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="T140">While the definition of .config variables may use</text:span><text:span text:style-name="T147"> variable references like</text:span><text:span text:style-name="T140"> $NAME or ${NAME} to include the </text:span><text:span text:style-name="T147">verbatim </text:span><text:span text:style-name="T140">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="T147">script</text:span><text:span text:style-name="T140"> that is supposed to be 'user-serviceable' 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="T147">Instead they will want to have a single, native script variable that is used throughout the job script, and that may be re-</text:span><text:soft-page-break/><text:span text:style-name="T147">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 $${NAME} in the configuration values, and re-formats them to the syntax of the current job script:</text:p>
<text:p text:style-name="P150"># joe1234.config</text:p>
<text:p text:style-name="P150">NAME = Joe User</text:p>
@@ -3402,7 +3390,7 @@
<text:p text:style-name="P153">#! /bin/sh</text:p>
<text:p text:style-name="P156">NAME='Joe User'</text:p>
<text:p text:style-name="P152">echo This experiment was generated by ${NAME}</text:p>
- <text:p text:style-name="P53"><text:span text:style-name="T244">T</text:span>o support variable reference<text:span text:style-name="T243">s for other script languages, a</text:span> job specific variable '.var_format' may be defined. <text:span text:style-name="T243">It defines an output format string where any occurrence </text:span><text:span text:style-name="T243">of '%s' will be replaced by the respective variable name. </text:span>For a Python based script, <text:span text:style-name="T228">this may look like:</text:span></text:p>
+ <text:p text:style-name="P53"><text:span text:style-name="T244">T</text:span>o support variable reference<text:span text:style-name="T243">s for other script languages, a</text:span> job specific variable '.var_format' may be defined. <text:span text:style-name="T243">It defines an output format string where any occurrence of '%s' will be replaced by the respective variable name. </text:span>For a Python based script, <text:span text:style-name="T228">this may look like:</text:span></text:p>
<text:p text:style-name="P155"># joe1234.config</text:p>
<text:p text:style-name="P155">NAME = Joe User</text:p>
<text:p text:style-name="P155">MESSAGE = This experiment was generated by $${NAME}</text:p>
@@ -3417,10 +3405,10 @@
<text:p text:style-name="P168">#! /usr/bin/env python </text:p>
<text:p text:style-name="P168">NAME = '<text:span text:style-name="T242">Joe User</text:span>' </text:p>
<text:p text:style-name="P169">print<text:span text:style-name="T279">(</text:span>'<text:span text:style-name="T140">This experiment was generated by </text:span><text:span text:style-name="T149">' + str(</text:span><text:span text:style-name="T140">NAME) </text:span><text:span text:style-name="T149">+ '</text:span>'<text:span text:style-name="T279">)</text:span></text:p>
- <text:h text:style-name="P338" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2574_1114405012"/><text:soft-page-break/>Initializing native script variables<text:bookmark-end text:name="__RefHeading__2574_1114405012"/></text:h>
+ <text:h text:style-name="P338" 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="P64">In the previous section, the native variables were initialized by an addition<text:span text:style-name="T246">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="P64"><text:span text:style-name="T247">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="T247"> maintains the special variable VARIABLES_. When generating output for</text:span></text:p>
- <text:p text:style-name="P157">NAME = Joe User</text:p>
+ <text:p text:style-name="P157"><text:soft-page-break/>NAME = Joe User</text:p>
<text:p text:style-name="P158">EMAIL = joe@domain.tld</text:p>
<text:p text:style-name="P170"><text:span text:style-name="T140">MESSAGE = This experiment was generated by $${NAME} </text:span><text:span text:style-name="T151"><$${EMAIL}></text:span></text:p>
<text:p text:style-name="P65"><text:span text:style-name="T48">mkexp</text:span><text:span text:style-name="T140"> will parse all values, recognize 'NAME' and 'EMAIL' as native variables, and </text:span><text:span text:style-name="T152">will </text:span><text:span text:style-name="T140">put their names in the VARIABLES_ list. Now we may use the 'for' template directive to generate an additional line for each member of VARIABLES_. To query the value for a given variable name, </text:span><text:span text:style-name="T48">mkexp</text:span><text:span text:style-name="T140"> provides the 'context' function, such that the template</text:span></text:p>
@@ -3439,9 +3427,9 @@
<text:p text:style-name="P63">Even the simplest user setup may contain an error. In this case, it is considered good practice to fix this error in the user setup, and to rerun <text:span text:style-name="T9">mkexp.</text:span><text:span text:style-name="T58"> If you want to be really good, you might even start a new experiment from the previous one's restart data.</text:span></text:p>
<text:p text:style-name="P91"><text:span text:style-name="T68">A</text:span><text:span text:style-name="T58">s a convenient short-cut, </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T58"> provides the script 'update' in the script directory. It may be called instead of going back to the 'run' and re-running </text:span><text:span text:style-name="T9">mkexp </text:span><text:span text:style-name="T58">directly. The update script records all command line settings and environment settings that were used for running </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T58"> so that './update' reg</text:span><text:span text:style-name="T103">e</text:span><text:span text:style-name="T58">nerates the scripts exactly as they were created, without having to re-construct the exact settings. Like mkexp, update allows to set or change variables on the command line, e.g.</text:span></text:p>
<text:p text:style-name="P147">./update FINAL_DATE=2015-12-31</text:p>
- <text:p text:style-name="P91"><text:soft-page-break/>may be used to regenerate scripts with a new final date. Note that these settings are also recorded, i.e. running just './update' the next time will again set FINAL_DATE.</text:p>
+ <text:p text:style-name="P91">may be used to regenerate scripts with a new final date. Note that these settings are also recorded, i.e. running just './update' the next time will again set FINAL_DATE.</text:p>
<text:p text:style-name="P63"><text:span text:style-name="T58">Of course, there is also the possibility to </text:span><text:span text:style-name="T68">change</text:span><text:span text:style-name="T58"> the </text:span><text:span text:style-name="T19">generated</text:span><text:span text:style-name="T67"> </text:span><text:span text:style-name="T58">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="T69">facing</text:span><text:span text:style-name="T58"> the next </text:span><text:span text:style-name="T69">change,</text:span><text:span text:style-name="T58"> this might not be the case, so eventually you </text:span><text:span text:style-name="T67">may</text:span><text:span text:style-name="T58"> 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="P63"><text:span text:style-name="T58">Whenever </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T58"> 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 'backup'. </text:span><text:span text:style-name="T67">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="T68">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="T103">after a necessary regeneration</text:span><text:span text:style-name="T68">.</text:span></text:p>
+ <text:p text:style-name="P63"><text:soft-page-break/><text:span text:style-name="T58">Whenever </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T58"> 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 'backup'. </text:span><text:span text:style-name="T67">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="T68">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="T103">after a necessary regeneration</text:span><text:span text:style-name="T68">.</text:span></text:p>
<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="T173">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="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>
@@ -3453,13 +3441,13 @@
<text:p text:style-name="P183"/>
<text:p text:style-name="P171"><text:s text:c="2"/>[[<text:span text:style-name="T260">namelist.echam</text:span>]] </text:p>
<text:p text:style-name="P171"><text:s text:c="4"/>[[[runctl]]] </text:p>
- <text:p text:style-name="P171"><text:soft-page-break/><text:s text:c="6"/>lamip = true</text:p>
+ <text:p text:style-name="P171"><text:s text:c="6"/>lamip = true</text:p>
<text:p text:style-name="P171"><text:s text:c="6"/><text:span text:style-name="T269">nproma = 48</text:span></text:p>
<text:p text:style-name="P175"><text:s text:c="6"/>earth_angular_velocity = 7.3e-5</text:p>
<text:p text:style-name="P175"><text:s text:c="6"/>out_expname = joe1234</text:p>
<text:p text:style-name="P175"><text:s text:c="6"/><text:span text:style-name="T261">dt_stop = 2009, 1, 1, 0, 0, 0</text:span></text:p>
<text:p text:style-name="P69"><text:span text:style-name="T58">defines </text:span><text:span text:style-name="T79">a single </text:span><text:span text:style-name="T58">namelist file, </text:span><text:span text:style-name="T82">'namelist.echam'</text:span><text:span text:style-name="T58">, </text:span><text:span text:style-name="T80">containing a single namelist group with four variables of different types. Note </text:span><text:span text:style-name="T99">that you do not </text:span><text:span text:style-name="T80">need to use quotes for strings nor periods for logical values.</text:span></text:p>
- <text:h text:style-name="P334" 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="P334" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2578_1114405012"/><text:soft-page-break/>Formatting the namelist information<text:bookmark-end text:name="__RefHeading__2578_1114405012"/></text:h>
<text:p text:style-name="P101"><text:span text:style-name="T78">The </text:span><text:span text:style-name="T79">names of the </text:span><text:span text:style-name="T78">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="T79">name</text:span><text:span text:style-name="T78">s, and their variables are formatted as fields of this namelist </text:span><text:span text:style-name="T79">group</text:span><text:span text:style-name="T78">. </text:span><text:span text:style-name="T79">In the example above, there is a single namelist group 'runctl', which will be converted to the Fortran namelist convention. </text:span><text:span text:style-name="T260">The values of the group'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="P75"><text:span text:style-name="T280">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="T82"> 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="P137">&runctl</text:p>
@@ -3473,9 +3461,9 @@
<text:h text:style-name="P343" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2580_1114405012"/><text:span text:style-name="T80">S</text:span><text:span text:style-name="T58">uppressing namelist </text:span><text:span text:style-name="T134">files, </text:span><text:span text:style-name="T58">groups, or variables</text:span><text:bookmark-end text:name="__RefHeading__2580_1114405012"/></text:h>
<text:p text:style-name="P106"><text:span text:style-name="T58">If you want to </text:span><text:span text:style-name="T122">disable</text:span><text:span text:style-name="T58"> a namelist group </text:span><text:span text:style-name="T134">or a whole namelist file </text:span><text:span text:style-name="T58">defined on a higher setup level, you may </text:span><text:span text:style-name="T134">set a</text:span><text:span text:style-name="T58"> special</text:span><text:span text:style-name="T134"> v</text:span><text:span text:style-name="T58">ariable '.hide' to </text:span><text:span text:style-name="T122">'</text:span><text:span text:style-name="T58">true</text:span><text:span text:style-name="T122">' </text:span><text:span text:style-name="T134">in the corresponding section</text:span><text:span text:style-name="T58">. </text:span><text:span text:style-name="T122">As you may suspect, setting '.hide' to 'false' for </text:span><text:span text:style-name="T135">elements</text:span><text:span text:style-name="T122"> that were hidden on a higher setup level will re-enable the</text:span><text:span text:style-name="T123">m</text:span><text:span text:style-name="T122">.</text:span></text:p>
<text:p text:style-name="P112"><text:span text:style-name="T122">T</text:span><text:span text:style-name="T129">o disable a </text:span><text:span text:style-name="T130">single </text:span><text:span text:style-name="T129">namelist variable, simply </text:span><text:span text:style-name="T341">omit the value after the equals sign. This is taken to be an empty string, causing the variable to not be written </text:span><text:span text:style-name="T342">to the namelist file</text:span><text:span text:style-name="T341">, so the default value is used instead. </text:span><text:span text:style-name="T342">Setting the variable to a non-empty value i</text:span><text:span text:style-name="T343">n a higher </text:span><text:span text:style-name="T342">level</text:span><text:span text:style-name="T343"> .</text:span><text:span text:style-name="T342">config file will re-enable it.</text:span></text:p>
- <text:p text:style-name="P110"><text:span text:style-name="T341">If the empty string is a valid value in </text:span><text:span text:style-name="T342">your namelist</text:span><text:span text:style-name="T341">, you may set the special variable '.default' to an alternative string to be used as default marker instead of the empty </text:span><text:soft-page-break/><text:span text:style-name="T341">string. This can be done both on namelist and group level.</text:span></text:p>
+ <text:p text:style-name="P110"><text:span text:style-name="T341">If the empty string is a valid value in </text:span><text:span text:style-name="T342">your namelist</text:span><text:span text:style-name="T341">, you may set the special variable '.default' to an alternative string to be used as default marker instead of the empty string. This can be done both on namelist and group level.</text:span></text:p>
<text:p text:style-name="P111"><text:span text:style-name="T130">As a legacy, t</text:span><text:span text:style-name="T58">he namelist group section also honors the special variable '.remove' which may be set to a list of names. Any variables listed in the '.remove' variable will be deleted from the namelist group definition. </text:span><text:span text:style-name="T130">Note that, w</text:span><text:span text:style-name="T131">hile '.remove' is useful to </text:span><text:span text:style-name="T89">suppress</text:span><text:span text:style-name="T131"> 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="T90">Therefore, its use in model setups is strongly discouraged.</text:span></text:p>
- <text:h text:style-name="P344" text:outline-level="3"><text:bookmark-start text:name="__RefHeading___Toc4310_4067847427"/>Comments in namelists<text:bookmark-end text:name="__RefHeading___Toc4310_4067847427"/></text:h>
+ <text:h text:style-name="P344" text:outline-level="3"><text:bookmark-start text:name="__RefHeading___Toc4310_4067847427"/><text:soft-page-break/>Comments in namelists<text:bookmark-end text:name="__RefHeading___Toc4310_4067847427"/></text:h>
<text:p text:style-name="P107">In general, <text:span text:style-name="T332">'#' </text:span>comments in namelist or group sections will by converted to Fortran 90 <text:span text:style-name="T332">'!' </text:span>comments. In-line comments for <text:span text:style-name="T332">individual</text:span> settings are also recognized.</text:p>
<text:p text:style-name="P139"># Run time settings</text:p>
<text:p text:style-name="P193">[[[runctl]]]</text:p>
@@ -3504,9 +3492,9 @@
<text:p text:style-name="P196"><text:s text:c="4"/>! lamip = .true. ! Stays with 'runctl'</text:p>
<text:p text:style-name="P198">/</text:p>
<text:p text:style-name="P196">&dynctl</text:p>
- <text:h text:style-name="P335" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2714_1114405012"/><text:soft-page-break/>Using the namelist text<text:bookmark-end text:name="__RefHeading__2714_1114405012"/></text:h>
+ <text:h text:style-name="P335" 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="P70"><text:span text:style-name="T80">T</text:span><text:span text:style-name="T82">he </text:span><text:span text:style-name="T71">formatted namelist text </text:span><text:span text:style-name="T58">is </text:span><text:span text:style-name="T82">stor</text:span><text:span text:style-name="T58">ed </text:span><text:span text:style-name="T82">in</text:span><text:span text:style-name="T58"> a global variable </text:span><text:span text:style-name="T82">that may be used by a template placeholder</text:span><text:span text:style-name="T58">. </text:span><text:span text:style-name="T80">This way, </text:span><text:span text:style-name="T58">all job information </text:span><text:span text:style-name="T82">available </text:span><text:span text:style-name="T80">is written to</text:span><text:span text:style-name="T58"> a single script or description file, </text:span><text:span text:style-name="T80">and </text:span><text:span text:style-name="T58">native script variables </text:span><text:span text:style-name="T80">may be used</text:span><text:span text:style-name="T58"> in the namelist definitions.</text:span></text:p>
- <text:p text:style-name="P72"><text:span text:style-name="T71">The name of </text:span><text:span text:style-name="T82">this </text:span><text:span text:style-name="T71">variable</text:span><text:span text:style-name="T72"> </text:span><text:span text:style-name="T82">is</text:span><text:span text:style-name="T71"> generated from </text:span><text:span text:style-name="T82">its</text:span><text:span text:style-name="T71"> </text:span><text:span text:style-name="T72">respective</text:span><text:span text:style-name="T71"> file name, </text:span><text:span text:style-name="T82">like</text:span><text:span text:style-name="T71"> 'namelist.echam', by </text:span><text:span text:style-name="T81">converting all letters to upper case </text:span><text:span text:style-name="T71">(</text:span><text:span text:style-name="T81">namelist.echam →</text:span><text:span text:style-name="T71"> </text:span><text:span text:style-name="T81">NAMELIST.ECHAM</text:span><text:span text:style-name="T71">) </text:span><text:span text:style-name="T72">and </text:span><text:span text:style-name="T71">replacing non-word characters by an underscore (NAMELIST.ECHAM → NAMELIST_ECHAM).</text:span></text:p>
+ <text:p text:style-name="P72"><text:span text:style-name="T71">The name of </text:span><text:span text:style-name="T82">this </text:span><text:span text:style-name="T71">variable</text:span><text:span text:style-name="T72"> </text:span><text:span text:style-name="T82">is</text:span><text:span text:style-name="T71"> generated from </text:span><text:span text:style-name="T82">its</text:span><text:span text:style-name="T71"> </text:span><text:span text:style-name="T72">respective</text:span><text:span text:style-name="T71"> file name, </text:span><text:span text:style-name="T82">like</text:span><text:span text:style-name="T71"> 'namelist.echam', by </text:span><text:span text:style-name="T81">converting all letters to upper case </text:span><text:span text:style-name="T71">(</text:span><text:span text:style-name="T81">namelist.echam →</text:span><text:span text:style-name="T71"> </text:span><text:soft-page-break/><text:span text:style-name="T81">NAMELIST.ECHAM</text:span><text:span text:style-name="T71">) </text:span><text:span text:style-name="T72">and </text:span><text:span text:style-name="T71">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">[namelists]</text:p>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="2"/><text:span text:style-name="T174">[[namelist.echam]]</text:span></text:p>
@@ -3525,7 +3513,7 @@
<text:p text:style-name="P128"><text:s text:c="4"/>out_expname = '${EXP_ID}'</text:p>
<text:p text:style-name="P136">/</text:p>
<text:p text:style-name="P123">EOF</text:p>
- <text:p text:style-name="P73"><text:span text:style-name="T82">Note how this setup uses the native script variable 'EXP_ID' to set the </text:span><text:span text:style-name="T78">namelist </text:span><text:span text:style-name="T78">contents.</text:span></text:p>
+ <text:p text:style-name="P73"><text:span text:style-name="T82">Note how this setup uses the native script variable 'EXP_ID' to set the </text:span><text:span text:style-name="T78">namelist contents.</text:span></text:p>
<text:p text:style-name="P103"><text:span text:style-name="T58">As an option, the namelist text may be formatted using the global function 'format_namelist', </text:span><text:span text:style-name="T121">taking the namelist section as argument.</text:span></text:p>
<text:p text:style-name="P173">#! /bin/sh</text:p>
<text:p text:style-name="P191">EXP_ID=%{EXP_ID}</text:p>
@@ -3536,11 +3524,11 @@
<text:p text:style-name="P104"><text:span text:style-name="T121">Additionally, </text:span><text:span text:style-name="T120">'format_namelist' can take the name of a group within the namelist as a second argument, allowing to format groups individually.</text:span></text:p>
<text:p text:style-name="P174">#! /bin/sh</text:p>
<text:p text:style-name="P192">EXP_ID=%{EXP_ID}</text:p>
- <text:p text:style-name="P126"><text:soft-page-break/>cat > namelist.echam << EOF</text:p>
+ <text:p text:style-name="P126">cat > namelist.echam << EOF</text:p>
<text:p text:style-name="P135">%<text:span text:style-name="T208">{</text:span><text:span text:style-name="T212">format_namelist(namelists['namelist.echam']</text:span><text:span text:style-name="T325">, 'runctl'</text:span><text:span text:style-name="T212">)</text:span><text:span text:style-name="T208">}</text:span></text:p>
<text:p text:style-name="P149">EOF</text:p>
<text:p text:style-name="P58">In this special case the result will still be the same, as 'runctl' is the only group within 'namelist.echam'.</text:p>
- <text:p text:style-name="P74"><text:span text:style-name="T83">As </text:span><text:span text:style-name="T119">shown </text:span><text:span text:style-name="T83">in the example</text:span><text:span text:style-name="T119">s</text:span><text:span text:style-name="T83"> above, the script template is responsible for writing the namelist text to an actual file. </text:span><text:span text:style-name="T82">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="T82"> </text:span><text:span text:style-name="T119">will not</text:span><text:span text:style-name="T82"> enforce this. The template needs to </text:span><text:span text:style-name="T82">be set up accordingly.</text:span></text:p>
+ <text:p text:style-name="P74"><text:span text:style-name="T83">As </text:span><text:span text:style-name="T119">shown </text:span><text:span text:style-name="T83">in the example</text:span><text:span text:style-name="T119">s</text:span><text:span text:style-name="T83"> above, the script template is responsible for writing the namelist text to an actual file. </text:span><text:span text:style-name="T82">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="T82"> </text:span><text:span text:style-name="T119">will not</text:span><text:span text:style-name="T82"> enforce this. The template needs to </text:span><text:soft-page-break/><text:span text:style-name="T82">be set up accordingly.</text:span></text:p>
<text:h text:style-name="P340" text:outline-level="3"><text:bookmark-start text:name="__RefHeading___Toc3662_1790556471"/>Using native script variables in namelists<text:bookmark-end text:name="__RefHeading___Toc3662_1790556471"/></text:h>
<text:p text:style-name="P92">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="P186">[namelists]</text:p>
@@ -3556,14 +3544,14 @@
<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="P337" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2584_1114405012"/>Non-namelist configuration files<text:bookmark-end text:name="__RefHeading__2584_1114405012"/></text:h>
<text:p text:style-name="P85"><text:span text:style-name="T93">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="T91">F</text:span><text:span text:style-name="T58">or any </text:span><text:span text:style-name="T93">of these</text:span><text:span text:style-name="T92"> files, the special section variable '.use_template' m</text:span><text:span text:style-name="T106">ay</text:span><text:span text:style-name="T92"> be set to 'true', </text:span><text:span text:style-name="T106">if </text:span><text:span text:style-name="T93">the model setup provid</text:span><text:span text:style-name="T106">es</text:span><text:span text:style-name="T93"> a template '</text:span><text:span text:style-name="T29">subsection</text:span><text:span text:style-name="T93">.tmpl', </text:span><text:span text:style-name="T106">or to an arbitrary template name, replacing </text:span><text:span text:style-name="T35">subsection,</text:span><text:span text:style-name="T106"> if a template is applicable to more than one section</text:span><text:span text:style-name="T93">. This template is expanded using the subsection's variables to create a suitably formatted text. </text:span><text:span text:style-name="T94">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:soft-page-break/><text:span text:style-name="T94">D</text:span><text:span text:style-name="T58">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="T94">D</text:span><text:span text:style-name="T58">efining input files for an experiment</text:span><text:bookmark-end text:name="__RefHeading__2831_1132221942"/></text:h>
<text:p text:style-name="P89"><text:span text:style-name="T58">While the namelist files determine the model properties, the model state </text:span><text:span text:style-name="T102">also </text:span><text:span text:style-name="T58">depends on input files for initial and boundary conditions or assimilation data. These files are defined in the [files] special section.</text:span></text:p>
<text:p text:style-name="P99"><text:span text:style-name="T58">Each </text:span><text:span text:style-name="T111">sub</text:span><text:span text:style-name="T58">section may define </text:span><text:span text:style-name="T110">or override </text:span><text:span text:style-name="T58">one of two special variables:</text:span></text:p>
<text:p text:style-name="List_20_Heading"><text:span text:style-name="T58">.</text:span><text:span text:style-name="T109">base_dir</text:span></text:p>
<text:p text:style-name="P232">file names are taken to be relative to this directory</text:p>
<text:p text:style-name="List_20_Heading"><text:span text:style-name="T58">.</text:span><text:span text:style-name="T109">sub_dir</text:span></text:p>
<text:p text:style-name="P261"><text:span text:style-name="T110">file names are taken to be relative to this subdirectory of </text:span><text:span text:style-name="T58">'.base_dir'</text:span></text:p>
- <text:p text:style-name="P66"><text:span text:style-name="T156">For expanding the resulting file path</text:span><text:span text:style-name="T140">, </text:span><text:span text:style-name="T48">mkexp</text:span><text:span text:style-name="T140"> provides </text:span><text:span text:style-name="T157">two</text:span><text:span text:style-name="T156"> global function</text:span><text:span text:style-name="T157">s</text:span><text:span text:style-name="T156">:</text:span></text:p>
+ <text:p text:style-name="P66"><text:soft-page-break/><text:span text:style-name="T156">For expanding the resulting file path</text:span><text:span text:style-name="T140">, </text:span><text:span text:style-name="T48">mkexp</text:span><text:span text:style-name="T140"> provides </text:span><text:span text:style-name="T157">two</text:span><text:span text:style-name="T156"> global function</text:span><text:span text:style-name="T157">s</text:span><text:span text:style-name="T156">:</text:span></text:p>
<text:p text:style-name="P293"><text:span text:style-name="T140">get_file</text:span><text:span text:style-name="T162">(</text:span><text:span text:style-name="T50">section</text:span><text:span text:style-name="T162">, </text:span><text:span text:style-name="T50">name</text:span><text:span text:style-name="T162">)</text:span></text:p>
<text:p text:style-name="P237">returns the full path for file <text:span text:style-name="T9">name</text:span> as given in the <text:span text:style-name="T9">section</text:span> object. Note that <text:span text:style-name="T9">section</text:span> is given as object reference, but <text:span text:style-name="Variable">name</text:span> is given as a string. <text:span text:style-name="T324">If the value of </text:span><text:span text:style-name="Variable"><text:span text:style-name="T324">name</text:span></text:span><text:span text:style-name="T324"> is an absolute file name, it will override .base_dir and .sub_dir. If it contains native script variables, they are expanded to their top-level configuration values; if none is found, the native script variables are formatted as described before.</text:span></text:p>
<text:p text:style-name="P301"><text:span text:style-name="T174">get_dir</text:span>(<text:span text:style-name="T9">section</text:span><text:span text:style-name="T58">)</text:span></text:p>
@@ -3582,7 +3570,7 @@
<text:p text:style-name="P119"><text:s text:c="6"/><text:span text:style-name="T226">[[</text:span>[[<text:span text:style-name="T284">echam</text:span>]]<text:span text:style-name="T226">]]</text:span></text:p>
<text:p text:style-name="P119"><text:s text:c="8"/><text:span text:style-name="T226">[[</text:span>[[[<text:span text:style-name="T284">restart</text:span>]]]<text:span text:style-name="T226">]]</text:span></text:p>
<text:p text:style-name="P120"><text:span text:style-name="T140"><text:s text:c="10"/></text:span><text:span text:style-name="T154">restart_myexp_echam.nc = restart_</text:span><text:span text:style-name="T160">another</text:span><text:span text:style-name="T161">exp</text:span><text:span text:style-name="T154">_echam_18491231.nc</text:span></text:p>
- <text:p text:style-name="P47"><text:soft-page-break/><text:span text:style-name="T146">This</text:span><text:span text:style-name="T154"> will result in a '.run_first' </text:span><text:span text:style-name="T155">script</text:span><text:span text:style-name="T154"> tha</text:span><text:span text:style-name="T155">t gets the model state from 'anotherexp', while the '.run' script</text:span><text:span text:style-name="T154"> </text:span><text:span text:style-name="T155">uses 'myexp'.</text:span></text:p>
+ <text:p text:style-name="P47"><text:span text:style-name="T146">This</text:span><text:span text:style-name="T154"> will result in a '.run_first' </text:span><text:span text:style-name="T155">script</text:span><text:span text:style-name="T154"> tha</text:span><text:span text:style-name="T155">t gets the model state from 'anotherexp', while the '.run' script</text:span><text:span text:style-name="T154"> </text:span><text:span text:style-name="T155">uses 'myexp'.</text:span></text:p>
</office:text>
</office:body>
-</office:document>
+</office:document>
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