diff --git a/CHANGES.txt b/CHANGES.txt
index 8ef3480b597c103dcac56d7045e0db78c57469c8..7634ca43b5401029fe8ff0dd38a26fc3ae3f9e64 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -6,7 +6,7 @@ Make Experiments!
Release Changes
---------------
-Release 1.1.2
+Release 1.2.0
=============
Global
@@ -18,6 +18,9 @@ Configuration
-------------
* Fixed job config corruption while overriding namelists in another job
+* Added full access to all other job configs for every job
+* Added overriding of global variables in jobs
+* Added job settings to global variable list (same as 'JOB' section)
Templates
---------
@@ -27,7 +30,7 @@ Templates
Release 1.1.1
=============
-* Replaced by 1.1.2
+* Replaced by 1.2.0
Version 1.1.1rc2
================
diff --git a/Makefile b/Makefile
index d58d87f44592cdac3832c0448632ac1acce7de4e..28f2d8f0cc217be6d967832f0ebc04da346a9ea4 100644
--- a/Makefile
+++ b/Makefile
@@ -5,7 +5,7 @@ PYTHON = python
all:
clean:
- $(RM) -r build dist MANIFEST *.pyc
+ $(RM) -r build dist MANIFEST *.pyc __pycache__
distclean: clean
$(RM) doc/*.pdf
diff --git a/doc/mkexp.fodt b/doc/mkexp.fodt
index 80481288148d0c79bb53eb2da33464a62d41cd6c..0e776ca1bf4cffda58e670146407f08db9cdd1c8 100644
--- a/doc/mkexp.fodt
+++ b/doc/mkexp.fodt
@@ -1,28 +1,28 @@
<?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>P12DT4H23M33S</meta:editing-duration><meta:editing-cycles>184</meta:editing-cycles><meta:generator>LibreOffice/6.4.7.2$Linux_X86_64 LibreOffice_project/40$Build-2</meta:generator><meta:initial-creator>Karl-Hermann Wieners</meta:initial-creator><dc:date>2021-11-01T15:29:03.073600672</dc:date><dc:creator>Karl-Hermann Wieners</dc:creator><meta:printed-by>Karl-Hermann Wieners</meta:printed-by><meta:print-date>2015-01-20T10:55:48.576690105</meta:print-date><dc:subject>Run-script generation for earth system models</dc:subject><meta:document-statistic meta:table-count="0" meta:image-count="0" meta:object-count="0" meta:page-count="29" meta:paragraph-count="639" meta:word-count="8826" meta:character-count="56108" meta:non-whitespace-character-count="47433"/><meta:template xlink:type="simple" xlink:actuate="onRequest" xlink:title="A4" xlink:href="../../../../../../home/m221078/.config/libreoffice/4/user/template/A4.ott" meta:date="2015-01-05T17:44:27.463210655"/></office:meta>
+ <office:meta><meta:creation-date>2015-01-05T17:44:27.618344249</meta:creation-date><dc:title>Make Experiments!</dc:title><meta:editing-duration>P12DT4H34M58S</meta:editing-duration><meta:editing-cycles>188</meta:editing-cycles><meta:generator>LibreOffice/6.4.7.2$Linux_X86_64 LibreOffice_project/40$Build-2</meta:generator><meta:initial-creator>Karl-Hermann Wieners</meta:initial-creator><dc:date>2021-12-23T10:36:26.040535318</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="641" meta:word-count="8844" meta:character-count="56197" meta:non-whitespace-character-count="47505"/><meta:template xlink:type="simple" xlink:actuate="onRequest" xlink:title="A4" xlink:href="../../../../../../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">438949</config:config-item>
+ <config:config-item config:name="ViewAreaTop" config:type="long">9347</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">22124</config:config-item>
- <config:config-item config:name="ViewAreaHeight" config:type="long">15572</config:config-item>
+ <config:config-item config:name="ViewAreaWidth" config:type="long">22026</config:config-item>
+ <config:config-item config:name="ViewAreaHeight" config:type="long">18690</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">15510</config:config-item>
- <config:config-item config:name="ViewTop" config:type="long">445172</config:config-item>
+ <config:config-item config:name="ViewLeft" config:type="long">12931</config:config-item>
+ <config:config-item config:name="ViewTop" config:type="long">15081</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">438949</config:config-item>
- <config:config-item config:name="VisibleRight" config:type="long">22123</config:config-item>
- <config:config-item config:name="VisibleBottom" config:type="long">454519</config:config-item>
+ <config:config-item config:name="VisibleTop" config:type="long">9347</config:config-item>
+ <config:config-item config:name="VisibleRight" config:type="long">22024</config:config-item>
+ <config:config-item config:name="VisibleBottom" config:type="long">28035</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>
- <config:config-item config:name="ZoomFactor" config:type="short">130</config:config-item>
+ <config:config-item config:name="ZoomFactor" config:type="short">111</config:config-item>
<config:config-item config:name="IsSelectedFrame" config:type="boolean">false</config:config-item>
<config:config-item config:name="AnchoredTextOverflowLegacy" config:type="boolean">false</config:config-item>
</config:config-item-map-entry>
@@ -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">swH+/0hQLU9mZmljZWpldC00NjIwLXNlcmllcwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAQ1VQUzpIUC1PZmZpY2VqZXQtNDYyMC1zZXJpZXMAAAAWAAMA0AAAAAAAAAAIAFZUAAAkbQAASm9iRGF0YSAxCnByaW50ZXI9SFAtT2ZmaWNlamV0LTQ2MjAtc2VyaWVzCm9yaWVudGF0aW9uPVBvcnRyYWl0CmNvcGllcz0xCmNvbGxhdGU9ZmFsc2UKbWFyZ2luZGFqdXN0bWVudD0wLDAsMCwwCmNvbG9yZGVwdGg9MjQKcHNsZXZlbD0wCnBkZmRldmljZT0xCmNvbG9yZGV2aWNlPTAKUFBEQ29udGV4RGF0YQpQYWdlU2l6ZTpMZXR0ZXIASW5wdXRTbG90OkF1dG8AABIAQ09NUEFUX0RVUExFWF9NT0RFEwBEdXBsZXhNb2RlOjpVbmtub3du</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">20483402</config:config-item>
+ <config:config-item config:name="Rsid" config:type="int">20661895</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>
@@ -147,7 +147,7 @@
<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:font-independent-line-spacing="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: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"/>
@@ -1487,73 +1487,106 @@
<style:paragraph-properties style:page-number="auto"/>
<style:text-properties officeooo:rsid="00cef9a3" officeooo:paragraph-rsid="00cef9a3"/>
</style:style>
- <style:style style:name="P350" style:family="paragraph" style:parent-style-name="Heading_20_1">
+ <style:style style:name="P350" 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="P351" 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="P352" 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="P353" style:family="paragraph" style:parent-style-name="Contents_20_Heading">
+ <style:paragraph-properties fo:break-before="page"/>
+ </style:style>
+ <style:style style:name="P354" 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="P351" style:family="paragraph" style:parent-style-name="Heading_20_1">
+ <style:style style:name="P355" 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="P352" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P356" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="00b17591"/>
</style:style>
- <style:style style:name="P353" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P357" 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="P354" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P358" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="012dcfed"/>
</style:style>
- <style:style style:name="P355" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P359" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="00f3a79a"/>
</style:style>
- <style:style style:name="P356" 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="0063d022"/>
</style:style>
- <style:style style:name="P357" 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 fo:font-style="normal" officeooo:paragraph-rsid="0086f697" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P358" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P362" 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="P359" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P363" 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="P360" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P364" 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="P361" style:family="paragraph" style:parent-style-name="Heading_20_3">
+ <style:style style:name="P365" 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="P362" 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 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="P363" 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 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="P364" 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 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="P365" 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 fo:font-style="normal" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P366" 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" officeooo:paragraph-rsid="00931d47" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P367" 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" officeooo:rsid="009715be" officeooo:paragraph-rsid="00c6886f" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
- <style:style style:name="P368" 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 officeooo:rsid="0063d022" officeooo:paragraph-rsid="0063d022"/>
</style:style>
- <style:style style:name="P369" 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 officeooo:paragraph-rsid="00fb6b92"/>
</style:style>
- <style:style style:name="P370" 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 officeooo:rsid="011bfd3c" officeooo:paragraph-rsid="011bfd3c"/>
</style:style>
- <style:style style:name="P371" 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 officeooo:rsid="00c6886f" officeooo:paragraph-rsid="00c6886f"/>
</style:style>
+ <style:style style:name="P376" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:text-properties officeooo:paragraph-rsid="0056317a"/>
+ </style:style>
+ <style:style style:name="P377" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:text-properties fo:font-style="normal" style:text-underline-style="none" officeooo:rsid="0053695f" officeooo:paragraph-rsid="0053695f" style:font-style-asian="normal" style:font-style-complex="normal"/>
+ </style:style>
+ <style:style style:name="P378" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:text-properties officeooo:paragraph-rsid="00551136"/>
+ </style:style>
<style:style style:name="T1" style:family="text">
<style:text-properties officeooo:rsid="000be205"/>
</style:style>
@@ -2008,641 +2041,668 @@
<style:text-properties fo:font-style="normal" style:text-underline-style="none" officeooo:rsid="010837cd" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
<style:style style:name="T152" style:family="text">
- <style:text-properties fo:font-style="normal" style:text-underline-style="none" fo:font-weight="bold" style:font-style-asian="normal" style:font-weight-asian="bold" style:font-style-complex="normal" style:font-weight-complex="bold"/>
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- <style:text-properties officeooo:rsid="00657146"/>
+ <style:text-properties officeooo:rsid="005fe3dc"/>
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+ <style:text-properties officeooo:rsid="0063d022"/>
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- <style:text-properties officeooo:rsid="00750ebf"/>
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<style:style style:name="T347" style:family="text">
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<style:style style:name="T349" style:family="text">
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<style:style style:name="T359" style:family="text">
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<style:style style:name="T363" style:family="text">
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<style:text-properties fo:color="#c0c0c0" fo:font-weight="bold" officeooo:rsid="00cfb468" style:font-weight-asian="bold" style:font-weight-complex="bold"/>
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+ <style:text-properties officeooo:rsid="013943dd"/>
+ </style:style>
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+ </style:style>
+ <style:style style:name="T370" style:family="text">
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+ </style:style>
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<style:style style:name="Sect1" style:family="section">
<style:section-properties style:editable="false">
<style:columns fo:column-count="1" fo:column-gap="0cm"/>
@@ -2690,7 +2750,7 @@
<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">16</text:page-number><text:tab/><text:tab/><text:modification-date style:data-style-name="N84">2021-11-01</text:modification-date>, <text:modification-time style:data-style-name="N41">15:29:03</text:modification-time></text:p>
+ <text:p text:style-name="Footer"><text:page-number text:select-page="current">29</text:page-number><text:tab/><text:tab/><text:modification-date style:data-style-name="N84">2021-12-23</text:modification-date>, <text:modification-time style:data-style-name="N41">10:36:26</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"/>
@@ -2708,8 +2768,8 @@
</text:sequence-decls>
<text:p text:style-name="P349">Make Experiments!</text:p>
<text:p text:style-name="P338">Run-script generation for earth system models</text:p>
- <text:p text:style-name="P339">Release 1.1.2</text:p>
- <text:p text:style-name="P312">Karl-Hermann Wieners<text:line-break/><text:span text:style-name="T274">Max-Planck-Institut für Meteorologie<text:line-break/>Hamburg</text:span></text:p>
+ <text:p text:style-name="P339">Release 1.2.0dev</text:p>
+ <text:p text:style-name="P312">Karl-Hermann Wieners<text:line-break/><text:span text:style-name="T276">Max-Planck-Institut für Meteorologie<text:line-break/>Hamburg</text:span></text:p>
<text:table-of-content text:style-name="Sect1" text:protected="true" text:name="Table of Contents1">
<text:table-of-content-source text:outline-level="10">
<text:index-title-template text:style-name="Contents_20_Heading">Table of Contents</text:index-title-template>
@@ -2798,65 +2858,66 @@
<text:index-title text:style-name="Sect1" text:name="Table of Contents1_Head">
<text:p text:style-name="P313">Table of Contents</text:p>
</text:index-title>
- <text:p text:style-name="P315"><text:a xlink:type="simple" xlink:href="#__RefHeading__2518_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1 <text:s/>Introduction<text:tab/>3</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2520_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1 <text:s/>Example: ECHAM experiment setup<text:tab/>3</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2522_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.1 <text:s/>Experiments are defined by custom and default settings<text:tab/>3</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2524_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.2 <text:s/>Job templates are completed by settings to create scripts<text:tab/>4</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2526_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.3 <text:s/>Generating scripts only refers to the custom settings' file<text:tab/>6</text:a></text:p>
- <text:p text:style-name="P315"><text:a xlink:type="simple" xlink:href="#__RefHeading__2528_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2 <text:s/>Details on experiment definition<text:tab/>6</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2530_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.1 <text:s/>Design<text:tab/>6</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2532_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.2 <text:s/>Tools<text:tab/>7</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2534_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3 <text:s/>Format of .config files<text:tab/>9</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__1669_1438093122" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.1 <text:s/>Variables<text:tab/>9</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2536_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.2 <text:s/>Sections<text:tab/>9</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2538_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.3 <text:s/>Special variables and sections<text:tab/>10</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2540_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.4 <text:s/>Variable interpolation<text:tab/>12</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2542_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.5 <text:s/>Evaluation of interpolation<text:tab/>12</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2544_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.6 <text:s/>Special expressions<text:tab/>13</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2546_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4 <text:s/>Format of .tmpl files<text:tab/>14</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2548_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.1 <text:s/>Placeholders<text:tab/>14</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2550_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.2 <text:s/>Variables in sections<text:tab/>15</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2552_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.3 <text:s/>Expressions<text:tab/>15</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2554_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.4 <text:s/>Loops<text:tab/>16</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2556_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.5 <text:s/>Conditions<text:tab/>17</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2558_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.6 <text:s/>Comments<text:tab/>17</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc3658_1790556471" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.7 <text:s/>Block statements and block comments<text:tab/>17</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2560_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.5 <text:s/>Standard experiments<text:tab/>18</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2562_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.6 <text:s/>Standard options<text:tab/>18</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc3660_1790556471" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.6.1 <text:s/>Options set due to model configuration<text:tab/>18</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__1508_1711940803" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7 <text:s/>Generating jobs<text:tab/>19</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.1 <text:s/></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">C</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">hanging the model job list</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:tab/>19</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2568_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.2 <text:s/>Pre-defined job variables<text:tab/>20</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.3 <text:s/>Overriding namelist settings in derived jobs<text:tab/>20</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2572_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.4 <text:s/>Native script variables<text:tab/>21</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2574_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.5 <text:s/>Initializing native script variables<text:tab/>22</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2576_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.6 <text:s/>Re-generation of scripts and backup<text:tab/>22</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2564_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8 <text:s/>Standard environments<text:tab/>23</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__1883_1672291846" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9 <text:s/>Defining namelists and other configuration files<text:tab/>23</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2578_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.1 <text:s/>Formatting the namelist information<text:tab/>24</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.2 <text:s/></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">S</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">uppressing namelist </text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">files, </text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">groups, or variables</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:tab/>24</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc4310_4067847427" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.3 <text:s/>Comments in namelists<text:tab/>25</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2714_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.4 <text:s/>Using the namelist text<text:tab/>26</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc3662_1790556471" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.5 <text:s/>Using native script variables in namelists<text:tab/>27</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2584_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.6 <text:s/>Non-namelist configuration files<text:tab/>27</text:a></text:p>
- <text:p text:style-name="P316"><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10 <text:s/></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">D</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">efining input files for an experiment</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:tab/>28</text:a></text:p>
- <text:p text:style-name="P317"><text:a xlink:type="simple" xlink:href="#__RefHeading__2833_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10.1 <text:s/>Overriding input files for certain jobs<text:tab/>28</text:a></text:p>
+ <text:p text:style-name="P350"><text:a xlink:type="simple" xlink:href="#__RefHeading__2518_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1 <text:s/>Introduction<text:tab/>3</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2520_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1 <text:s/>Example: ECHAM experiment setup<text:tab/>3</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2522_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.1 <text:s/>Experiments are defined by custom and default settings<text:tab/>3</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2524_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.2 <text:s/>Job templates are completed by settings to create scripts<text:tab/>4</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2526_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.3 <text:s/>Generating scripts only refers to the custom settings' file<text:tab/>6</text:a></text:p>
+ <text:p text:style-name="P350"><text:a xlink:type="simple" xlink:href="#__RefHeading__2528_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2 <text:s/>Details on experiment definition<text:tab/>6</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2530_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.1 <text:s/>Design<text:tab/>6</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2532_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.2 <text:s/>Tools<text:tab/>7</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2534_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3 <text:s/>Format of .config files<text:tab/>9</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__1669_1438093122" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.1 <text:s/>Variables<text:tab/>9</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2536_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.2 <text:s/>Sections<text:tab/>9</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2538_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.3 <text:s/>Special variables and sections<text:tab/>10</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2540_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.4 <text:s/>Variable interpolation<text:tab/>12</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2542_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.5 <text:s/>Evaluation of interpolation<text:tab/>12</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2544_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.6 <text:s/>Special expressions<text:tab/>13</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2546_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4 <text:s/>Format of .tmpl files<text:tab/>14</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2548_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.1 <text:s/>Placeholders<text:tab/>14</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2550_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.2 <text:s/>Variables in sections<text:tab/>15</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2552_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.3 <text:s/>Expressions<text:tab/>15</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2554_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.4 <text:s/>Loops<text:tab/>16</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2556_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.5 <text:s/>Conditions<text:tab/>17</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2558_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.6 <text:s/>Comments<text:tab/>17</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc3658_1790556471" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.7 <text:s/>Block statements and block comments<text:tab/>17</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2560_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.5 <text:s/>Standard experiments<text:tab/>18</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2562_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.6 <text:s/>Standard options<text:tab/>18</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc3660_1790556471" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.6.1 <text:s/>Options set due to model configuration<text:tab/>19</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__1508_1711940803" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7 <text:s/>Generating jobs<text:tab/>19</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.1 <text:s/></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">C</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">hanging the model job list</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:tab/>19</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc4462_1592844343" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.2 <text:s/>Creating derived jobs<text:tab/>20</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2568_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.3 <text:s/>Pre-defined job variables<text:tab/>20</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.4 <text:s/></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">Overriding </text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">global</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56"> </text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">or </text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">derived</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56"> </text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">settings in jobs</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:tab/>20</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2572_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.5 <text:s/>Native script variables<text:tab/>21</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2574_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.6 <text:s/>Initializing native script variables<text:tab/>22</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2576_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7.7 <text:s/>Re-generation of scripts and backup<text:tab/>23</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2564_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8 <text:s/>Standard environments<text:tab/>23</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__1883_1672291846" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9 <text:s/>Defining namelists and other configuration files<text:tab/>24</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2578_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.1 <text:s/>Formatting the namelist information<text:tab/>24</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.2 <text:s/></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">S</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">uppressing namelist </text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">files, </text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">groups, or variables</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:tab/>25</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc4310_4067847427" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.3 <text:s/>Comments in namelists<text:tab/>25</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2714_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.4 <text:s/>Using the namelist text<text:tab/>26</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading___Toc3662_1790556471" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.5 <text:s/>Using native script variables in namelists<text:tab/>27</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2584_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.6 <text:s/>Non-namelist configuration files<text:tab/>28</text:a></text:p>
+ <text:p text:style-name="P351"><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10 <text:s/></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">D</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:span text:style-name="T56">efining input files for an experiment</text:span></text:a><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link"><text:tab/>28</text:a></text:p>
+ <text:p text:style-name="P352"><text:a xlink:type="simple" xlink:href="#__RefHeading__2833_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10.1 <text:s/>Overriding input files for certain jobs<text:tab/>28</text:a></text:p>
</text:index-body>
</text:table-of-content>
<text:p text:style-name="P86"/>
<text:h text:style-name="P314" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2518_1114405012"/>Introduction<text:bookmark-end text:name="__RefHeading__2518_1114405012"/></text:h>
<text:p text:style-name="Text_20_body">Running a numerical earth system model experiment requires a number of preparatory and processing steps like staging input data files, providing namelists and other configuration data, housekeeping duties like model-time management, post-processing and storing <text:span text:style-name="T1">of </text:span>output data. These steps are usually put into scripts or another kind of job description that is finally executed on some high-performance computing system.</text:p>
- <text:p text:style-name="P1">The <text:span text:style-name="T185">Make Experiments! (</text:span>mkexp<text:span text:style-name="T185">)</text:span> toolbox provides a generic interface to setting up such a<text:span text:style-name="T1">n experiment</text:span>. At the heart of this <text:span text:style-name="T1">lies</text:span> the so-called .config file. This is a simple <text:span text:style-name="T1">text </text:span>file that contains the model settings for your experiment in a way that is <text:span text:style-name="T1">largely </text:span>independent of the job description that is later used to run it.</text:p>
+ <text:p text:style-name="P1">The <text:span text:style-name="T187">Make Experiments! (</text:span>mkexp<text:span text:style-name="T187">)</text:span> toolbox provides a generic interface to setting up such a<text:span text:style-name="T1">n experiment</text:span>. At the heart of this <text:span text:style-name="T1">lies</text:span> the so-called .config file. This is a simple <text:span text:style-name="T1">text </text:span>file that contains the model settings for your experiment in a way that is <text:span text:style-name="T1">largely </text:span>independent of the job description that is later used to run it.</text:p>
<text:p text:style-name="P4">To make this an easy task, MPI-M's models are delivered with a number of standard experiment types. Your own .config file will chose one of these, thus inheriting their settings for use in your experiment. Typically, it will also override or amend these settings for the purpose of your experiment.</text:p>
<text:p text:style-name="P2">While the .config fil<text:span text:style-name="T2">e contains all necessary settings, there is much more to the actual job description. Therefore, the standard experiment types also provide templates (.tmpl files) for the jobs to run, that are then converted to the final job step descriptions, using the .config file settings. Besides, the .config file contains a 'jobs' section, where the job control flow and parameters of the job description itself may be adjusted, e.g. requiring more resources or disabling certain job steps.</text:span></text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2520_1114405012"/>Example: <text:span text:style-name="T3">ECHAM experiment setup</text:span><text:bookmark-end text:name="__RefHeading__2520_1114405012"/></text:h>
<text:p text:style-name="P32">To illustrate the way <text:span text:style-name="T9">mkexp</text:span> works, let us look at the way that experiments with ECHAM, MPI-M's atmospheric circulation model, are set up.</text:p>
<text:h text:style-name="P321" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2522_1114405012"/>Experiments are defined by custom and default settings<text:bookmark-end text:name="__RefHeading__2522_1114405012"/></text:h>
- <text:p text:style-name="P3">ECHAM comes with five <text:span text:style-name="T244">pre-defined </text:span>experiment types, amip-LR, amip-MR, amip-HR, sstClim-LR and sstClim-MR. <text:span text:style-name="T3">To set up an experiment based on one of these, like amip-LR, all you have to do is create your own experiment configuration file within ECHAM's run subdirectory, e.g. 'joe1234.config', setting amip-LR as experiment type and providing an experiment description with the header comment:</text:span></text:p>
+ <text:p text:style-name="P3">ECHAM comes with five <text:span text:style-name="T246">pre-defined </text:span>experiment types, amip-LR, amip-MR, amip-HR, sstClim-LR and sstClim-MR. <text:span text:style-name="T3">To set up an experiment based on one of these, like amip-LR, all you have to do is create your own experiment configuration file within ECHAM's run subdirectory, e.g. 'joe1234.config', setting amip-LR as experiment type and providing an experiment description with the header comment:</text:span></text:p>
<text:p text:style-name="P116"># Standard AMIP experiment as baseline for further experiments (LR)</text:p>
<text:p text:style-name="P116"/>
<text:p text:style-name="P116">EXP_TYPE = amip-LR</text:p>
- <text:p text:style-name="P3">For each <text:span text:style-name="T4">experiment type</text:span>, you will find a .config file in the run/standard_experiments subdirectory. For instance, <text:span text:style-name="T243">'</text:span>amip-LR.config<text:span text:style-name="T243">'</text:span> includes these settings</text:p>
+ <text:p text:style-name="P3">For each <text:span text:style-name="T4">experiment type</text:span>, you will find a .config file in the run/standard_experiments subdirectory. For instance, <text:span text:style-name="T245">'</text:span>amip-LR.config<text:span text:style-name="T245">'</text:span> includes these settings</text:p>
<text:p text:style-name="P115"># Default definitions for amip-LR experiments </text:p>
<text:p text:style-name="P114"><text:soft-page-break/></text:p>
<text:p text:style-name="P114">RES = 63 </text:p>
@@ -2870,58 +2931,58 @@
<text:p text:style-name="P117"><text:s text:c="2"/>[[namelist.jsbach]] </text:p>
<text:p text:style-name="P117"><text:s text:c="4"/>[[[jsbach_ctl]]] </text:p>
<text:p text:style-name="P117"><text:s text:c="6"/>use_dynveg <text:s/>= false </text:p>
- <text:p text:style-name="P5">As you can see, settings are simple name = value pairs that may be organized in sections. Sections are defined by a bracketed section name. They may contain subsections, where the number of brackets define<text:span text:style-name="T183">s</text:span> the hierarchy depth. The pre-defined sections [namelists] and [jobs] are used for special purposes within <text:span text:style-name="T9">mkexp</text:span>.</text:p>
- <text:p text:style-name="P5"><text:span text:style-name="T243">Some s</text:span>ettings apply to all <text:span text:style-name="T243">ECHAM </text:span>experiment types. <text:span text:style-name="T243">They</text:span> go into a file named <text:span text:style-name="T243">'</text:span>DEFAULT.config<text:span text:style-name="T243">'</text:span>. <text:span text:style-name="T9">mkexp</text:span> will <text:span text:style-name="T243">always </text:span>read this file <text:span text:style-name="T243">first, </text:span>before applying <text:span text:style-name="T243">any </text:span>settings from <text:span text:style-name="T243">a specific experiment type like 'amip-LR.config'.</text:span> <text:span text:style-name="T243">Such settings might be default paths for input data, as in</text:span></text:p>
- <text:p text:style-name="P121"># <text:span text:style-name="T243">Default definitions for all </text:span>ECHAM experiment<text:span text:style-name="T243">s</text:span></text:p>
+ <text:p text:style-name="P5">As you can see, settings are simple name = value pairs that may be organized in sections. Sections are defined by a bracketed section name. They may contain subsections, where the number of brackets define<text:span text:style-name="T185">s</text:span> the hierarchy depth. The pre-defined sections [namelists] and [jobs] are used for special purposes within <text:span text:style-name="T9">mkexp</text:span>.</text:p>
+ <text:p text:style-name="P5"><text:span text:style-name="T245">Some s</text:span>ettings apply to all <text:span text:style-name="T245">ECHAM </text:span>experiment types. <text:span text:style-name="T245">They</text:span> go into a file named <text:span text:style-name="T245">'</text:span>DEFAULT.config<text:span text:style-name="T245">'</text:span>. <text:span text:style-name="T9">mkexp</text:span> will <text:span text:style-name="T245">always </text:span>read this file <text:span text:style-name="T245">first, </text:span>before applying <text:span text:style-name="T245">any </text:span>settings from <text:span text:style-name="T245">a specific experiment type like 'amip-LR.config'.</text:span> <text:span text:style-name="T245">Such settings might be default paths for input data, as in</text:span></text:p>
+ <text:p text:style-name="P121"># <text:span text:style-name="T245">Default definitions for all </text:span>ECHAM experiment<text:span text:style-name="T245">s</text:span></text:p>
<text:p text:style-name="P121"/>
<text:p text:style-name="P121">ATMO_INPUT_ROOT = /pool/data/ECHAM6/input/r0004 </text:p>
<text:p text:style-name="P121">LAND_INPUT_ROOT = /pool/data/JSBACH/input/r0004 </text:p>
<text:p text:style-name="P6">The final configuration is then merged from all of these three sources, where the experiment configuration may override <text:span text:style-name="T53">or amend </text:span>settings from the experiment type, and the type config may in turn change the model defaults.</text:p>
<text:h text:style-name="P322" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2524_1114405012"/>Job templates are completed by settings to create scripts<text:bookmark-end text:name="__RefHeading__2524_1114405012"/></text:h>
- <text:p text:style-name="P6"><text:span text:style-name="T243">Now the experiment configuration is finalized, the </text:span>settings are used to fill in <text:span text:style-name="T243">a kind of job description forms, so called </text:span><text:span text:style-name="T9">templates</text:span><text:span text:style-name="T243">, </text:span>from which eventually the <text:span text:style-name="T243">actual </text:span>job description files are created. As the structure of<text:span text:style-name="T243"> </text:span>jobs is largely independent of the model resolution, all amip- experiment types share the same set of template files. One of them is <text:span text:style-name="T264">'</text:span>amip.run.tmpl<text:span text:style-name="T264">'</text:span>, also within the run/standard_experiments subdirectory. <text:span text:style-name="T6">The excerpt below shows that t</text:span>his looks mostly like a shell script, but contains <text:span text:style-name="T184">placeholders</text:span> that are filled using the .config file information:</text:p>
+ <text:p text:style-name="P6"><text:span text:style-name="T245">Now the experiment configuration is finalized, the </text:span>settings are used to fill in <text:span text:style-name="T245">a kind of job description forms, so called </text:span><text:span text:style-name="T9">templates</text:span><text:span text:style-name="T245">, </text:span>from which eventually the <text:span text:style-name="T245">actual </text:span>job description files are created. As the structure of<text:span text:style-name="T245"> </text:span>jobs is largely independent of the model resolution, all amip- experiment types share the same set of template files. One of them is <text:span text:style-name="T266">'</text:span>amip.run.tmpl<text:span text:style-name="T266">'</text:span>, also within the run/standard_experiments subdirectory. <text:span text:style-name="T6">The excerpt below shows that t</text:span>his looks mostly like a shell script, but contains <text:span text:style-name="T186">placeholders</text:span> that are filled using the .config file information:</text:p>
<text:p text:style-name="P121">#! /bin/bash</text:p>
<text:p text:style-name="P121"/>
<text:p text:style-name="P121"># Job file to run ECHAM 6 </text:p>
<text:p text:style-name="P121"/>
- <text:p text:style-name="P127">EXP=<text:span text:style-name="T168">%{EXP_ID}</text:span> # experiment identifier </text:p>
+ <text:p text:style-name="P127">EXP=<text:span text:style-name="T170">%{EXP_ID}</text:span> # experiment identifier </text:p>
<text:p text:style-name="P121"/>
- <text:p text:style-name="P121">RES=<text:span text:style-name="T168">%{RES}</text:span> <text:span text:style-name="T184"># experiment truncation</text:span></text:p>
+ <text:p text:style-name="P121">RES=<text:span text:style-name="T170">%{RES}</text:span> <text:span text:style-name="T186"># experiment truncation</text:span></text:p>
<text:p text:style-name="P121"/>
<text:p text:style-name="P127"># absolute paths to directories with initial data: </text:p>
- <text:p text:style-name="P127">ATMO_DATA=<text:span text:style-name="T168">%{ATMO_INPUT_ROOT}</text:span> </text:p>
+ <text:p text:style-name="P127">ATMO_DATA=<text:span text:style-name="T170">%{ATMO_INPUT_ROOT}</text:span> </text:p>
<text:p text:style-name="P127">ATMO_MAP_DATA=$ATMO_DATA/T${RES} </text:p>
<text:p text:style-name="P127"><text:soft-page-break/></text:p>
<text:p text:style-name="P127"># absolute path to directory with initial data for JSBACH: </text:p>
- <text:p text:style-name="P127">LAND_MAP_DATA=<text:span text:style-name="T168">%{LAND_INPUT_ROOT}</text:span>/T${RES} </text:p>
+ <text:p text:style-name="P127">LAND_MAP_DATA=<text:span text:style-name="T170">%{LAND_INPUT_ROOT}</text:span>/T${RES} </text:p>
<text:p text:style-name="P122"/>
<text:p text:style-name="P122"># </text:p>
<text:p text:style-name="P121"># ECHAM6 namelist </text:p>
<text:p text:style-name="P121"># </text:p>
<text:p text:style-name="P121">cat > namelist.echam << EOF </text:p>
- <text:p text:style-name="P121"><text:span text:style-name="T168">%{NAMELIST_ECHAM}</text:span> </text:p>
+ <text:p text:style-name="P121"><text:span text:style-name="T170">%{NAMELIST_ECHAM}</text:span> </text:p>
<text:p text:style-name="P121">EOF </text:p>
<text:p text:style-name="P121"/>
<text:p text:style-name="P121"># </text:p>
<text:p text:style-name="P121"># JSBACH namelist</text:p>
<text:p text:style-name="P121"># </text:p>
<text:p text:style-name="P121">cat > namelist.jsbach << EOF </text:p>
- <text:p text:style-name="P121"><text:span text:style-name="T168">%{NAMELIST_JSBACH}</text:span> </text:p>
+ <text:p text:style-name="P121"><text:span text:style-name="T170">%{NAMELIST_JSBACH}</text:span> </text:p>
<text:p text:style-name="P121">EOF </text:p>
- <text:p text:style-name="P7"><text:span text:style-name="T244">T</text:span>h<text:span text:style-name="T244">e</text:span>se <text:span text:style-name="T244">'</text:span>%{...}<text:span text:style-name="T244">'</text:span> construct<text:span text:style-name="T7">s</text:span> correspond to the configuration settings shown in the previous section. The value for <text:span text:style-name="T264">the setting </text:span>given <text:span text:style-name="T244">by the variable name between '%{' and '}'</text:span> is pasted into the template, replacing the placeholder. The special names 'NAMELIST_ECHAM' and 'NAMELIST_JSBACH' contain the contents of the 'namelists' subsections, with each setting taken to be a Fortran namelist setting, and formatted accordingly. 'EXP_ID' is taken to be the base filename of the experiment's .config file. The result of this operation is then written to the final job script, in our case <text:span text:style-name="T244">'</text:span>joe1234.run<text:span text:style-name="T244">'</text:span>:</text:p>
+ <text:p text:style-name="P7"><text:span text:style-name="T246">T</text:span>h<text:span text:style-name="T246">e</text:span>se <text:span text:style-name="T246">'</text:span>%{...}<text:span text:style-name="T246">'</text:span> construct<text:span text:style-name="T7">s</text:span> correspond to the configuration settings shown in the previous section. The value for <text:span text:style-name="T266">the setting </text:span>given <text:span text:style-name="T246">by the variable name between '%{' and '}'</text:span> is pasted into the template, replacing the placeholder. The special names 'NAMELIST_ECHAM' and 'NAMELIST_JSBACH' contain the contents of the 'namelists' subsections, with each setting taken to be a Fortran namelist setting, and formatted accordingly. 'EXP_ID' is taken to be the base filename of the experiment's .config file. The result of this operation is then written to the final job script, in our case <text:span text:style-name="T246">'</text:span>joe1234.run<text:span text:style-name="T246">'</text:span>:</text:p>
<text:p text:style-name="P122">#! /bin/bash</text:p>
<text:p text:style-name="P122"/>
<text:p text:style-name="P122"># Job file to run ECHAM 6 </text:p>
<text:p text:style-name="P122"/>
- <text:p text:style-name="P127">EXP=<text:span text:style-name="T168">joe1234</text:span> # experiment identifier </text:p>
+ <text:p text:style-name="P127">EXP=<text:span text:style-name="T170">joe1234</text:span> # experiment identifier </text:p>
<text:p text:style-name="P122"/>
- <text:p text:style-name="P122">RES=<text:span text:style-name="T169">63</text:span><text:span text:style-name="T6"> # experiment truncation</text:span></text:p>
+ <text:p text:style-name="P122">RES=<text:span text:style-name="T171">63</text:span><text:span text:style-name="T6"> # experiment truncation</text:span></text:p>
<text:p text:style-name="P122"/>
<text:p text:style-name="P122">#<text:span text:style-name="T6"> absolute paths to directories with initial data: </text:span></text:p>
- <text:p text:style-name="P127">ATMO_DATA=<text:span text:style-name="T170">/pool/data/ECHAM6/input/r0004</text:span><text:span text:style-name="T5"> </text:span></text:p>
+ <text:p text:style-name="P127">ATMO_DATA=<text:span text:style-name="T172">/pool/data/ECHAM6/input/r0004</text:span><text:span text:style-name="T5"> </text:span></text:p>
<text:p text:style-name="P127">ATMO_MAP_DATA=$ATMO_DATA/T${RES} </text:p>
<text:p text:style-name="P127"/>
<text:p text:style-name="P127"># absolute path to directory with initial data for JSBACH: </text:p>
- <text:p text:style-name="P127">LAND_MAP_DATA=<text:span text:style-name="T170">/pool/data/JSBACH/input/r0004</text:span>/T${RES} </text:p>
+ <text:p text:style-name="P127">LAND_MAP_DATA=<text:span text:style-name="T172">/pool/data/JSBACH/input/r0004</text:span>/T${RES} </text:p>
<text:p text:style-name="P127"/>
<text:p text:style-name="P127">#</text:p>
<text:p text:style-name="P122"># ECHAM6 namelist </text:p>
@@ -2940,24 +3001,24 @@
<text:p text:style-name="P130"><text:s text:c="4"/>use_dynveg = .false.</text:p>
<text:p text:style-name="P130"><text:soft-page-break/>/</text:p>
<text:p text:style-name="P122">EOF </text:p>
- <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2526_1114405012"/><text:span text:style-name="T244">G</text:span>enerat<text:span text:style-name="T244">ing scripts only refers to the custom settings' file</text:span><text:bookmark-end text:name="__RefHeading__2526_1114405012"/></text:h>
- <text:p text:style-name="P13"><text:span text:style-name="T243">So, as soon as</text:span> <text:span text:style-name="T243">you have set up '</text:span>joe1234.config<text:span text:style-name="T243">'</text:span>, you may create the job scripts that are needed to run your experiment. Still within ECHAM's <text:span text:style-name="T245">'</text:span>run<text:span text:style-name="T245">'</text:span> subdirectory, type the following into your terminal:</text:p>
+ <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2526_1114405012"/><text:span text:style-name="T246">G</text:span>enerat<text:span text:style-name="T246">ing scripts only refers to the custom settings' file</text:span><text:bookmark-end text:name="__RefHeading__2526_1114405012"/></text:h>
+ <text:p text:style-name="P13"><text:span text:style-name="T245">So, as soon as</text:span> <text:span text:style-name="T245">you have set up '</text:span>joe1234.config<text:span text:style-name="T245">'</text:span>, you may create the job scripts that are needed to run your experiment. Still within ECHAM's <text:span text:style-name="T247">'</text:span>run<text:span text:style-name="T247">'</text:span> subdirectory, type the following into your terminal:</text:p>
<text:p text:style-name="Preformatted_20_Text">../util/mkexp/mkexp joe1234.config</text:p>
- <text:p text:style-name="P14">This will <text:span text:style-name="T185">read all configuration information and </text:span>create all job scripts that are defined within your experiment's setup, <text:span text:style-name="T185">using their respective templates as shown in the previous section</text:span>. <text:span text:style-name="T9">mkexp</text:span> will put these <text:span text:style-name="T185">scripts </text:span>in <text:span text:style-name="T185">a common</text:span> directory defined by the .config variable <text:span text:style-name="T245">'</text:span>SCRIPT_DIR<text:span text:style-name="T245">'</text:span>, and <text:span text:style-name="T245">print</text:span> the name of this directory on your terminal.</text:p>
- <text:h text:style-name="P318" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2528_1114405012"/>Details on <text:span text:style-name="T263">experiment</text:span> <text:span text:style-name="T263">definition</text:span><text:bookmark-end text:name="__RefHeading__2528_1114405012"/></text:h>
+ <text:p text:style-name="P14">This will <text:span text:style-name="T187">read all configuration information and </text:span>create all job scripts that are defined within your experiment's setup, <text:span text:style-name="T187">using their respective templates as shown in the previous section</text:span>. <text:span text:style-name="T9">mkexp</text:span> will put these <text:span text:style-name="T187">scripts </text:span>in <text:span text:style-name="T187">a common</text:span> directory defined by the .config variable <text:span text:style-name="T247">'</text:span>SCRIPT_DIR<text:span text:style-name="T247">'</text:span>, and <text:span text:style-name="T247">print</text:span> the name of this directory on your terminal.</text:p>
+ <text:h text:style-name="P318" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2528_1114405012"/>Details on <text:span text:style-name="T265">experiment</text:span> <text:span text:style-name="T265">definition</text:span><text:bookmark-end text:name="__RefHeading__2528_1114405012"/></text:h>
<text:p text:style-name="P15">With the introductory example of the previous section in mind, this section will give some more detailed information on specific aspects of <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T56">.</text:span></text:p>
<text:h text:style-name="P340" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2530_1114405012"/>Design<text:bookmark-end text:name="__RefHeading__2530_1114405012"/></text:h>
- <text:p text:style-name="P34">Experiment definition with <text:span text:style-name="T9">mkexp</text:span> <text:span text:style-name="T217">is organized</text:span> <text:span text:style-name="T217">in</text:span> three levels.</text:p>
- <text:p text:style-name="P34">The first level is the <text:span text:style-name="T9">mkexp</text:span> toolbox. It provides the front end to create an executable job description from a generic experiment configuration, <text:span text:style-name="T216">but does not contain any model specific information. Instead a basic set of conventions is defined that should be applicable to a very large range of model systems. When this document uses the term </text:span><text:span text:style-name="T18">mkexp</text:span><text:span text:style-name="T62">, it refers to this system level.</text:span></text:p>
- <text:p text:style-name="P34"><text:span text:style-name="T216">At a second level, a model needs to provide a number of files containing the information needed by </text:span><text:span text:style-name="T17">mkexp</text:span><text:span text:style-name="T216">: the required job steps and their interaction, the basic contents of job scripts, model specific information, and building blocks that may be combined to define a specific experiment. This is called the </text:span><text:span text:style-name="T17">model setup</text:span><text:span text:style-name="T61">. The files must maintain the naming conventions prescribed by </text:span><text:span text:style-name="T17">mkexp</text:span><text:span text:style-name="T61">.</text:span></text:p>
+ <text:p text:style-name="P34">Experiment definition with <text:span text:style-name="T9">mkexp</text:span> <text:span text:style-name="T219">is organized</text:span> <text:span text:style-name="T219">in</text:span> three levels.</text:p>
+ <text:p text:style-name="P34">The first level is the <text:span text:style-name="T9">mkexp</text:span> toolbox. It provides the front end to create an executable job description from a generic experiment configuration, <text:span text:style-name="T218">but does not contain any model specific information. Instead a basic set of conventions is defined that should be applicable to a very large range of model systems. When this document uses the term </text:span><text:span text:style-name="T18">mkexp</text:span><text:span text:style-name="T62">, it refers to this system level.</text:span></text:p>
+ <text:p text:style-name="P34"><text:span text:style-name="T218">At a second level, a model needs to provide a number of files containing the information needed by </text:span><text:span text:style-name="T17">mkexp</text:span><text:span text:style-name="T218">: the required job steps and their interaction, the basic contents of job scripts, model specific information, and building blocks that may be combined to define a specific experiment. This is called the </text:span><text:span text:style-name="T17">model setup</text:span><text:span text:style-name="T61">. The files must maintain the naming conventions prescribed by </text:span><text:span text:style-name="T17">mkexp</text:span><text:span text:style-name="T61">.</text:span></text:p>
<text:p text:style-name="P35"><text:span text:style-name="T56">Finally, the third level is the actual experiment definition. Here the user decides which of the building blocks from the previous level are needed, and </text:span><text:span text:style-name="T93">defines</text:span><text:span text:style-name="T56"> experiment specific settings that override or amend the information from the model setup. It is also essential to supply an experiment description and a – possibly unique – experiment identifier. All this is called the </text:span><text:span text:style-name="T9">user setup</text:span><text:span text:style-name="T56">.</text:span></text:p>
<text:p text:style-name="P36"><text:span text:style-name="T56">All levels should make a clear distinction </text:span><text:span text:style-name="T63">between </text:span><text:span text:style-name="T56">the .config files, containing the experiment's configuration information, </text:span><text:span text:style-name="T63">and </text:span><text:span text:style-name="T56">the .tmpl files, containing the actual job description and job control syntax.</text:span></text:p>
<text:h text:style-name="P341" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2532_1114405012"/><text:soft-page-break/>Tools<text:bookmark-end text:name="__RefHeading__2532_1114405012"/></text:h>
- <text:p text:style-name="P87"><text:span text:style-name="T185">The </text:span><text:span text:style-name="T32">mkexp</text:span><text:span text:style-name="T185"> package provides a number of tools for working with script configurations and setups.</text:span></text:p>
- <text:p text:style-name="Preformatted_20_List_20_Heading">mkexp <text:span text:style-name="T293">[-m] [-g] </text:span><text:span text:style-name="T23">file</text:span><text:span text:style-name="T74">.</text:span><text:span text:style-name="T56">config</text:span> [<text:span text:style-name="T9">name</text:span>=<text:span text:style-name="T9">value</text:span> ...]</text:p>
- <text:p text:style-name="P239"><text:span text:style-name="T185">This is the main tool for generating an experiment setup. It </text:span>takes <text:span text:style-name="T246">the given</text:span> <text:span text:style-name="T246">user setup</text:span> and <text:span text:style-name="T265">the model setup that is referenced by the user setup </text:span>to generate <text:span text:style-name="T246">the</text:span> <text:span text:style-name="T246">job description files or</text:span> scripts that <text:span text:style-name="T265">are required to run a model experiment as specified in </text:span><text:span text:style-name="T21">file.</text:span><text:span text:style-name="T74">config</text:span><text:span text:style-name="T246">.</text:span></text:p>
+ <text:p text:style-name="P87"><text:span text:style-name="T187">The </text:span><text:span text:style-name="T32">mkexp</text:span><text:span text:style-name="T187"> package provides a number of tools for working with script configurations and setups.</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_List_20_Heading">mkexp <text:span text:style-name="T295">[-m] [-g] </text:span><text:span text:style-name="T23">file</text:span><text:span text:style-name="T74">.</text:span><text:span text:style-name="T56">config</text:span> [<text:span text:style-name="T9">name</text:span>=<text:span text:style-name="T9">value</text:span> ...]</text:p>
+ <text:p text:style-name="P239"><text:span text:style-name="T187">This is the main tool for generating an experiment setup. It </text:span>takes <text:span text:style-name="T248">the given</text:span> <text:span text:style-name="T248">user setup</text:span> and <text:span text:style-name="T267">the model setup that is referenced by the user setup </text:span>to generate <text:span text:style-name="T248">the</text:span> <text:span text:style-name="T248">job description files or</text:span> scripts that <text:span text:style-name="T267">are required to run a model experiment as specified in </text:span><text:span text:style-name="T21">file.</text:span><text:span text:style-name="T74">config</text:span><text:span text:style-name="T248">.</text:span></text:p>
<text:p text:style-name="P243">When running, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T56"> creates three directories, one each for the job scripts, run-time data, and output data, as defined by the setup. The names of these are printed, plus warnings if they already exist.</text:span></text:p>
- <text:p text:style-name="P242">mkexp<text:span text:style-name="T56"> allows to override </text:span><text:span text:style-name="T72">or amend </text:span><text:span text:style-name="T56">the .config file settings on the command line </text:span><text:span text:style-name="T72">by defining or re-defining a variable </text:span><text:span text:style-name="T247">name</text:span><text:span text:style-name="T72"> set to </text:span><text:span text:style-name="T247">value</text:span><text:span text:style-name="T72">. Section variables are referenced as </text:span><text:span text:style-name="T247">sectionname</text:span><text:span text:style-name="T72">.</text:span><text:span text:style-name="T247">variablename</text:span><text:span text:style-name="T72">. Any periods in the variable name have to be duplicated, e.g. to set '.remove' in section 'jobs' to 'post', use 'jobs...remove=post'. Note that three periods will always be read as '.' followed by '..', thus it is not possible to use variable names th</text:span><text:span text:style-name="T94">at</text:span><text:span text:style-name="T72"> </text:span><text:span text:style-name="T247">end</text:span><text:span text:style-name="T72"> </text:span><text:span text:style-name="T94">i</text:span><text:span text:style-name="T72">n a period.</text:span></text:p>
+ <text:p text:style-name="P242">mkexp<text:span text:style-name="T56"> allows to override </text:span><text:span text:style-name="T72">or amend </text:span><text:span text:style-name="T56">the .config file settings on the command line </text:span><text:span text:style-name="T72">by defining or re-defining a variable </text:span><text:span text:style-name="T249">name</text:span><text:span text:style-name="T72"> set to </text:span><text:span text:style-name="T249">value</text:span><text:span text:style-name="T72">. Section variables are referenced as </text:span><text:span text:style-name="T249">sectionname</text:span><text:span text:style-name="T72">.</text:span><text:span text:style-name="T249">variablename</text:span><text:span text:style-name="T72">. Any periods in the variable name have to be duplicated, e.g. to set '.remove' in section 'jobs' to 'post', use 'jobs...remove=post'. Note that three periods will always be read as '.' followed by '..', thus it is not possible to use variable names th</text:span><text:span text:style-name="T94">at</text:span><text:span text:style-name="T72"> </text:span><text:span text:style-name="T249">end</text:span><text:span text:style-name="T72"> </text:span><text:span text:style-name="T94">i</text:span><text:span text:style-name="T72">n a period.</text:span></text:p>
<text:p text:style-name="P259"><text:span text:style-name="T72">W</text:span><text:span text:style-name="T56">hen given the '-m' or '--no-make-dirs' option, only the </text:span><text:span text:style-name="T73">script</text:span><text:span text:style-name="T56"> directory is created while creation of the </text:span><text:span text:style-name="T73">run-time and outpu</text:span><text:span text:style-name="T56">t directories is skipped.</text:span></text:p>
<text:p text:style-name="P261">With '-g' or '--getexp', instead of a .config file, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T56"> expects a dump generated by </text:span><text:span text:style-name="T9">getexp -vv</text:span><text:span text:style-name="T56"> (see below). The experiment setup is regenerated from this dump, overriding any model setup.</text:span></text:p>
<text:p text:style-name="P278"><text:span text:style-name="T72">g</text:span><text:span text:style-name="T56">etexp [-v ...] </text:span><text:span text:style-name="T105">[-R]</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T111">[-k </text:span><text:span text:style-name="T39">key</text:span><text:span text:style-name="T111">] </text:span><text:span text:style-name="T9">file</text:span><text:span text:style-name="T56">.config [</text:span><text:span text:style-name="T9">name</text:span><text:span text:style-name="T56">=</text:span><text:span text:style-name="T9">value ...</text:span><text:span text:style-name="T56">]</text:span></text:p>
@@ -2965,34 +3026,34 @@
<text:p text:style-name="P244"><text:span text:style-name="T56">When given the '-v' </text:span><text:span text:style-name="T105">or '--</text:span><text:span text:style-name="T56">verbose</text:span><text:span text:style-name="T105">'</text:span><text:span text:style-name="T56"> option, all </text:span><text:span text:style-name="T9">global</text:span><text:span text:style-name="T56"> configuration variables and their values are printed in alphabetical order. </text:span><text:span text:style-name="T105">When given twice, the whole configuration is dumped </text:span><text:span text:style-name="T110">to the screen</text:span><text:span text:style-name="T105">. </text:span><text:span text:style-name="T110">Save this to a file for use with </text:span><text:span text:style-name="T38">mkexp -g</text:span><text:span text:style-name="T110">.</text:span></text:p>
<text:p text:style-name="P230">When given the '-R' or '--readme' option, the header comment text is printed.</text:p>
<text:p text:style-name="P264">When given the '-k' or '--key' option, only the configured value for <text:span text:style-name="T9">key</text:span> is printed. Section variables may be referenced as described above for <text:span text:style-name="T9">name</text:span>=<text:span text:style-name="T9">value</text:span><text:span text:style-name="T56">. </text:span><text:span text:style-name="T113">This option may be used more than once to print additional values.</text:span><text:span text:style-name="T56"> </text:span></text:p>
- <text:p text:style-name="P290">diffexp <text:span text:style-name="T22">file</text:span><text:span text:style-name="T23">1</text:span><text:span text:style-name="T248">.config </text:span><text:span text:style-name="T22">file2</text:span><text:span text:style-name="T73">.</text:span><text:span text:style-name="T74">config</text:span></text:p>
+ <text:p text:style-name="P290">diffexp <text:span text:style-name="T22">file</text:span><text:span text:style-name="T23">1</text:span><text:span text:style-name="T250">.config </text:span><text:span text:style-name="T22">file2</text:span><text:span text:style-name="T73">.</text:span><text:span text:style-name="T74">config</text:span></text:p>
<text:p text:style-name="P227">For an easy comparison of the whole set of generated scripts for two different experiments, this tool takes the directories defined in each configuration, locates the job scripts corresponding to each other (e.g. exp0001.run and exp0002.run), equalizes all occurrences of the experiment name in the scripts and then uses the diff tool to show differences. The environment variable 'DIFF' may be set to an alternative tool to be called instead.</text:p>
- <text:p text:style-name="P279">rmexp <text:span text:style-name="T24">file</text:span><text:span text:style-name="T249">.config</text:span><text:span text:style-name="T75"> [</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T75">]</text:span></text:p>
- <text:p text:style-name="P246">This allows <text:span text:style-name="T252">interactive </text:span>remov<text:span text:style-name="T252">al for </text:span>all data of an experiment without having to <text:soft-page-break/>deal with path names, as these are read from the configuration.</text:p>
- <text:p text:style-name="P292"><text:span text:style-name="T294">cp</text:span>exp <text:span text:style-name="T329">[-n] </text:span><text:span text:style-name="T24">file</text:span><text:span text:style-name="T249">.config</text:span><text:span text:style-name="T75"> </text:span><text:span text:style-name="T37">new_name</text:span><text:span text:style-name="T106"> </text:span><text:span text:style-name="T75">[</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T75">]</text:span></text:p>
- <text:p text:style-name="P262"><text:span text:style-name="T295">Replicates all data </text:span>of an experiment <text:span text:style-name="T294">to a new experiment name; also updates text files by rewriting references to the old name</text:span>. <text:span text:style-name="T329">With '-n', shows what would be done instead of actually doing it</text:span></text:p>
- <text:p text:style-name="P293"><text:span text:style-name="T304">du</text:span>exp <text:span text:style-name="T24">file</text:span><text:span text:style-name="T249">.config</text:span><text:span text:style-name="T75"> [</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T75">]</text:span></text:p>
+ <text:p text:style-name="P279">rmexp <text:span text:style-name="T24">file</text:span><text:span text:style-name="T251">.config</text:span><text:span text:style-name="T75"> [</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T75">]</text:span></text:p>
+ <text:p text:style-name="P246">This allows <text:span text:style-name="T254">interactive </text:span>remov<text:span text:style-name="T254">al for </text:span>all data of an experiment without having to <text:soft-page-break/>deal with path names, as these are read from the configuration.</text:p>
+ <text:p text:style-name="P292"><text:span text:style-name="T296">cp</text:span>exp <text:span text:style-name="T331">[-n] </text:span><text:span text:style-name="T24">file</text:span><text:span text:style-name="T251">.config</text:span><text:span text:style-name="T75"> </text:span><text:span text:style-name="T37">new_name</text:span><text:span text:style-name="T106"> </text:span><text:span text:style-name="T75">[</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T75">]</text:span></text:p>
+ <text:p text:style-name="P262"><text:span text:style-name="T297">Replicates all data </text:span>of an experiment <text:span text:style-name="T296">to a new experiment name; also updates text files by rewriting references to the old name</text:span>. <text:span text:style-name="T331">With '-n', shows what would be done instead of actually doing it</text:span></text:p>
+ <text:p text:style-name="P293"><text:span text:style-name="T306">du</text:span>exp <text:span text:style-name="T24">file</text:span><text:span text:style-name="T251">.config</text:span><text:span text:style-name="T75"> [</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T75">]</text:span></text:p>
<text:p text:style-name="P266"><text:span text:style-name="T116">Shows disk usage for all data that has been created by</text:span><text:span text:style-name="T75"> </text:span><text:span text:style-name="T116">an</text:span><text:span text:style-name="T75"> experiment.</text:span></text:p>
- <text:p text:style-name="P295"><text:span text:style-name="T315">upexp </text:span><text:span text:style-name="Variable"><text:span text:style-name="T315">file</text:span></text:span><text:span text:style-name="T315">.config </text:span><text:span text:style-name="T75">[</text:span><text:span text:style-name="Variable">name</text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="Variable">value</text:span><text:span text:style-name="Variable"><text:span text:style-name="T24"> </text:span></text:span><text:span text:style-name="T24">...</text:span><text:span text:style-name="T75">]</text:span></text:p>
+ <text:p text:style-name="P295"><text:span text:style-name="T317">upexp </text:span><text:span text:style-name="Variable"><text:span text:style-name="T317">file</text:span></text:span><text:span text:style-name="T317">.config </text:span><text:span text:style-name="T75">[</text:span><text:span text:style-name="Variable">name</text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="Variable">value</text:span><text:span text:style-name="Variable"><text:span text:style-name="T24"> </text:span></text:span><text:span text:style-name="T24">...</text:span><text:span text:style-name="T75">]</text:span></text:p>
<text:p text:style-name="P232">Update generated scripts for the given experiment with the same mkexp version, environment and command line, as saved in the corresponding 'update' script.</text:p>
- <text:p text:style-name="P294">edit<text:span text:style-name="T314">exp</text:span> [<text:span text:style-name="Variable">file</text:span>]</text:p>
- <text:p text:style-name="P267">Reads <text:span text:style-name="T313">the</text:span> update script <text:span text:style-name="Variable">file</text:span> ('update' by default) and <text:span text:style-name="T313">launches a program to edit the </text:span>corresponding config file. <text:span text:style-name="T313">The program is taken from the environment variables 'VISUAL' or 'EDITOR' if defined, otherwise </text:span><text:span text:style-name="T42">vi</text:span><text:span text:style-name="T313"> is launched.</text:span></text:p>
- <text:p text:style-name="P292"><text:span text:style-name="T312">getconfig</text:span> <text:span text:style-name="T312">[</text:span><text:span text:style-name="Variable">file</text:span><text:span text:style-name="T249">]</text:span></text:p>
- <text:p text:style-name="P267">Documentation tool for experiments that were created using command line assignments. Reads <text:span text:style-name="T315">the</text:span> update script <text:span text:style-name="Variable">file</text:span> ('update' by default) and prints the corresponding config file with command line settings from the update script included.</text:p>
- <text:p text:style-name="Preformatted_20_List_20_Heading"><text:span text:style-name="T322">setconfig</text:span> <text:span text:style-name="T323">[-d </text:span><text:span text:style-name="Variable"><text:span text:style-name="T323">key</text:span></text:span><text:span text:style-name="T323">] [-H </text:span><text:span text:style-name="Variable"><text:span text:style-name="T323">text</text:span></text:span><text:span text:style-name="T323">] [-a </text:span><text:span text:style-name="Variable"><text:span text:style-name="T324">file</text:span></text:span>.<text:span text:style-name="T324">config] [</text:span><text:span text:style-name="Variable">file</text:span>.<text:span text:style-name="T324">config</text:span><text:span text:style-name="T75"> [</text:span><text:span text:style-name="Variable"><text:span text:style-name="T249">name</text:span></text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="Variable"><text:span text:style-name="T249">value</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T24"> </text:span></text:span><text:span text:style-name="T24">...</text:span><text:span text:style-name="T75">]</text:span><text:span text:style-name="T124">]</text:span></text:p>
- <text:p text:style-name="P269"><text:span text:style-name="T322">Filter tool to alter configuration files via command line. Reads </text:span><text:span text:style-name="Variable"><text:span text:style-name="T322">file</text:span></text:span><text:span text:style-name="T322">.config (standard input by default or if </text:span><text:span text:style-name="Variable"><text:span text:style-name="T322">file</text:span></text:span><text:span text:style-name="T322">.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="T322">=</text:span><text:span text:style-name="T43">value </text:span><text:span text:style-name="T322">as described before. With '-d' or '--delete', the variable </text:span><text:span text:style-name="Variable"><text:span text:style-name="T322">key</text:span></text:span><text:span text:style-name="T322"> is removed from the configuration. </text:span><text:span text:style-name="T123">With '-H' or '--header', </text:span><text:span text:style-name="Variable"><text:span text:style-name="T323">text</text:span></text:span> <text:span text:style-name="T323">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="T322">file</text:span></text:span><text:span text:style-name="T322">.config.</text:span></text:p>
- <text:p text:style-name="P300"><text:span text:style-name="T322">se</text:span><text:span text:style-name="T348">l</text:span><text:span text:style-name="T322">config</text:span><text:span text:style-name="T323"> [-</text:span><text:span text:style-name="T227">t</text:span><text:span text:style-name="T323">]</text:span> <text:span text:style-name="T323">[-</text:span><text:span text:style-name="T348">c</text:span><text:span text:style-name="T323">] </text:span><text:span text:style-name="Variable">section</text:span> <text:span text:style-name="T324">[</text:span><text:span text:style-name="Variable">file</text:span>.<text:span text:style-name="T324">config</text:span><text:span text:style-name="T124">]</text:span></text:p>
- <text:p text:style-name="P272"><text:span text:style-name="T322">Filter tool to </text:span><text:span text:style-name="T342">extract</text:span><text:span text:style-name="T348"> sections from </text:span><text:span text:style-name="T322">configuration files via command line. Reads </text:span><text:span text:style-name="Variable"><text:span text:style-name="T322">file</text:span></text:span><text:span text:style-name="T322">.config (standard input by default or if </text:span><text:span text:style-name="Variable"><text:span text:style-name="T322">file</text:span></text:span><text:span text:style-name="T322">.config = '-') and prints the filtered configuration to standard output. </text:span><text:span text:style-name="Variable"><text:span text:style-name="T348">section</text:span></text:span><text:span text:style-name="T348"> is specified as described for </text:span><text:span text:style-name="T45">mkexp. </text:span><text:span text:style-name="T322">With '-</text:span><text:span text:style-name="T348">t</text:span><text:span text:style-name="T322">' or '--trailing-space', t</text:span><text:span text:style-name="T348">railing space is </text:span><text:span text:style-name="T322">removed from the </text:span><text:span text:style-name="T348">output lines</text:span><text:span text:style-name="T322">. </text:span><text:span text:style-name="T123">With '-</text:span><text:span text:style-name="T130">c</text:span><text:span text:style-name="T123">' or '--</text:span><text:span text:style-name="T337">inline-comments</text:span><text:span text:style-name="T123">', </text:span><text:span text:style-name="T130">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="P299">namelist2config [-d <text:span text:style-name="T331">[-c]</text:span> [-v]<text:span text:style-name="T333">]</text:span></text:p>
- <text:p text:style-name="P271">Tries to extract namelist settings from shell scripts or log files and converts them to <text:span text:style-name="T332">the </text:span>.config format. <text:span text:style-name="T332">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="T333">printed directly, in original order</text:span><text:span text:style-name="T332">. </text:span><text:span text:style-name="T333">In this mode, </text:span><text:span text:style-name="T332">'-c' enables comments, '-v' will output non-namelist lines from input files as comments, prefixed with '###'.</text:span></text:p>
- <text:p text:style-name="P301"><text:span text:style-name="T228">files</text:span><text:span text:style-name="T347">2config [-d</text:span><text:span text:style-name="T349">]</text:span><text:span text:style-name="T347"> </text:span><text:span text:style-name="T331">[-</text:span><text:span text:style-name="T349">x</text:span><text:span text:style-name="T331">]</text:span></text:p>
- <text:p text:style-name="P273"><text:soft-page-break/><text:span text:style-name="T350">Tries to extract </text:span><text:span text:style-name="T349">input file operations </text:span><text:span text:style-name="T350">from shell scripts or log files and converts them to </text:span><text:span text:style-name="T332">the </text:span><text:span text:style-name="T350">.config format. </text:span><text:span text:style-name="T332">By default, </text:span><text:span text:style-name="T349">file </text:span><text:span text:style-name="T332">names </text:span><text:span text:style-name="T341">are</text:span><text:span text:style-name="T332"> sorted to allow easier comparisons. With '-d', namelists are </text:span><text:span text:style-name="T333">printed directly, in original order</text:span><text:span text:style-name="T332">. </text:span><text:span text:style-name="T349">Use '-x' when processing log files from shell scripts run with the 'xtrace' or '-x' option.</text:span></text:p>
- <text:h text:style-name="P347" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2534_1114405012"/><text:span text:style-name="T191">F</text:span>ormat of .config files<text:bookmark-end text:name="__RefHeading__2534_1114405012"/></text:h>
- <text:p text:style-name="P15">The .config files are simple text files containing a dictionary of variables with their respective values. They may be structured using sections and comments. <text:span text:style-name="T186">For reading these files, </text:span><text:span text:style-name="T12">mkexp</text:span><text:span text:style-name="T186"> uses the </text:span><text:span text:style-name="T12">configobj</text:span><text:span text:style-name="T186"> Python library. All settings found in the .config files are handled as Python variables internally.</text:span></text:p>
+ <text:p text:style-name="P294">edit<text:span text:style-name="T316">exp</text:span> [<text:span text:style-name="Variable">file</text:span>]</text:p>
+ <text:p text:style-name="P267">Reads <text:span text:style-name="T315">the</text:span> update script <text:span text:style-name="Variable">file</text:span> ('update' by default) and <text:span text:style-name="T315">launches a program to edit the </text:span>corresponding config file. <text:span text:style-name="T315">The program is taken from the environment variables 'VISUAL' or 'EDITOR' if defined, otherwise </text:span><text:span text:style-name="T42">vi</text:span><text:span text:style-name="T315"> is launched.</text:span></text:p>
+ <text:p text:style-name="P292"><text:span text:style-name="T314">getconfig</text:span> <text:span text:style-name="T314">[</text:span><text:span text:style-name="Variable">file</text:span><text:span text:style-name="T251">]</text:span></text:p>
+ <text:p text:style-name="P267">Documentation tool for experiments that were created using command line assignments. Reads <text:span text:style-name="T317">the</text:span> update script <text:span text:style-name="Variable">file</text:span> ('update' by default) and prints the corresponding config file with command line settings from the update script included.</text:p>
+ <text:p text:style-name="Preformatted_20_List_20_Heading"><text:span text:style-name="T324">setconfig</text:span> <text:span text:style-name="T325">[-d </text:span><text:span text:style-name="Variable"><text:span text:style-name="T325">key</text:span></text:span><text:span text:style-name="T325">] [-H </text:span><text:span text:style-name="Variable"><text:span text:style-name="T325">text</text:span></text:span><text:span text:style-name="T325">] [-a </text:span><text:span text:style-name="Variable"><text:span text:style-name="T326">file</text:span></text:span>.<text:span text:style-name="T326">config] [</text:span><text:span text:style-name="Variable">file</text:span>.<text:span text:style-name="T326">config</text:span><text:span text:style-name="T75"> [</text:span><text:span text:style-name="Variable"><text:span text:style-name="T251">name</text:span></text:span><text:span text:style-name="T75">=</text:span><text:span text:style-name="Variable"><text:span text:style-name="T251">value</text:span></text:span><text:span text:style-name="Variable"><text:span text:style-name="T24"> </text:span></text:span><text:span text:style-name="T24">...</text:span><text:span text:style-name="T75">]</text:span><text:span text:style-name="T124">]</text:span></text:p>
+ <text:p text:style-name="P269"><text:span text:style-name="T324">Filter tool to alter configuration files via command line. Reads </text:span><text:span text:style-name="Variable"><text:span text:style-name="T324">file</text:span></text:span><text:span text:style-name="T324">.config (standard input by default or if </text:span><text:span text:style-name="Variable"><text:span text:style-name="T324">file</text:span></text:span><text:span text:style-name="T324">.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="T324">=</text:span><text:span text:style-name="T43">value </text:span><text:span text:style-name="T324">as described before. With '-d' or '--delete', the variable </text:span><text:span text:style-name="Variable"><text:span text:style-name="T324">key</text:span></text:span><text:span text:style-name="T324"> is removed from the configuration. </text:span><text:span text:style-name="T123">With '-H' or '--header', </text:span><text:span text:style-name="Variable"><text:span text:style-name="T325">text</text:span></text:span> <text:span text:style-name="T325">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="T324">file</text:span></text:span><text:span text:style-name="T324">.config.</text:span></text:p>
+ <text:p text:style-name="P300"><text:span text:style-name="T324">se</text:span><text:span text:style-name="T352">l</text:span><text:span text:style-name="T324">config</text:span><text:span text:style-name="T325"> [-</text:span><text:span text:style-name="T229">t</text:span><text:span text:style-name="T325">]</text:span> <text:span text:style-name="T325">[-</text:span><text:span text:style-name="T352">c</text:span><text:span text:style-name="T325">] </text:span><text:span text:style-name="Variable">section</text:span> <text:span text:style-name="T326">[</text:span><text:span text:style-name="Variable">file</text:span>.<text:span text:style-name="T326">config</text:span><text:span text:style-name="T124">]</text:span></text:p>
+ <text:p text:style-name="P272"><text:span text:style-name="T324">Filter tool to </text:span><text:span text:style-name="T346">extract</text:span><text:span text:style-name="T352"> sections from </text:span><text:span text:style-name="T324">configuration files via command line. Reads </text:span><text:span text:style-name="Variable"><text:span text:style-name="T324">file</text:span></text:span><text:span text:style-name="T324">.config (standard input by default or if </text:span><text:span text:style-name="Variable"><text:span text:style-name="T324">file</text:span></text:span><text:span text:style-name="T324">.config = '-') and prints the filtered configuration to standard output. </text:span><text:span text:style-name="Variable"><text:span text:style-name="T352">section</text:span></text:span><text:span text:style-name="T352"> is specified as described for </text:span><text:span text:style-name="T45">mkexp. </text:span><text:span text:style-name="T324">With '-</text:span><text:span text:style-name="T352">t</text:span><text:span text:style-name="T324">' or '--trailing-space', t</text:span><text:span text:style-name="T352">railing space is </text:span><text:span text:style-name="T324">removed from the </text:span><text:span text:style-name="T352">output lines</text:span><text:span text:style-name="T324">. </text:span><text:span text:style-name="T123">With '-</text:span><text:span text:style-name="T130">c</text:span><text:span text:style-name="T123">' or '--</text:span><text:span text:style-name="T339">inline-comments</text:span><text:span text:style-name="T123">', </text:span><text:span text:style-name="T130">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="P299">namelist2config [-d <text:span text:style-name="T333">[-c]</text:span> [-v]<text:span text:style-name="T335">]</text:span></text:p>
+ <text:p text:style-name="P271">Tries to extract namelist settings from shell scripts or log files and converts them to <text:span text:style-name="T334">the </text:span>.config format. <text:span text:style-name="T334">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="T335">printed directly, in original order</text:span><text:span text:style-name="T334">. </text:span><text:span text:style-name="T335">In this mode, </text:span><text:span text:style-name="T334">'-c' enables comments, '-v' will output non-namelist lines from input files as comments, prefixed with '###'.</text:span></text:p>
+ <text:p text:style-name="P301"><text:span text:style-name="T230">files</text:span><text:span text:style-name="T351">2config [-d</text:span><text:span text:style-name="T353">]</text:span><text:span text:style-name="T351"> </text:span><text:span text:style-name="T333">[-</text:span><text:span text:style-name="T353">x</text:span><text:span text:style-name="T333">]</text:span></text:p>
+ <text:p text:style-name="P273"><text:soft-page-break/><text:span text:style-name="T354">Tries to extract </text:span><text:span text:style-name="T353">input file operations </text:span><text:span text:style-name="T354">from shell scripts or log files and converts them to </text:span><text:span text:style-name="T334">the </text:span><text:span text:style-name="T354">.config format. </text:span><text:span text:style-name="T334">By default, </text:span><text:span text:style-name="T353">file </text:span><text:span text:style-name="T334">names </text:span><text:span text:style-name="T345">are</text:span><text:span text:style-name="T334"> sorted to allow easier comparisons. With '-d', namelists are </text:span><text:span text:style-name="T335">printed directly, in original order</text:span><text:span text:style-name="T334">. </text:span><text:span text:style-name="T353">Use '-x' when processing log files from shell scripts run with the 'xtrace' or '-x' option.</text:span></text:p>
+ <text:h text:style-name="P347" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2534_1114405012"/><text:span text:style-name="T193">F</text:span>ormat of .config files<text:bookmark-end text:name="__RefHeading__2534_1114405012"/></text:h>
+ <text:p text:style-name="P15">The .config files are simple text files containing a dictionary of variables with their respective values. They may be structured using sections and comments. <text:span text:style-name="T188">For reading these files, </text:span><text:span text:style-name="T12">mkexp</text:span><text:span text:style-name="T188"> uses the </text:span><text:span text:style-name="T12">configobj</text:span><text:span text:style-name="T188"> 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="T187">configuration variable is set by simply assigning a text value to a name, as in</text:span></text:p>
+ <text:p text:style-name="P18">A <text:span text:style-name="T189">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="P19">Note that <text:span text:style-name="T188">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="P19">Note that <text:span text:style-name="T190">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">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>
@@ -3002,19 +3063,19 @@
<text:p text:style-name="P146">[section1]</text:p>
<text:p text:style-name="P146"><text:s text:c="4"/>description = This is the first section</text:p>
<text:p text:style-name="P22">will be stored as a dictionary section1 with section1['description'] set to 'This is the first section'.</text:p>
- <text:p text:style-name="P22">Sections may be nested to arbitrary depth by incrementing the number of bracket pairs <text:span text:style-name="T189">as in</text:span></text:p>
+ <text:p text:style-name="P22">Sections may be nested to arbitrary depth by incrementing the number of bracket pairs <text:span text:style-name="T191">as in</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text">[section1]</text:p>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="4"/>description = This is the first section</text:p>
<text:p text:style-name="Preformatted_20_Text"><text:soft-page-break/><text:s text:c="4"/>[[subsection1a]]</text:p>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="8"/>description = This is the first sub section of the first section</text:p>
- <text:p text:style-name="P141"><text:s text:c="4"/>[[subsection1<text:span text:style-name="T189">b</text:span>]]</text:p>
- <text:p text:style-name="P141"><text:s text:c="8"/>description = This is the <text:span text:style-name="T189">second</text:span> sub section of the first section</text:p>
+ <text:p text:style-name="P141"><text:s text:c="4"/>[[subsection1<text:span text:style-name="T191">b</text:span>]]</text:p>
+ <text:p text:style-name="P141"><text:s text:c="8"/>description = This is the <text:span text:style-name="T191">second</text:span> sub section of the first section</text:p>
<text:p text:style-name="P140">[section2]</text:p>
<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="T250">A s</text:span>ection <text:span text:style-name="T250">is</text:span> closed by the beginning of a new section of the same level, by a section <text:span text:style-name="T250">of </text:span>l<text:span text:style-name="T250">ower</text:span> <text:span text:style-name="T250">nesting </text:span>depth, <text:span text:style-name="T250">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="T190">long</text:span> to the respective subsection.</text:p>
+ <text:p text:style-name="P23"><text:span text:style-name="T252">A s</text:span>ection <text:span text:style-name="T252">is</text:span> closed by the beginning of a new section of the same level, by a section <text:span text:style-name="T252">of </text:span>l<text:span text:style-name="T252">ower</text:span> <text:span text:style-name="T252">nesting </text:span>depth, <text:span text:style-name="T252">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="T192">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"/>Special <text:span text:style-name="T242">v</text:span>ariables <text:span text:style-name="T242">and sections</text:span><text:bookmark-end text:name="__RefHeading__2538_1114405012"/></text:h>
+ <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="T244">v</text:span>ariables <text:span text:style-name="T244">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="T56">There are a number of special variables that influence the way </text:span>mkexp<text:span text:style-name="T56"> works. They must be present in one of the .config files, unless noted otherwise below. </text:span><text:span text:style-name="T60">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="T60">T</text:span><text:span text:style-name="T56">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>
@@ -3024,9 +3085,9 @@
<text:p text:style-name="P206">DATA_DIR</text:p>
<text:p text:style-name="P221">Directory for storing output data. When a model run finishes, output will be stored there for further processing. Will also be created when non-existent.</text:p>
<text:p text:style-name="P210">VERSION_</text:p>
- <text:p text:style-name="P228">Each .config file in the model setup <text:span text:style-name="T280">should</text:span> set this variable to a suitable value, e.g. version control information. The values are collected in a variable 'VERSIONS_' which is usually written to the resulting job descriptions.</text:p>
+ <text:p text:style-name="P228">Each .config file in the model setup <text:span text:style-name="T282">should</text:span> set this variable to a suitable value, e.g. version control information. The values are collected in a variable 'VERSIONS_' which is usually written to the resulting job descriptions.</text:p>
<text:p text:style-name="P211">SETUP_OPTIONS (<text:span text:style-name="T9">optional</text:span>)</text:p>
- <text:p text:style-name="P225">Subset of the model's standard options that should be applied to <text:span text:style-name="T289">all</text:span> experiment<text:span text:style-name="T289">s using the same model version</text:span>. </text:p>
+ <text:p text:style-name="P225">Subset of the model's standard options that should be applied to <text:span text:style-name="T291">all</text:span> experiment<text:span text:style-name="T291">s using the same model version</text:span>. </text:p>
<text:p text:style-name="P41">There is a second set of variables that belongs in the user setup:</text:p>
<text:p text:style-name="P208"><text:soft-page-break/>EXP_TYPE</text:p>
<text:p text:style-name="P223">Selects one of the standard experiments that are pre-defined in the model setup as basis of the current experiment definition.</text:p>
@@ -3036,8 +3097,8 @@
<text:p text:style-name="P224">Subset of the model's standard options that should be applied to the current experiment definition.</text:p>
<text:p text:style-name="P215">EXP_ID (<text:span text:style-name="T9">optional</text:span>)</text:p>
<text:p text:style-name="P237">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="T215">(</text:span><text:span text:style-name="T16">optional</text:span><text:span text:style-name="T215">)</text:span></text:p>
- <text:p text:style-name="P222">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="T309">as well as </text:span>leading and trailing empty lines <text:span text:style-name="T309">or comment boilerplate </text:span>are removed. Note that <text:span text:style-name="T266">both header comment and </text:span>EXP_DESCRIPTION may reference any other global variable defined in the experiment configuration <text:span text:style-name="T266">(see section </text:span><text:span text:style-name="T266"><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="T266">)</text:span>.</text:p>
+ <text:p text:style-name="P203">EXP_DESCRIPTION <text:span text:style-name="T217">(</text:span><text:span text:style-name="T16">optional</text:span><text:span text:style-name="T217">)</text:span></text:p>
+ <text:p text:style-name="P222">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="T311">as well as </text:span>leading and trailing empty lines <text:span text:style-name="T311">or comment boilerplate </text:span>are removed. Note that <text:span text:style-name="T268">both header comment and </text:span>EXP_DESCRIPTION may reference any other global variable defined in the experiment configuration <text:span text:style-name="T268">(see section </text:span><text:span text:style-name="T268"><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="T268">)</text:span>.</text:p>
<text:p text:style-name="P222">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="T56">Another set of variables is automatically added to the job specific experiment configuration. </text:span><text:span text:style-name="T71">These are considered read-only</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T64">and may not be altered</text:span><text:span text:style-name="T56">.</text:span></text:p>
<text:p text:style-name="P202">JOB</text:p>
@@ -3052,14 +3113,14 @@
<text:p text:style-name="List_20_Heading">[jobs]</text:p>
<text:p text:style-name="P238">This section defines the job description set needed for an experiment. It also provides job specific settings. Details are given in section <text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__1508_1711940803">2.7</text:bookmark-ref>, '<text:bookmark-ref text:reference-format="text" text:ref-name="__RefHeading__1508_1711940803">Generating jobs</text:bookmark-ref>'.</text:p>
<text:p text:style-name="List_20_Heading">[namelists]</text:p>
- <text:p text:style-name="P238">Information that is contained in model configuration or namelist files is set in this section. For further details see section <text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__1883_1672291846">2.9</text:bookmark-ref>, <text:span text:style-name="T255">'</text:span><text:span text:style-name="T255"><text:bookmark-ref text:reference-format="text" text:ref-name="__RefHeading__1883_1672291846">Defining namelists and other configuration files</text:bookmark-ref></text:span><text:span text:style-name="T255">'.</text:span></text:p>
+ <text:p text:style-name="P238">Information that is contained in model configuration or namelist files is set in this section. For further details see section <text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__1883_1672291846">2.9</text:bookmark-ref>, <text:span text:style-name="T257">'</text:span><text:span text:style-name="T257"><text:bookmark-ref text:reference-format="text" text:ref-name="__RefHeading__1883_1672291846">Defining namelists and other configuration files</text:bookmark-ref></text:span><text:span text:style-name="T257">'.</text:span></text:p>
<text:p text:style-name="P217">[files]</text:p>
- <text:p text:style-name="P252">All input files that are needed for an experiment and <text:span text:style-name="T277">information</text:span> to provide them go into this section. <text:span text:style-name="T277">See section </text:span><text:span text:style-name="T277"><text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__2831_1132221942">2.10</text:bookmark-ref></text:span><text:span text:style-name="T277">, '</text:span><text:span text:style-name="T277"><text:bookmark-ref text:reference-format="text" text:ref-name="__RefHeading__2831_1132221942">Defining input files for an experiment</text:bookmark-ref></text:span><text:span text:style-name="T277">'.</text:span></text:p>
+ <text:p text:style-name="P252">All input files that are needed for an experiment and <text:span text:style-name="T279">information</text:span> to provide them go into this section. <text:span text:style-name="T279">See section </text:span><text:span text:style-name="T279"><text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__2831_1132221942">2.10</text:bookmark-ref></text:span><text:span text:style-name="T279">, '</text:span><text:span text:style-name="T279"><text:bookmark-ref text:reference-format="text" text:ref-name="__RefHeading__2831_1132221942">Defining input files for an experiment</text:bookmark-ref></text:span><text:span text:style-name="T279">'.</text:span></text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2540_1114405012"/><text:soft-page-break/>Variable interpolation<text:bookmark-end text:name="__RefHeading__2540_1114405012"/></text:h>
- <text:p text:style-name="P76">The value of a .config variable may reference the value of another variable by prefixing its name with <text:span text:style-name="T256">a </text:span>dollar sign. <text:span text:style-name="T256">This is called </text:span><text:span text:style-name="T26">interpolation</text:span><text:span text:style-name="T82"> of variables. E.g.</text:span></text:p>
+ <text:p text:style-name="P76">The value of a .config variable may reference the value of another variable by prefixing its name with <text:span text:style-name="T258">a </text:span>dollar sign. <text:span text:style-name="T258">This is called </text:span><text:span text:style-name="T26">interpolation</text:span><text:span text:style-name="T82"> of variables. E.g.</text:span></text:p>
<text:p text:style-name="P178"># joe1234.config</text:p>
<text:p text:style-name="P184">WORK_ROOT = /scratch/joe</text:p>
- <text:p text:style-name="Preformatted_20_Text">WORK_DIR = $WORK_ROOT/experiments/<text:span text:style-name="T257">$EXP_ID</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text">WORK_DIR = $WORK_ROOT/experiments/<text:span text:style-name="T259">$EXP_ID</text:span></text:p>
<text:p text:style-name="P78">will set 'WORK_DIR' to '/scratch/joe/experiments/joe1234'.</text:p>
<text:p text:style-name="P77">Interpolation only works for variables of the current section or its ancestor sections.</text:p>
<text:p text:style-name="Preformatted_20_Text">[ensembles] </text:p>
@@ -3070,141 +3131,141 @@
<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">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/$EXP_ID_test <text:s text:c="3"/><text:span text:style-name="T257"># ERROR: missing option "EXP_ID_test"</text:span></text:p>
- <text:p text:style-name="P179"><text:span text:style-name="T257">WORK_DIR = /tmp/</text:span><text:span text:style-name="T175">${EXP_ID}_test</text:span><text:span text:style-name="T257"> <text:s/># OK</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text">WORK_DIR = /tmp/$EXP_ID_test <text:s text:c="3"/><text:span text:style-name="T259"># ERROR: missing option "EXP_ID_test"</text:span></text:p>
+ <text:p text:style-name="P179"><text:span text:style-name="T259">WORK_DIR = /tmp/</text:span><text:span text:style-name="T177">${EXP_ID}_test</text:span><text:span text:style-name="T259"> <text:s/># OK</text:span></text:p>
<text:p text:style-name="P178"/>
- <text:p text:style-name="P178">SPACY <text:span text:style-name="T258">VAR</text:span> = Whew! </text:p>
- <text:p text:style-name="P178"><text:span text:style-name="T258">MESSAGE</text:span> = He said: $SPACY VAR <text:s text:c="2"/><text:span text:style-name="T258"># ERROR: missing option </text:span>"<text:span text:style-name="T258">SPACY</text:span>"</text:p>
- <text:p text:style-name="P180">MESSAGE = <text:span text:style-name="T257">He said: </text:span><text:span text:style-name="T175">$</text:span><text:span text:style-name="T168">{</text:span><text:span text:style-name="T175">SPACY VAR</text:span><text:span text:style-name="T168">}</text:span> # OK</text:p>
- <text:p text:style-name="P79">The user<text:span text:style-name="T267">'</text:span>s <text:span text:style-name="T9">environment variables</text:span> may be referenced as global variables in a .config file. Thus a user may write something like</text:p>
+ <text:p text:style-name="P178">SPACY <text:span text:style-name="T260">VAR</text:span> = Whew! </text:p>
+ <text:p text:style-name="P178"><text:span text:style-name="T260">MESSAGE</text:span> = He said: $SPACY VAR <text:s text:c="2"/><text:span text:style-name="T260"># ERROR: missing option </text:span>"<text:span text:style-name="T260">SPACY</text:span>"</text:p>
+ <text:p text:style-name="P180">MESSAGE = <text:span text:style-name="T259">He said: </text:span><text:span text:style-name="T177">$</text:span><text:span text:style-name="T170">{</text:span><text:span text:style-name="T177">SPACY VAR</text:span><text:span text:style-name="T170">}</text:span> # OK</text:p>
+ <text:p text:style-name="P79">The user<text:span text:style-name="T269">'</text:span>s <text:span text:style-name="T9">environment variables</text:span> may be referenced as global variables in a .config file. Thus a user may write something like</text:p>
<text:p text:style-name="Preformatted_20_Text">SCRIPT_ROOT = $HOME/experiments/$EXP_ID</text:p>
<text:p text:style-name="P79">setting 'SCRIPT_ROOT' to a subdirectory of the user's home directory.</text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2542_1114405012"/>Evaluation of interpolation<text:bookmark-end text:name="__RefHeading__2542_1114405012"/></text:h>
<text:p text:style-name="P80">While interpolation looks a lot like in shell scripts, there is a major difference: interpolation is – as in Makefiles – only evaluated when the final value is written or passed on. This has the advantage that the model setup may define settings based on variables that are only defined later in the user setup.</text:p>
<text:p text:style-name="P181"># model setup</text:p>
- <text:p text:style-name="P303"><text:soft-page-break/><text:span text:style-name="T259">MODEL</text:span>_<text:span text:style-name="T259">DIR</text:span> = $HOME/<text:span text:style-name="T259">$MODEL_SUBDIR</text:span></text:p>
+ <text:p text:style-name="P303"><text:soft-page-break/><text:span text:style-name="T261">MODEL</text:span>_<text:span text:style-name="T261">DIR</text:span> = $HOME/<text:span text:style-name="T261">$MODEL_SUBDIR</text:span></text:p>
<text:p text:style-name="P182"># user setup</text:p>
<text:p text:style-name="P182">MODEL_SUBDIR = echam</text:p>
- <text:p text:style-name="P81">Here, as the model setup is read before the user setup, 'MODEL_SUBDIR' is not set when 'MODEL_ROOT' is defined. <text:span text:style-name="T260">This works, because i</text:span>nterpolation of 'MODEL_ROOT's value is postponed until all levels of setup have been read.</text:p>
+ <text:p text:style-name="P81">Here, as the model setup is read before the user setup, 'MODEL_SUBDIR' is not set when 'MODEL_ROOT' is defined. <text:span text:style-name="T262">This works, because i</text:span>nterpolation of 'MODEL_ROOT's value is postponed until all levels of setup have been read.</text:p>
<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"/>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="T56"> includes some special expressions, that are evaluated when interpolation occurs.</text:span></text:p>
- <text:p text:style-name="P280"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T56"> = </text:span><text:span text:style-name="T158">eval(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T158">)</text:span><text:span text:style-name="T56"><text:line-break/></text:span><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T56"> = </text:span><text:span text:style-name="T158">evals(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T158">)</text:span></text:p>
- <text:p text:style-name="P276"><text:span text:style-name="T86">I</text:span><text:span text:style-name="T115">nterpret </text:span><text:span text:style-name="T41">expression</text:span><text:span text:style-name="T115"> 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="T115"> as a string. </text:span><text:span text:style-name="T114">The modules </text:span><text:span text:style-name="T309">'</text:span>os<text:span text:style-name="T309">'</text:span>, <text:span text:style-name="T309">'</text:span>re<text:span text:style-name="T309">'</text:span> and <text:span text:style-name="T309">'</text:span>time<text:span text:style-name="T309">'</text:span> <text:span text:style-name="T114">may be used in </text:span><text:span text:style-name="T40">expression</text:span><text:span text:style-name="T114">. </text:span><text:span text:style-name="T131">Besides, a </text:span><text:span text:style-name="T338">predicate</text:span><text:span text:style-name="T131"> 'is_set' is available to </text:span><text:span text:style-name="T164">test if a string evaluates to</text:span><text:span text:style-name="T51"> true</text:span><text:span text:style-name="T164"> when used as namelist </text:span><text:span text:style-name="T339">logical, </text:span><text:span text:style-name="T340">r</text:span><text:span text:style-name="T339">eturn</text:span><text:span text:style-name="T340">ing</text:span><text:span text:style-name="T344"> false</text:span><text:span text:style-name="T339"> when used on </text:span><text:span text:style-name="T340">'None'.</text:span></text:p>
+ <text:p text:style-name="P280"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T56"> = </text:span><text:span text:style-name="T160">eval(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T160">)</text:span><text:span text:style-name="T56"><text:line-break/></text:span><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T56"> = </text:span><text:span text:style-name="T160">evals(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T160">)</text:span></text:p>
+ <text:p text:style-name="P276"><text:span text:style-name="T86">I</text:span><text:span text:style-name="T115">nterpret </text:span><text:span text:style-name="T41">expression</text:span><text:span text:style-name="T115"> 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="T115"> as a string. </text:span><text:span text:style-name="T114">The modules </text:span><text:span text:style-name="T311">'</text:span>os<text:span text:style-name="T311">'</text:span>, <text:span text:style-name="T311">'</text:span>re<text:span text:style-name="T311">'</text:span> and <text:span text:style-name="T311">'</text:span>time<text:span text:style-name="T311">'</text:span> <text:span text:style-name="T114">may be used in </text:span><text:span text:style-name="T40">expression</text:span><text:span text:style-name="T114">. </text:span><text:span text:style-name="T131">Besides, a </text:span><text:span text:style-name="T340">predicate</text:span><text:span text:style-name="T131"> 'is_set' is available to </text:span><text:span text:style-name="T166">test if a string evaluates to</text:span><text:span text:style-name="T51"> true</text:span><text:span text:style-name="T166"> when used as namelist </text:span><text:span text:style-name="T341">logical, </text:span><text:span text:style-name="T342">r</text:span><text:span text:style-name="T341">eturn</text:span><text:span text:style-name="T342">ing</text:span><text:span text:style-name="T348"> false</text:span><text:span text:style-name="T341"> when used on </text:span><text:span text:style-name="T342">'None'.</text:span></text:p>
<text:p text:style-name="P248"><text:span text:style-name="T56">When the result is a list, </text:span><text:span text:style-name="T9">eval</text:span><text:span text:style-name="T56"> will return a list of strings, while </text:span><text:span text:style-name="T9">evals</text:span><text:span text:style-name="T56"> will return a single string, where elements are joined by a comma and a space.</text:span></text:p>
<text:p text:style-name="P247"><text:span text:style-name="T56">Note that interpolation does not work for list values; if you need this, consider to set the original variable </text:span><text:span text:style-name="T83">to a string containing a Python list expression</text:span><text:span text:style-name="T56">, and </text:span><text:span text:style-name="T83">then </text:span><text:span text:style-name="T56">use </text:span><text:span text:style-name="T9">eval</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T96">a</text:span><text:span text:style-name="T56">round the interpolation expression:</text:span></text:p>
- <text:p text:style-name="P304">DATE_<text:span text:style-name="T268">STRING</text:span> = '[2010, 10, 20]' # need quotes here!</text:p>
- <text:p text:style-name="P304">DATE_<text:span text:style-name="T268">LIST</text:span> = eval($DATE_<text:span text:style-name="T269">STRING</text:span>) # becomes a 3 element list</text:p>
- <text:p text:style-name="P281">variable<text:span text:style-name="T56"> = </text:span><text:span text:style-name="T158">read(</text:span>file_name<text:span text:style-name="T158">)</text:span></text:p>
+ <text:p text:style-name="P304">DATE_<text:span text:style-name="T270">STRING</text:span> = '[2010, 10, 20]' # need quotes here!</text:p>
+ <text:p text:style-name="P304">DATE_<text:span text:style-name="T270">LIST</text:span> = eval($DATE_<text:span text:style-name="T271">STRING</text:span>) # becomes a 3 element list</text:p>
+ <text:p text:style-name="P281">variable<text:span text:style-name="T56"> = </text:span><text:span text:style-name="T160">read(</text:span>file_name<text:span text:style-name="T160">)</text:span></text:p>
<text:p text:style-name="P241"><text:span text:style-name="T56">Read the contents of the file </text:span>file_name<text:span text:style-name="T56"> and assign its contents to </text:span>variable<text:span text:style-name="T56"> as a string.</text:span></text:p>
- <text:p text:style-name="P282"><text:span text:style-name="T27">variable</text:span><text:span text:style-name="T84"> = </text:span><text:span text:style-name="T160">split_date(</text:span><text:span text:style-name="T27">timestamp</text:span><text:span text:style-name="T160">)</text:span></text:p>
- <text:p text:style-name="P249"><text:span text:style-name="T261">T</text:span>ake <text:span text:style-name="T9">timestamp</text:span><text:span text:style-name="T56"> and split it into a list of numerical date/time elements. </text:span><text:soft-page-break/><text:span text:style-name="T9">tim</text:span><text:span text:style-name="T28">e</text:span><text:span text:style-name="T9">stamp</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T85">must have </text:span><text:span text:style-name="T56">an ISO-like format (date elements separated by '-'; 'T' or space as date/time separator; time elements separated by ':</text:span><text:span text:style-name="T85">'; </text:span><text:span text:style-name="T56">trailing time elements </text:span><text:span text:style-name="T86">and their separators </text:span><text:span text:style-name="T85">are optional</text:span><text:span text:style-name="T56">; time zone indicator is not supported). </text:span><text:span text:style-name="T98">Unlike ISO, </text:span><text:span text:style-name="T31">split_date</text:span><text:span text:style-name="T98"> also</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T98">allows the date to be in the form YYYYMMDD</text:span><text:span text:style-name="T56">. </text:span><text:span text:style-name="T86">Unset fields default to zero.</text:span></text:p>
- <text:p text:style-name="P283"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T56"> = </text:span><text:span text:style-name="T158">sec2time(</text:span><text:span text:style-name="T9">second_of_day</text:span><text:span text:style-name="T158">)</text:span></text:p>
+ <text:p text:style-name="P282"><text:span text:style-name="T27">variable</text:span><text:span text:style-name="T84"> = </text:span><text:span text:style-name="T162">split_date(</text:span><text:span text:style-name="T27">timestamp</text:span><text:span text:style-name="T162">)</text:span></text:p>
+ <text:p text:style-name="P249"><text:span text:style-name="T263">T</text:span>ake <text:span text:style-name="T9">timestamp</text:span><text:span text:style-name="T56"> and split it into a list of numerical date/time elements. </text:span><text:soft-page-break/><text:span text:style-name="T9">tim</text:span><text:span text:style-name="T28">e</text:span><text:span text:style-name="T9">stamp</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T85">must have </text:span><text:span text:style-name="T56">an ISO-like format (date elements separated by '-'; 'T' or space as date/time separator; time elements separated by ':</text:span><text:span text:style-name="T85">'; </text:span><text:span text:style-name="T56">trailing time elements </text:span><text:span text:style-name="T86">and their separators </text:span><text:span text:style-name="T85">are optional</text:span><text:span text:style-name="T56">; time zone indicator is not supported). </text:span><text:span text:style-name="T98">Unlike ISO, </text:span><text:span text:style-name="T31">split_date</text:span><text:span text:style-name="T98"> also</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T98">allows the date to be in the form YYYYMMDD</text:span><text:span text:style-name="T56">. </text:span><text:span text:style-name="T86">Unset fields default to zero.</text:span></text:p>
+ <text:p text:style-name="P283"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T56"> = </text:span><text:span text:style-name="T160">sec2time(</text:span><text:span text:style-name="T9">second_of_day</text:span><text:span text:style-name="T160">)</text:span></text:p>
<text:p text:style-name="P233">Take integer <text:span text:style-name="T9">second_of_day</text:span> (from 0 to 86399) and return the corresponding time stamp as string of the form HH:MM:SS.</text:p>
- <text:p text:style-name="P284"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T168">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="P284"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T170">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="P250">Take integer <text:span text:style-name="T9">offset</text:span><text:span text:style-name="T56"> (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="T56"> and return the resulting date string.</text:span></text:p>
- <text:p text:style-name="P285"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T168">add_</text:span><text:span text:style-name="T176">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="P285"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T170">add_</text:span><text:span text:style-name="T178">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="P251"><text:span text:style-name="T56">Take integer </text:span><text:span text:style-name="T9">offset</text:span><text:span text:style-name="T56"> (may be negative), add it to the </text:span><text:span text:style-name="T99">day</text:span><text:span text:style-name="T56"> portion of </text:span><text:span text:style-name="T9">datestamp</text:span><text:span text:style-name="T56"> and return the resulting date string. </text:span><text:span text:style-name="T99">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"/>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>
- <text:p text:style-name="P25">The simplest interaction in a template is replacing a template's placeholder by a value from a .config file. <text:span text:style-name="T192">Any name enclosed by '%{' and '}' is taken to be a configuration variable, like in the snippets below:</text:span></text:p>
+ <text:p text:style-name="P25">The simplest interaction in a template is replacing a template's placeholder by a value from a .config file. <text:span text:style-name="T194">Any name enclosed by '%{' and '}' is taken to be a configuration variable, like in the snippets below:</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text">#! /bin/ksh</text:p>
- <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T193">#</text:span> This script was <text:span text:style-name="T193">crea</text:span>ted by %{NAME}</text:p>
- <text:p text:style-name="P33">Here, the placehol<text:span text:style-name="T251">d</text:span>er requests the 'NAME' variable which was set to 'Joe User' in the example .config file <text:span text:style-name="T251">of section </text:span><text:span text:style-name="T251"><text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__1669_1438093122">2.3.1</text:bookmark-ref></text:span>. This value is now looked up in the <text:span text:style-name="T251">configuration</text:span> and used to textually replace the placeholder expression, yield<text:span text:style-name="T251">ing</text:span> the final text:</text:p>
+ <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T195">#</text:span> This script was <text:span text:style-name="T195">crea</text:span>ted by %{NAME}</text:p>
+ <text:p text:style-name="P33">Here, the placehol<text:span text:style-name="T253">d</text:span>er requests the 'NAME' variable which was set to 'Joe User' in the example .config file <text:span text:style-name="T253">of section </text:span><text:span text:style-name="T253"><text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__1669_1438093122">2.3.1</text:bookmark-ref></text:span>. This value is now looked up in the <text:span text:style-name="T253">configuration</text:span> and used to textually replace the placeholder expression, yield<text:span text:style-name="T253">ing</text:span> the final text:</text:p>
<text:p text:style-name="P143">#! /bin/ksh</text:p>
- <text:p text:style-name="P142"><text:span text:style-name="T194"># </text:span>This script was <text:span text:style-name="T194">crea</text:span>ted by <text:span text:style-name="T192">Joe User</text:span></text:p>
- <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2550_1114405012"/><text:soft-page-break/><text:span text:style-name="T196">V</text:span>ariables in sections<text:bookmark-end text:name="__RefHeading__2550_1114405012"/></text:h>
+ <text:p text:style-name="P142"><text:span text:style-name="T196"># </text:span>This script was <text:span text:style-name="T196">crea</text:span>ted by <text:span text:style-name="T194">Joe User</text:span></text:p>
+ <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2550_1114405012"/><text:soft-page-break/><text:span text:style-name="T198">V</text:span>ariables in sections<text:bookmark-end text:name="__RefHeading__2550_1114405012"/></text:h>
<text:p text:style-name="P26">To request a variable within a section, simply prepend the section name to the variable name, using '.' as separator, as in</text:p>
<text:p text:style-name="Preformatted_20_Text"># %{section1.description}</text:p>
<text:p text:style-name="P26">This is also used for nested sections:</text:p>
- <text:p text:style-name="Preformatted_20_Text"># %{section1.s<text:span text:style-name="T194">ubs</text:span>ection1a.description}</text:p>
- <text:p text:style-name="P27">For section names that contain a '.' or spaces (like 'namelist.echam' in the introductory example), instead of the '.' separator, the section name is given as a quoted string in brackets (similar to <text:span text:style-name="T251">Python's dictionary</text:span> syntax):</text:p>
+ <text:p text:style-name="Preformatted_20_Text"># %{section1.s<text:span text:style-name="T196">ubs</text:span>ection1a.description}</text:p>
+ <text:p text:style-name="P27">For section names that contain a '.' or spaces (like 'namelist.echam' in the introductory example), instead of the '.' separator, the section name is given as a quoted string in brackets (similar to <text:span text:style-name="T253">Python's dictionary</text:span> syntax):</text:p>
<text:p text:style-name="P201">IS_AMIP_RUN=%{namelists['namelist.echam'].runctl.lamip}</text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2552_1114405012"/>Expressions<text:bookmark-end text:name="__RefHeading__2552_1114405012"/></text:h>
- <text:p text:style-name="P26">The placeholders may <text:span text:style-name="T195">also contain more complex expressions, using a limited set of operations that is defined in the </text:span><text:span text:style-name="T13">Jinja</text:span><text:span text:style-name="T195"> documentation. Among these are</text:span></text:p>
+ <text:p text:style-name="P26">The placeholders may <text:span text:style-name="T197">also contain more complex expressions, using a limited set of operations that is defined in the </text:span><text:span text:style-name="T13">Jinja</text:span><text:span text:style-name="T197"> documentation. Among these are</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text">LITERAL_STRING=%{'hello'}</text:p>
<text:p text:style-name="Preformatted_20_Text">LITERAL_INTEGER=%{42}</text:p>
<text:p text:style-name="Preformatted_20_Text">LITERAL_FLOAT=%{21.5}</text:p>
<text:p text:style-name="Preformatted_20_Text">LITERAL_LIST=%{['hello', 42, 21.5]}</text:p>
<text:p text:style-name="Preformatted_20_Text">LITERAL_BOOLEANS=%{false} <text:s/># Always lower-case!</text:p>
<text:p text:style-name="Preformatted_20_Text">ARITHMETIC=%{2 + 2 * 2 – 2 / 2} <text:s/># is 5</text:p>
- <text:p text:style-name="Preformatted_20_Text">STRING_TOGETHER=%{NAME ~ ', employee number ' ~ 42} <text:s/># Converts <text:span text:style-name="T196">42</text:span> to string</text:p>
+ <text:p text:style-name="Preformatted_20_Text">STRING_TOGETHER=%{NAME ~ ', employee number ' ~ 42} <text:s/># Converts <text:span text:style-name="T198">42</text:span> to string</text:p>
<text:p text:style-name="P145">LIST_ELEMENT=%{PATH[0]} <text:s/># indices start with 0</text:p>
<text:p text:style-name="P145">LIST_SUBLIST=%{PATH[1:3]}</text:p>
- <text:p text:style-name="Preformatted_20_Text">FILTERED_STRING=%{NAME | <text:span text:style-name="T196">lower()} <text:s/># is 'joe user'</text:span></text:p>
- <text:p text:style-name="P96">The last example allows for <text:span text:style-name="T214">a </text:span>number of predefined filters instead of 'lower'. These are described in the <text:span text:style-name="T9">Jinja</text:span> documentation (List of Builtin Filters). <text:span text:style-name="T284">Besides, </text:span><text:span text:style-name="T9">mkexp</text:span> defines <text:s/><text:span text:style-name="T287">a number of </text:span>additional filters:</text:p>
- <text:p text:style-name="P286">split<text:span text:style-name="T202">(</text:span><text:span text:style-name="T49">s</text:span><text:span text:style-name="T52">=none</text:span><text:span text:style-name="T161">, </text:span><text:span text:style-name="T49">m</text:span><text:span text:style-name="T161">=-1)</text:span></text:p>
- <text:p text:style-name="P234">cuts <text:span text:style-name="T286">the input </text:span>string <text:span text:style-name="T286">at all occurrences of </text:span><text:span text:style-name="T34">s</text:span><text:span text:style-name="T286">, returning</text:span> a list of substrings. <text:span text:style-name="T355">If </text:span><text:span text:style-name="Variable"><text:span text:style-name="T355">s </text:span></text:span><text:span text:style-name="T356">is</text:span><text:span text:style-name="Variable"><text:span text:style-name="T356"> none</text:span></text:span><text:span text:style-name="T355">, substrings are delimited by white space. </text:span><text:span text:style-name="T285">If </text:span><text:span text:style-name="T33">m</text:span><text:span text:style-name="T285"> is positive or zero, it cuts only at the first </text:span><text:span text:style-name="T33">m</text:span><text:span text:style-name="T285"> occurrences; the last element contains the remaining substring:</text:span></text:p>
- <text:p text:style-name="P311">%{ 'A<text:span text:style-name="T359">·</text:span>B<text:span text:style-name="T359">··</text:span>C' | <text:span text:style-name="T168">split</text:span><text:span text:style-name="T202">('</text:span><text:span text:style-name="T360">·</text:span><text:span text:style-name="T202">') }<text:tab/><text:tab/>→</text:span><text:span text:style-name="T205"> </text:span><text:span text:style-name="T204">['A', 'B', </text:span><text:span text:style-name="T211">'', </text:span><text:span text:style-name="T204">'C']</text:span></text:p>
- <text:p text:style-name="P311">%{ 'A<text:span text:style-name="T359">·</text:span>B<text:span text:style-name="T359">··</text:span>C' | <text:span text:style-name="T202">split</text:span><text:span text:style-name="T168">()</text:span><text:span text:style-name="T202"> }<text:tab/><text:tab/>→</text:span><text:span text:style-name="T205"> </text:span><text:span text:style-name="T204">['A', 'B',</text:span><text:span text:style-name="T211"> </text:span><text:span text:style-name="T204">'C']</text:span></text:p>
- <text:p text:style-name="P311"><text:span text:style-name="T204">%{ 'A</text:span><text:span text:style-name="T362">·</text:span><text:span text:style-name="T204">B</text:span><text:span text:style-name="T361">··</text:span><text:span text:style-name="T204">C' | split('</text:span><text:span text:style-name="T361">·</text:span><text:span text:style-name="T204">', </text:span><text:span text:style-name="T178">1</text:span><text:span text:style-name="T204">) } <text:tab/></text:span><text:span text:style-name="T205">→ </text:span><text:span text:style-name="T204">['A', </text:span><text:span text:style-name="T178">'B</text:span><text:span text:style-name="T363">··</text:span><text:span text:style-name="T178">C'</text:span><text:span text:style-name="T204">]</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text">FILTERED_STRING=%{NAME | <text:span text:style-name="T198">lower()} <text:s/># is 'joe user'</text:span></text:p>
+ <text:p text:style-name="P96">The last example allows for <text:span text:style-name="T216">a </text:span>number of predefined filters instead of 'lower'. These are described in the <text:span text:style-name="T9">Jinja</text:span> documentation (List of Builtin Filters). <text:span text:style-name="T286">Besides, </text:span><text:span text:style-name="T9">mkexp</text:span> defines <text:s/><text:span text:style-name="T289">a number of </text:span>additional filters:</text:p>
+ <text:p text:style-name="P286">split<text:span text:style-name="T204">(</text:span><text:span text:style-name="T49">s</text:span><text:span text:style-name="T52">=none</text:span><text:span text:style-name="T163">, </text:span><text:span text:style-name="T49">m</text:span><text:span text:style-name="T163">=-1)</text:span></text:p>
+ <text:p text:style-name="P234">cuts <text:span text:style-name="T288">the input </text:span>string <text:span text:style-name="T288">at all occurrences of </text:span><text:span text:style-name="T34">s</text:span><text:span text:style-name="T288">, returning</text:span> a list of substrings. <text:span text:style-name="T359">If </text:span><text:span text:style-name="Variable"><text:span text:style-name="T359">s </text:span></text:span><text:span text:style-name="T360">is</text:span><text:span text:style-name="Variable"><text:span text:style-name="T360"> none</text:span></text:span><text:span text:style-name="T359">, substrings are delimited by white space. </text:span><text:span text:style-name="T287">If </text:span><text:span text:style-name="T33">m</text:span><text:span text:style-name="T287"> is positive or zero, it cuts only at the first </text:span><text:span text:style-name="T33">m</text:span><text:span text:style-name="T287"> occurrences; the last element contains the remaining substring:</text:span></text:p>
+ <text:p text:style-name="P311">%{ 'A<text:span text:style-name="T363">·</text:span>B<text:span text:style-name="T363">··</text:span>C' | <text:span text:style-name="T170">split</text:span><text:span text:style-name="T204">('</text:span><text:span text:style-name="T364">·</text:span><text:span text:style-name="T204">') }<text:tab/><text:tab/>→</text:span><text:span text:style-name="T207"> </text:span><text:span text:style-name="T206">['A', 'B', </text:span><text:span text:style-name="T213">'', </text:span><text:span text:style-name="T206">'C']</text:span></text:p>
+ <text:p text:style-name="P311">%{ 'A<text:span text:style-name="T363">·</text:span>B<text:span text:style-name="T363">··</text:span>C' | <text:span text:style-name="T204">split</text:span><text:span text:style-name="T170">()</text:span><text:span text:style-name="T204"> }<text:tab/><text:tab/>→</text:span><text:span text:style-name="T207"> </text:span><text:span text:style-name="T206">['A', 'B',</text:span><text:span text:style-name="T213"> </text:span><text:span text:style-name="T206">'C']</text:span></text:p>
+ <text:p text:style-name="P311"><text:span text:style-name="T206">%{ 'A</text:span><text:span text:style-name="T366">·</text:span><text:span text:style-name="T206">B</text:span><text:span text:style-name="T365">··</text:span><text:span text:style-name="T206">C' | split('</text:span><text:span text:style-name="T365">·</text:span><text:span text:style-name="T206">', </text:span><text:span text:style-name="T180">1</text:span><text:span text:style-name="T206">) } <text:tab/></text:span><text:span text:style-name="T207">→ </text:span><text:span text:style-name="T206">['A', </text:span><text:span text:style-name="T180">'B</text:span><text:span text:style-name="T367">··</text:span><text:span text:style-name="T180">C'</text:span><text:span text:style-name="T206">]</text:span></text:p>
<text:p text:style-name="P253"/>
- <text:p text:style-name="P138">filter<text:span text:style-name="T202">()</text:span></text:p>
- <text:p text:style-name="P255">removes empty elements from <text:span text:style-name="T286">the input</text:span> list:</text:p>
- <text:p text:style-name="P308"><text:span text:style-name="T204">%{ ['A', '', 'C'] | </text:span><text:span text:style-name="T178">filter</text:span><text:span text:style-name="T204">() }<text:tab/>→</text:span><text:span text:style-name="T202"> ['A', 'C']</text:span></text:p>
- <text:p text:style-name="P287"><text:soft-page-break/>match<text:span text:style-name="T202">(</text:span><text:span text:style-name="T49">regexp</text:span><text:span text:style-name="T202">, </text:span><text:span text:style-name="T49">default</text:span><text:span text:style-name="T202">='')</text:span></text:p>
- <text:p text:style-name="P256"><text:span text:style-name="T202">returns the input string</text:span><text:span text:style-name="T161">, if </text:span><text:span text:style-name="T49">regexp</text:span><text:span text:style-name="T161"> matches somewhere in it. If </text:span><text:span text:style-name="T49">regexp</text:span><text:span text:style-name="T161"> contains matching groups (parentheses), the substring matching the first group is returned. If no match is found, the </text:span><text:span text:style-name="T49">default</text:span><text:span text:style-name="T161"> string is returned:</text:span></text:p>
- <text:p text:style-name="P308"><text:span text:style-name="T161">%{ 'Douglas Adams' | </text:span><text:span text:style-name="T158">match</text:span><text:span text:style-name="T161">('Adam') }<text:tab/><text:tab/>→ 'Douglas Adams'</text:span></text:p>
- <text:p text:style-name="P308"><text:span text:style-name="T161">%{ 'Douglas Adams' | match(</text:span><text:span text:style-name="T158">'Eve'</text:span><text:span text:style-name="T161">) }<text:tab/><text:tab/>→ ''</text:span></text:p>
- <text:p text:style-name="P308"><text:span text:style-name="T161">%{ 'Douglas Adams' | match('Abel', </text:span><text:span text:style-name="T158">'Cain'</text:span><text:span text:style-name="T161">) }<text:tab/>→ 'Cain'</text:span></text:p>
- <text:p text:style-name="P308"><text:span text:style-name="T161">%{ 'Douglas Adams' | match('l</text:span><text:span text:style-name="T158">(.*)</text:span><text:span text:style-name="T161">m') }<text:tab/><text:tab/>→ 'as Ada'</text:span></text:p>
- <text:p text:style-name="P289"><text:span text:style-name="T158">wordwrap</text:span><text:span text:style-name="T161">(width=79, break_long_words=true, break_on_hyphens=true, <text:s text:c="2"/><text:line-break/> <text:s text:c="8"/>wrapstring=none)</text:span></text:p>
- <text:p text:style-name="P258"><text:span text:style-name="T161">replaces the </text:span><text:span text:style-name="T162">builtin </text:span><text:span text:style-name="T50">Jinja </text:span><text:span text:style-name="T162">filter 'wordwrap' <text:s/>by a private version that allows to suppress breaks on hyphens:</text:span></text:p>
- <text:p text:style-name="P305">%{'long-hyphenated-text'|<text:span text:style-name="T168">wordwrap</text:span>(15, false)}</text:p>
- <text:p text:style-name="P309"><text:span text:style-name="T162">→</text:span><text:span text:style-name="T161"> 'long- </text:span></text:p>
+ <text:p text:style-name="P138">filter<text:span text:style-name="T204">()</text:span></text:p>
+ <text:p text:style-name="P255">removes empty elements from <text:span text:style-name="T288">the input</text:span> list:</text:p>
+ <text:p text:style-name="P308"><text:span text:style-name="T206">%{ ['A', '', 'C'] | </text:span><text:span text:style-name="T180">filter</text:span><text:span text:style-name="T206">() }<text:tab/>→</text:span><text:span text:style-name="T204"> ['A', 'C']</text:span></text:p>
+ <text:p text:style-name="P287"><text:soft-page-break/>match<text:span text:style-name="T204">(</text:span><text:span text:style-name="T49">regexp</text:span><text:span text:style-name="T204">, </text:span><text:span text:style-name="T49">default</text:span><text:span text:style-name="T204">='')</text:span></text:p>
+ <text:p text:style-name="P256"><text:span text:style-name="T204">returns the input string</text:span><text:span text:style-name="T163">, if </text:span><text:span text:style-name="T49">regexp</text:span><text:span text:style-name="T163"> matches somewhere in it. If </text:span><text:span text:style-name="T49">regexp</text:span><text:span text:style-name="T163"> contains matching groups (parentheses), the substring matching the first group is returned. If no match is found, the </text:span><text:span text:style-name="T49">default</text:span><text:span text:style-name="T163"> string is returned:</text:span></text:p>
+ <text:p text:style-name="P308"><text:span text:style-name="T163">%{ 'Douglas Adams' | </text:span><text:span text:style-name="T160">match</text:span><text:span text:style-name="T163">('Adam') }<text:tab/><text:tab/>→ 'Douglas Adams'</text:span></text:p>
+ <text:p text:style-name="P308"><text:span text:style-name="T163">%{ 'Douglas Adams' | match(</text:span><text:span text:style-name="T160">'Eve'</text:span><text:span text:style-name="T163">) }<text:tab/><text:tab/>→ ''</text:span></text:p>
+ <text:p text:style-name="P308"><text:span text:style-name="T163">%{ 'Douglas Adams' | match('Abel', </text:span><text:span text:style-name="T160">'Cain'</text:span><text:span text:style-name="T163">) }<text:tab/>→ 'Cain'</text:span></text:p>
+ <text:p text:style-name="P308"><text:span text:style-name="T163">%{ 'Douglas Adams' | match('l</text:span><text:span text:style-name="T160">(.*)</text:span><text:span text:style-name="T163">m') }<text:tab/><text:tab/>→ 'as Ada'</text:span></text:p>
+ <text:p text:style-name="P289"><text:span text:style-name="T160">wordwrap</text:span><text:span text:style-name="T163">(width=79, break_long_words=true, break_on_hyphens=true, <text:s text:c="2"/><text:line-break/> <text:s text:c="8"/>wrapstring=none)</text:span></text:p>
+ <text:p text:style-name="P258"><text:span text:style-name="T163">replaces the </text:span><text:span text:style-name="T164">builtin </text:span><text:span text:style-name="T50">Jinja </text:span><text:span text:style-name="T164">filter 'wordwrap' <text:s/>by a private version that allows to suppress breaks on hyphens:</text:span></text:p>
+ <text:p text:style-name="P305">%{'long-hyphenated-text'|<text:span text:style-name="T170">wordwrap</text:span>(15, false)}</text:p>
+ <text:p text:style-name="P309"><text:span text:style-name="T164">→</text:span><text:span text:style-name="T163"> 'long- </text:span></text:p>
<text:p text:style-name="P306"><text:s text:c="3"/>hyphenated-text'</text:p>
<text:p text:style-name="P309"/>
- <text:p text:style-name="P305">%{'long-hyphenated-text'|wordwrap(15, false, <text:span text:style-name="T168">false</text:span>)} </text:p>
- <text:p text:style-name="P309"><text:span text:style-name="T162">→</text:span><text:span text:style-name="T161"> 'long-</text:span><text:span text:style-name="T162">hyphenated-text'</text:span></text:p>
+ <text:p text:style-name="P305">%{'long-hyphenated-text'|wordwrap(15, false, <text:span text:style-name="T170">false</text:span>)} </text:p>
+ <text:p text:style-name="P309"><text:span text:style-name="T164">→</text:span><text:span text:style-name="T163"> 'long-</text:span><text:span text:style-name="T164">hyphenated-text'</text:span></text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2554_1114405012"/>Loops<text:bookmark-end text:name="__RefHeading__2554_1114405012"/></text:h>
- <text:p text:style-name="P28">Text in a template may be used repeatedly, like a classical 'for' loop. Loops are defined by structured comments <text:span text:style-name="T270">i.e. lines </text:span>beginning with '#%'. <text:span text:style-name="T270">They </text:span>start with '#% for … <text:span text:style-name="T199">in …:</text:span>' and end in '#% endfor':</text:p>
- <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T168">#% for</text:span> countdown <text:span text:style-name="T168">in</text:span> [3, 2, 1, '<text:span text:style-name="T270">liftoff</text:span>']<text:span text:style-name="T168">:</text:span></text:p>
+ <text:p text:style-name="P28">Text in a template may be used repeatedly, like a classical 'for' loop. Loops are defined by structured comments <text:span text:style-name="T272">i.e. lines </text:span>beginning with '#%'. <text:span text:style-name="T272">They </text:span>start with '#% for … <text:span text:style-name="T201">in …:</text:span>' and end in '#% endfor':</text:p>
+ <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T170">#% for</text:span> countdown <text:span text:style-name="T170">in</text:span> [3, 2, 1, '<text:span text:style-name="T272">liftoff</text:span>']<text:span text:style-name="T170">:</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text">echo %{countdown}</text:p>
<text:p text:style-name="P128">#% endfor</text:p>
- <text:p text:style-name="P28">will <text:span text:style-name="T197">be expanded by </text:span><text:span text:style-name="T30">mkexp</text:span><text:span text:style-name="T197"> to </text:span>yield</text:p>
+ <text:p text:style-name="P28">will <text:span text:style-name="T199">be expanded by </text:span><text:span text:style-name="T30">mkexp</text:span><text:span text:style-name="T199"> to </text:span>yield</text:p>
<text:p text:style-name="Preformatted_20_Text">echo 3</text:p>
<text:p text:style-name="Preformatted_20_Text">echo 2</text:p>
<text:p text:style-name="Preformatted_20_Text">echo 1</text:p>
- <text:p text:style-name="Preformatted_20_Text">echo <text:span text:style-name="T270">liftoff</text:span></text:p>
- <text:p text:style-name="P31"><text:span text:style-name="T199">You may of course use expressions in the loop definition. </text:span>For classical, index based loops, there is a 'range' function as in Python, <text:span text:style-name="T199">and the size of a list is queried with the 'length' filter</text:span>.</text:p>
- <text:p text:style-name="P144">#% for index in <text:span text:style-name="T168">range(1, </text:span><text:span text:style-name="T171">PATH|length()</text:span><text:span text:style-name="T168">)</text:span> <text:s/><text:span text:style-name="T199"># PATH was defined in </text:span><text:span text:style-name="T199"><text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__1669_1438093122">2.3.1</text:bookmark-ref></text:span></text:p>
- <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T199">echo</text:span> %<text:span text:style-name="T200">{index}: </text:span>%{<text:span text:style-name="T199">PATH[</text:span>index<text:span text:style-name="T199">]</text:span>} <text:s/></text:p>
+ <text:p text:style-name="Preformatted_20_Text">echo <text:span text:style-name="T272">liftoff</text:span></text:p>
+ <text:p text:style-name="P31"><text:span text:style-name="T201">You may of course use expressions in the loop definition. </text:span>For classical, index based loops, there is a 'range' function as in Python, <text:span text:style-name="T201">and the size of a list is queried with the 'length' filter</text:span>.</text:p>
+ <text:p text:style-name="P144">#% for index in <text:span text:style-name="T170">range(1, </text:span><text:span text:style-name="T173">PATH|length()</text:span><text:span text:style-name="T170">)</text:span> <text:s/><text:span text:style-name="T201"># PATH was defined in </text:span><text:span text:style-name="T201"><text:bookmark-ref text:reference-format="chapter" text:ref-name="__RefHeading__1669_1438093122">2.3.1</text:bookmark-ref></text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T201">echo</text:span> %<text:span text:style-name="T202">{index}: </text:span>%{<text:span text:style-name="T201">PATH[</text:span>index<text:span text:style-name="T201">]</text:span>} <text:s/></text:p>
<text:p text:style-name="Preformatted_20_Text">#% endfor</text:p>
- <text:p text:style-name="Text_20_body">Note that <text:span text:style-name="T198">indexing of lists starts at 0,</text:span> <text:span text:style-name="T198">i.e. the first element of the PATH list is skipped. Besides, </text:span>the stop index <text:span text:style-name="T200">is</text:span> not included, i.e. <text:span text:style-name="T199">as PATH has a length of 3, </text:span>the last looping has index <text:span text:style-name="T198">2</text:span>:</text:p>
- <text:p text:style-name="Preformatted_20_Text">echo <text:span text:style-name="T200">1: </text:span>/usr/bin </text:p>
- <text:p text:style-name="Preformatted_20_Text"><text:soft-page-break/>echo <text:span text:style-name="T200">2: </text:span>/usr/local/bin </text:p>
- <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2556_1114405012"/>Condition<text:span text:style-name="T197">s</text:span><text:bookmark-end text:name="__RefHeading__2556_1114405012"/></text:h>
- <text:p text:style-name="P29">A template may contain alternative parts <text:span text:style-name="T200">that are selected depending on the .config data</text:span>, <text:span text:style-name="T200">similar to an 'if' statement. This is useful for e.g. skipping certain parts of the script template that are not applicable to runs of a given resolution but required for others. They are also implemented as structured comments, starting with '#% if …:' and ending in '#% endif', with optional '#% elif …:' and '#% else:' parts.</text:span></text:p>
- <text:p text:style-name="P30"><text:span text:style-name="T200">For testing, you may use expressions with comparisons (==, !=, >, >=, <, <=), querying a certain list element (… in …), and logical operators (and, or, not). Sub-expressions may be parenthesized to change the order of evaluation. Besides, </text:span><text:span text:style-name="T14">Jinja</text:span><text:span text:style-name="T200"> provides a number of named tests that use the '… is …' Syntax.</text:span></text:p>
- <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T168">#% if </text:span><text:span text:style-name="T203">PATH|length()</text:span><text:span text:style-name="T201"> </text:span><text:span text:style-name="T172">is divisibleby 3:</text:span></text:p>
+ <text:p text:style-name="Text_20_body">Note that <text:span text:style-name="T200">indexing of lists starts at 0,</text:span> <text:span text:style-name="T200">i.e. the first element of the PATH list is skipped. Besides, </text:span>the stop index <text:span text:style-name="T202">is</text:span> not included, i.e. <text:span text:style-name="T201">as PATH has a length of 3, </text:span>the last looping has index <text:span text:style-name="T200">2</text:span>:</text:p>
+ <text:p text:style-name="Preformatted_20_Text">echo <text:span text:style-name="T202">1: </text:span>/usr/bin </text:p>
+ <text:p text:style-name="Preformatted_20_Text"><text:soft-page-break/>echo <text:span text:style-name="T202">2: </text:span>/usr/local/bin </text:p>
+ <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2556_1114405012"/>Condition<text:span text:style-name="T199">s</text:span><text:bookmark-end text:name="__RefHeading__2556_1114405012"/></text:h>
+ <text:p text:style-name="P29">A template may contain alternative parts <text:span text:style-name="T202">that are selected depending on the .config data</text:span>, <text:span text:style-name="T202">similar to an 'if' statement. This is useful for e.g. skipping certain parts of the script template that are not applicable to runs of a given resolution but required for others. They are also implemented as structured comments, starting with '#% if …:' and ending in '#% endif', with optional '#% elif …:' and '#% else:' parts.</text:span></text:p>
+ <text:p text:style-name="P30"><text:span text:style-name="T202">For testing, you may use expressions with comparisons (==, !=, >, >=, <, <=), querying a certain list element (… in …), and logical operators (and, or, not). Sub-expressions may be parenthesized to change the order of evaluation. Besides, </text:span><text:span text:style-name="T14">Jinja</text:span><text:span text:style-name="T202"> provides a number of named tests that use the '… is …' Syntax.</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T170">#% if </text:span><text:span text:style-name="T205">PATH|length()</text:span><text:span text:style-name="T203"> </text:span><text:span text:style-name="T174">is divisibleby 3:</text:span></text:p>
<text:p text:style-name="P162">diff3 %{PATH[:3]|join(' ')}</text:p>
- <text:p text:style-name="P131">#% elif <text:span text:style-name="T203">PATH|length()</text:span> is even:</text:p>
+ <text:p text:style-name="P131">#% elif <text:span text:style-name="T205">PATH|length()</text:span> is even:</text:p>
<text:p text:style-name="P145">diff %{PATH[:2]|join(' ')}</text:p>
<text:p text:style-name="P128">#% else:</text:p>
- <text:p text:style-name="Preformatted_20_Text">echo <text:span text:style-name="T212">cannot handle PATH</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text">echo <text:span text:style-name="T214">cannot handle PATH</text:span></text:p>
<text:p text:style-name="P128">#% endif</text:p>
<text:p text:style-name="P37">If PATH is defined as in the examples above, this will result in</text:p>
<text:p text:style-name="Preformatted_20_Text">diff3 /bin /usr/bin /usr/local/bin</text:p>
- <text:p text:style-name="P113"><text:span text:style-name="T200">For a list of available tests, see the </text:span><text:span text:style-name="T15">Jinja</text:span><text:span text:style-name="T213"> documentation. </text:span><text:span text:style-name="T284">Besides, </text:span><text:span text:style-name="T15">mkexp</text:span><text:span text:style-name="T213"> defines </text:span><text:span text:style-name="T287">a</text:span><text:span text:style-name="T352">n</text:span><text:span text:style-name="T287"> </text:span><text:span text:style-name="T213">additional </text:span><text:span text:style-name="T343">test</text:span><text:span text:style-name="T213">:</text:span></text:p>
- <text:p text:style-name="P302"><text:span text:style-name="T234">set</text:span><text:span text:style-name="T204">(</text:span><text:span text:style-name="T163">)</text:span></text:p>
- <text:p text:style-name="P274"><text:span text:style-name="T164">tests if a string evaluates to</text:span><text:span text:style-name="T51"> true</text:span><text:span text:style-name="T164"> when used as namelist </text:span><text:span text:style-name="T339">logical</text:span><text:span text:style-name="T164">. Returns</text:span><text:span text:style-name="T51"> false</text:span><text:span text:style-name="T164"> when used on an undefined variable:</text:span></text:p>
- <text:p text:style-name="P310"><text:span text:style-name="T352">'</text:span><text:span text:style-name="T210">.true.</text:span><text:span text:style-name="T352">' </text:span><text:span text:style-name="T182">is set</text:span><text:span text:style-name="T202"><text:tab/><text:tab/>→</text:span><text:span text:style-name="T205"> </text:span><text:span text:style-name="T230">true</text:span></text:p>
- <text:p text:style-name="P310"><text:span text:style-name="T210">'T' </text:span><text:span text:style-name="T182">is set<text:tab/><text:tab/></text:span><text:span text:style-name="T204"><text:tab/></text:span><text:span text:style-name="T205">→ </text:span><text:span text:style-name="T230">true</text:span></text:p>
- <text:p text:style-name="P310"><text:span text:style-name="T230">'fAlSe' </text:span><text:span text:style-name="T234">is set<text:tab/><text:tab/></text:span><text:span text:style-name="T231">→ </text:span><text:span text:style-name="T230">false</text:span></text:p>
- <text:p text:style-name="P310"><text:span text:style-name="T230">un</text:span><text:span text:style-name="T232">known_var</text:span><text:span text:style-name="T230"> </text:span><text:span text:style-name="T234">is set<text:tab/></text:span><text:span text:style-name="T231">→ </text:span><text:span text:style-name="T230">false</text:span></text:p>
+ <text:p text:style-name="P113"><text:span text:style-name="T202">For a list of available tests, see the </text:span><text:span text:style-name="T15">Jinja</text:span><text:span text:style-name="T215"> documentation. </text:span><text:span text:style-name="T286">Besides, </text:span><text:span text:style-name="T15">mkexp</text:span><text:span text:style-name="T215"> defines </text:span><text:span text:style-name="T289">a</text:span><text:span text:style-name="T356">n</text:span><text:span text:style-name="T289"> </text:span><text:span text:style-name="T215">additional </text:span><text:span text:style-name="T347">test</text:span><text:span text:style-name="T215">:</text:span></text:p>
+ <text:p text:style-name="P302"><text:span text:style-name="T236">set</text:span><text:span text:style-name="T206">(</text:span><text:span text:style-name="T165">)</text:span></text:p>
+ <text:p text:style-name="P274"><text:span text:style-name="T166">tests if a string evaluates to</text:span><text:span text:style-name="T51"> true</text:span><text:span text:style-name="T166"> when used as namelist </text:span><text:span text:style-name="T341">logical</text:span><text:span text:style-name="T166">. Returns</text:span><text:span text:style-name="T51"> false</text:span><text:span text:style-name="T166"> when used on an undefined variable:</text:span></text:p>
+ <text:p text:style-name="P310"><text:span text:style-name="T356">'</text:span><text:span text:style-name="T212">.true.</text:span><text:span text:style-name="T356">' </text:span><text:span text:style-name="T184">is set</text:span><text:span text:style-name="T204"><text:tab/><text:tab/>→</text:span><text:span text:style-name="T207"> </text:span><text:span text:style-name="T232">true</text:span></text:p>
+ <text:p text:style-name="P310"><text:span text:style-name="T212">'T' </text:span><text:span text:style-name="T184">is set<text:tab/><text:tab/></text:span><text:span text:style-name="T206"><text:tab/></text:span><text:span text:style-name="T207">→ </text:span><text:span text:style-name="T232">true</text:span></text:p>
+ <text:p text:style-name="P310"><text:span text:style-name="T232">'fAlSe' </text:span><text:span text:style-name="T236">is set<text:tab/><text:tab/></text:span><text:span text:style-name="T233">→ </text:span><text:span text:style-name="T232">false</text:span></text:p>
+ <text:p text:style-name="P310"><text:span text:style-name="T232">un</text:span><text:span text:style-name="T234">known_var</text:span><text:span text:style-name="T232"> </text:span><text:span text:style-name="T236">is set<text:tab/></text:span><text:span text:style-name="T233">→ </text:span><text:span text:style-name="T232">false</text:span></text:p>
<text:p text:style-name="P254"/>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2558_1114405012"/>Comments<text:bookmark-end text:name="__RefHeading__2558_1114405012"/></text:h>
- <text:p text:style-name="P61"><text:span text:style-name="T9">Jinj</text:span>a also allows template comments that are removed when the template is expanded. This is implemented as another kind of structured comment starting with <text:span text:style-name="T271">'#%</text:span>#':</text:p>
+ <text:p text:style-name="P61"><text:span text:style-name="T9">Jinj</text:span>a also allows template comments that are removed when the template is expanded. This is implemented as another kind of structured comment starting with <text:span text:style-name="T273">'#%</text:span>#':</text:p>
<text:p text:style-name="Preformatted_20_Text"># This comment will make it to the expanded script</text:p>
- <text:p text:style-name="Preformatted_20_Text">#%# This one will not make it <text:span text:style-name="T222">and is for template documentation only</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text">#%# This one will not make it <text:span text:style-name="T224">and is for template documentation only</text:span></text:p>
<text:h text:style-name="P334" text:outline-level="3"><text:bookmark-start text:name="__RefHeading___Toc3658_1790556471"/>Block statements and block comments<text:bookmark-end text:name="__RefHeading___Toc3658_1790556471"/></text:h>
<text:p text:style-name="P100">For templates that contain more <text:span text:style-name="T9">Jinja</text:span><text:span text:style-name="T56"> code than actual output lines, a variant of the </text:span><text:soft-page-break/><text:span text:style-name="T56">standard </text:span><text:span text:style-name="T9">Jinja </text:span><text:span text:style-name="T56">block synta</text:span><text:span text:style-name="T112">x i</text:span><text:span text:style-name="T56">s available for both statements and comments</text:span><text:span text:style-name="T56"><text:note text:id="ftn1" text:note-class="footnote"><text:note-citation>1</text:note-citation><text:note-body>
- <text:p text:style-name="P348">The standard <text:span text:style-name="T9">Jinja</text:span><text:span text:style-name="T56"> comment syntax '{#' collides with the Bourne shell idiom for variable size, '$â </text:span><text:span text:style-name="T166">{#</text:span><text:span text:style-name="T161">var</text:span><text:span text:style-name="T56">}'. </text:span><text:span text:style-name="T112">Standard b</text:span><text:span text:style-name="T56">lock statement syntax '{%' gives problems when </text:span><text:span text:style-name="T112">mkexp </text:span><text:span text:style-name="T56">template variables </text:span><text:span text:style-name="T112">'%{var}' </text:span><text:span text:style-name="T56">are used </text:span><text:span text:style-name="T112">in</text:span><text:span text:style-name="T56"> shell variable </text:span><text:span text:style-name="T112">expansions</text:span><text:span text:style-name="T56">, like '$</text:span><text:span text:style-name="T166">{%</text:span><text:span text:style-name="T56">{</text:span><text:span text:style-name="T112">var}:-default}'</text:span></text:p></text:note-body></text:note></text:span><text:span text:style-name="T56">. Block statements begin with '{%__mkexp__' and end with '%}', block comments begin with '{#__mkexp__' and end with '#}'.</text:span></text:p>
+ <text:p text:style-name="P348">The standard <text:span text:style-name="T9">Jinja</text:span><text:span text:style-name="T56"> comment syntax '{#' collides with the Bourne shell idiom for variable size, '$â </text:span><text:span text:style-name="T168">{#</text:span><text:span text:style-name="T163">var</text:span><text:span text:style-name="T56">}'. </text:span><text:span text:style-name="T112">Standard b</text:span><text:span text:style-name="T56">lock statement syntax '{%' gives problems when </text:span><text:span text:style-name="T112">mkexp </text:span><text:span text:style-name="T56">template variables </text:span><text:span text:style-name="T112">'%{var}' </text:span><text:span text:style-name="T56">are used </text:span><text:span text:style-name="T112">in</text:span><text:span text:style-name="T56"> shell variable </text:span><text:span text:style-name="T112">expansions</text:span><text:span text:style-name="T56">, like '$</text:span><text:span text:style-name="T168">{%</text:span><text:span text:style-name="T56">{</text:span><text:span text:style-name="T112">var}:-default}'</text:span></text:p></text:note-body></text:note></text:span><text:span text:style-name="T56">. Block statements begin with '{%__mkexp__' and end with '%}', block comments begin with '{#__mkexp__' and end with '#}'.</text:span></text:p>
<text:h text:style-name="P346" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2560_1114405012"/>Standard experiment<text:span text:style-name="T54">s</text:span><text:bookmark-end text:name="__RefHeading__2560_1114405012"/></text:h>
<text:p text:style-name="P16">When generating an experiment setup, <text:span text:style-name="T9">mkexp</text:span> expects the .config and .tmpl files to reside in a subdirectory of the current working directory, called 'standard_experiments'.</text:p>
<text:p text:style-name="P10"><text:span text:style-name="T8">The definition of a standard experiment type </text:span><text:span text:style-name="T10">typename</text:span><text:span text:style-name="T8"> may consist of a configuration in </text:span><text:span text:style-name="T10">typename</text:span><text:span text:style-name="T8">.config and a number of </text:span><text:span text:style-name="T10">typename</text:span><text:span text:style-name="T8">.</text:span><text:span text:style-name="T10">jobname</text:span><text:span text:style-name="T8">.tmpl files, one for each subsection </text:span><text:span text:style-name="T10">jobname</text:span><text:span text:style-name="T8"> of the jobs section. Before reading </text:span><text:span text:style-name="T10">typename</text:span><text:span text:style-name="T8">.config, the special DEFAULT.config is loaded, containing the model default settings. Both .config and .tmpl files may be missing; the default is to read only DEFAULT.config or the corresponding DEFAULT.</text:span><text:span text:style-name="T10">jobname</text:span><text:span text:style-name="T8">.tmpl file instead.</text:span></text:p>
@@ -3214,12 +3275,12 @@
<text:p text:style-name="P11">Besides the standard experiment types, <text:span text:style-name="T9">mkexp</text:span> also supports option sets that are independent of the experiment type chosen.</text:p>
<text:p text:style-name="P11">Usually these option sets contain a number of settings needed for a certain technical aspect, e.g. for changing the output interval or aggregation method for output data, or providing resolution dependent model settings. They reside in a subdirectory 'standard_options' of the current working directory, each in their respective <text:span text:style-name="T9">optionname</text:span>.config file.</text:p>
<text:p text:style-name="P11">Within the experiment's .config file, options are selected by setting the variable EXP_OPTIONS to the list of required option names. These settings are loaded after the experiment type configuration but before the user defined experiment configuration.</text:p>
- <text:h text:style-name="P333" text:outline-level="3"><text:bookmark-start text:name="__RefHeading___Toc3660_1790556471"/><text:soft-page-break/><text:span text:style-name="T291">O</text:span>ptions set due to model configuration <text:bookmark-end text:name="__RefHeading___Toc3660_1790556471"/></text:h>
- <text:p text:style-name="P97">Some options may need to be set <text:span text:style-name="T290">for all experiments that use a given </text:span>model configuration. <text:span text:style-name="T290">If e.g. a part of the model is disabled at build time, the corresponding option set should also be disabled for all experiments.</text:span></text:p>
+ <text:h text:style-name="P333" text:outline-level="3"><text:bookmark-start text:name="__RefHeading___Toc3660_1790556471"/><text:soft-page-break/><text:span text:style-name="T293">O</text:span>ptions set due to model configuration <text:bookmark-end text:name="__RefHeading___Toc3660_1790556471"/></text:h>
+ <text:p text:style-name="P97">Some options may need to be set <text:span text:style-name="T292">for all experiments that use a given </text:span>model configuration. <text:span text:style-name="T292">If e.g. a part of the model is disabled at build time, the corresponding option set should also be disabled for all experiments.</text:span></text:p>
<text:p text:style-name="P98">For this, the build process may write an optional file 'SETUP.config' <text:s/>that is read before any type or user configuration. If this file contains the variable SETUP_OPTIONS, the options listed there will be loaded before loading the EXP_OPTIONS list. Do not override SETUP_OPTIONS in the user configuration unless you know what you are doing!</text:p>
- <text:h text:style-name="P343" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1508_1711940803"/>Generating <text:span text:style-name="T238">j</text:span>obs<text:bookmark-end text:name="__RefHeading__1508_1711940803"/></text:h>
- <text:p text:style-name="P42">When<text:span text:style-name="T218"> </text:span>running <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T134">, </text:span><text:span text:style-name="T135">the special configuration section [jobs]</text:span><text:span text:style-name="T47"> </text:span><text:span text:style-name="T135">is read and evaluated. Each of its subsections, e.g. [[run]], defines a job definition file or job script to be created.</text:span></text:p>
- <text:p text:style-name="P163"># <text:span text:style-name="T219">model setup: experiment type 'control'</text:span></text:p>
+ <text:h text:style-name="P343" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1508_1711940803"/>Generating <text:span text:style-name="T240">j</text:span>obs<text:bookmark-end text:name="__RefHeading__1508_1711940803"/></text:h>
+ <text:p text:style-name="P42">When<text:span text:style-name="T220"> </text:span>running <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T134">, </text:span><text:span text:style-name="T135">the special configuration section [jobs]</text:span><text:span text:style-name="T47"> </text:span><text:span text:style-name="T135">is read and evaluated. Each of its subsections, e.g. [[run]], defines a job definition file or job script to be created.</text:span></text:p>
+ <text:p text:style-name="P163"># <text:span text:style-name="T221">model setup: experiment type 'control'</text:span></text:p>
<text:p text:style-name="P150">[jobs]</text:p>
<text:p text:style-name="P150"><text:s text:c="2"/>[[pre]]</text:p>
<text:p text:style-name="P150"><text:s text:c="2"/>[[run]]</text:p>
@@ -3235,12 +3296,13 @@
<text:p text:style-name="P150"><text:s text:c="2"/>[[my_pre]]</text:p>
<text:p text:style-name="P150"><text:soft-page-break/><text:s text:c="2"/>[[my_post]]</text:p>
<text:p text:style-name="P49">This way, the 'pre' and 'post' jobs will not be created in favor of two new jobs, 'my_pre' and 'my_post'. In this case, the user setup must provide two templates 'joe1234.my_pre.tmpl' and 'joe1234.my_post.tmpl', together with the .config file.</text:p>
- <text:p text:style-name="P45">Alternatively, you may want to introduce a new 'my_p<text:span text:style-name="T220">ost</text:span>' job, that is basically the same as the old 'p<text:span text:style-name="T220">ost</text:span>' job but uses a slightly different configuration. This may be done using the special section variable '.extends'.</text:p>
+ <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading___Toc4462_1592844343"/>Creating derived jobs<text:bookmark-end text:name="__RefHeading___Toc4462_1592844343"/></text:h>
+ <text:p text:style-name="P378">Alternatively, you may want to introduce a new 'my_p<text:span text:style-name="T222">ost</text:span>' job, that is basically the same as the old 'p<text:span text:style-name="T222">ost</text:span>' job but uses a slightly different configuration. This may be done using the special section variable '.extends'.</text:p>
<text:p text:style-name="P150">[jobs]</text:p>
<text:p text:style-name="P164"><text:span text:style-name="T134"><text:s text:c="2"/>[[my_p</text:span><text:span text:style-name="T139">ost</text:span><text:span text:style-name="T134">]]</text:span></text:p>
<text:p text:style-name="P164"><text:span text:style-name="T134"><text:s text:c="4"/>.</text:span><text:span text:style-name="T138">extends</text:span><text:span text:style-name="T134"> = p</text:span><text:span text:style-name="T139">ost</text:span></text:p>
<text:p text:style-name="P151"><text:s text:c="4"/>command = $HOME/bin/my_special_command</text:p>
- <text:p text:style-name="P50">With this configuration, an additional 'joe1234.my_post' is created based on the existing 'post' template. A dedicated 'joe1234.my_post.tmpl' file is not needed here. The 'command' setting is <text:span text:style-name="T221">made available </text:span>to <text:span text:style-name="T221">the template via the</text:span> 'JOB' dictionary.</text:p>
+ <text:p text:style-name="P50">With this configuration, an additional 'joe1234.my_post' is created based on the existing 'post' template. A dedicated 'joe1234.my_post.tmpl' file is not needed here. The 'command' setting is <text:span text:style-name="T223">made available </text:span>to <text:span text:style-name="T223">the template </text:span><text:span text:style-name="T371">both as a global setting and </text:span><text:span text:style-name="T223">via the</text:span> 'JOB' dictionary.</text:p>
<text:h text:style-name="P324" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2568_1114405012"/>Pre-defined job variables<text:bookmark-end text:name="__RefHeading__2568_1114405012"/></text:h>
<text:p text:style-name="P55">While <text:span text:style-name="T9">mkexp</text:span> in general does not impose any naming convention on the variable names used in the job sections and leaves the details to the respective model setup, there are a few exceptions.</text:p>
<text:p text:style-name="P212">tasks</text:p>
@@ -3249,19 +3311,19 @@
<text:p text:style-name="P235">Number of computing nodes required on the computing system. Needed if 'tasks' is not set.</text:p>
<text:p text:style-name="P213">tasks_per_node</text:p>
<text:p text:style-name="P235">Number of parallel (MPI) tasks on a single node. Needed if 'tasks' is not set.</text:p>
- <text:h text:style-name="P323" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2570_1114405012"/>Overriding namelist settings in derived jobs<text:bookmark-end text:name="__RefHeading__2570_1114405012"/></text:h>
- <text:p text:style-name="P50">There is special provision to change namelist files settings for a specific job. Consider this setting from the introductory example.</text:p>
+ <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2570_1114405012"/><text:span text:style-name="T134">Overriding </text:span><text:span text:style-name="T369">global</text:span><text:span text:style-name="T134"> </text:span><text:span text:style-name="T152">or </text:span><text:span text:style-name="T370">derived</text:span><text:span text:style-name="T152"> </text:span><text:span text:style-name="T134">settings in jobs</text:span><text:bookmark-end text:name="__RefHeading__2570_1114405012"/></text:h>
+ <text:p text:style-name="P376"><text:span text:style-name="T139">There is special provision to change </text:span><text:span text:style-name="T343">global or </text:span><text:span text:style-name="T344">derived</text:span><text:span text:style-name="T343"> </text:span><text:span text:style-name="T139">settings for a specific job. Consider this setting from the introductory example.</text:span></text:p>
<text:p text:style-name="P165">[namelists]</text:p>
<text:p text:style-name="P118"><text:s text:c="2"/>[[namelist.jsbach]]</text:p>
<text:p text:style-name="P118"><text:s text:c="4"/>[[[jsbach_ctl]]]</text:p>
<text:p text:style-name="P118"><text:s text:c="6"/>use_dynveg = false</text:p>
- <text:p text:style-name="P46"><text:span text:style-name="T134">If – for some reason – your experiments needs 'use_dynveg' set to 'true' for the first year only, you may create an additional 'run_first' job, </text:span><text:span text:style-name="T140">with a job specific namelists subsection that – apart from the addition</text:span><text:span text:style-name="T142">al</text:span><text:span text:style-name="T140"> brackets – has the same structure as</text:span><text:span text:style-name="T134"> </text:span><text:span text:style-name="T140">the global namelists section.</text:span></text:p>
- <text:p text:style-name="P165"><text:soft-page-break/>[jobs]</text:p>
+ <text:p text:style-name="P46"><text:span text:style-name="T134">If – for some reason – your experiments needs 'use_dynveg' set to 'true' for the first </text:span><text:soft-page-break/><text:span text:style-name="T134">year only, you may create an additional 'run_first' job, </text:span><text:span text:style-name="T140">with a job specific namelists subsection that – apart from the addition</text:span><text:span text:style-name="T142">al</text:span><text:span text:style-name="T140"> brackets – has the same structure as</text:span><text:span text:style-name="T134"> </text:span><text:span text:style-name="T140">the global namelists section.</text:span></text:p>
+ <text:p text:style-name="P165">[jobs]</text:p>
<text:p text:style-name="P165"><text:s text:c="2"/>[[run_first]]</text:p>
<text:p text:style-name="P165"><text:s text:c="4"/>.extends = run</text:p>
- <text:p text:style-name="P165"><text:s text:c="4"/><text:span text:style-name="T168">[[[namelists]]</text:span><text:span text:style-name="T177">]</text:span></text:p>
- <text:p text:style-name="P118"><text:s text:c="6"/><text:span text:style-name="T220">[[</text:span>[[namelist.jsbach]]<text:span text:style-name="T220">]]</text:span></text:p>
- <text:p text:style-name="P118"><text:s text:c="8"/><text:span text:style-name="T220">[[</text:span>[[[jsbach_ctl]]]<text:span text:style-name="T220">]]</text:span></text:p>
+ <text:p text:style-name="P165"><text:s text:c="4"/><text:span text:style-name="T170">[[[namelists]]</text:span><text:span text:style-name="T179">]</text:span></text:p>
+ <text:p text:style-name="P118"><text:s text:c="6"/><text:span text:style-name="T222">[[</text:span>[[namelist.jsbach]]<text:span text:style-name="T222">]]</text:span></text:p>
+ <text:p text:style-name="P118"><text:s text:c="8"/><text:span text:style-name="T222">[[</text:span>[[[jsbach_ctl]]]<text:span text:style-name="T222">]]</text:span></text:p>
<text:p text:style-name="P118"><text:span text:style-name="T134"><text:s text:c="10"/>use_dynveg = </text:span><text:span text:style-name="T139">true</text:span></text:p>
<text:p text:style-name="P46"><text:span text:style-name="T140">This</text:span><text:span text:style-name="T134"> 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="P323" 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>
@@ -3274,108 +3336,108 @@
<text:p text:style-name="P150">#! /bin/sh</text:p>
<text:p text:style-name="P154">NAME='%{NAME}'</text:p>
<text:p text:style-name="P150">echo %{MESSAGE}</text:p>
- <text:p text:style-name="P52">By default, <text:span text:style-name="T222">native variables are formatted as </text:span>shell script, namely ${NAME}:</text:p>
+ <text:p text:style-name="P52">By default, <text:span text:style-name="T224">native variables are formatted as </text:span>shell script, namely ${NAME}:</text:p>
<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="T237">T</text:span>o support variable reference<text:span text:style-name="T236">s for other script languages, a</text:span> job specific variable '.var_format' may be defined. <text:span text:style-name="T236">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="T222">this may look like:</text:span></text:p>
+ <text:p text:style-name="P53"><text:span text:style-name="T239">T</text:span>o support variable reference<text:span text:style-name="T238">s for other script languages, a</text:span> job specific variable '.var_format' may be defined. <text:span text:style-name="T238">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="T224">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>
<text:p text:style-name="P167">[jobs]</text:p>
- <text:p text:style-name="Preformatted_20_Text"><text:s text:c="2"/>[[job]]</text:p>
- <text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="4"/>.var_format = <text:span text:style-name="T225">"</text:span><text:span text:style-name="T223">' + str(</text:span>%s<text:span text:style-name="T235">)</text:span> <text:span text:style-name="T223">+ '</text:span><text:span text:style-name="T225">"</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text"><text:soft-page-break/><text:s text:c="2"/>[[job]]</text:p>
+ <text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="4"/>.var_format = <text:span text:style-name="T227">"</text:span><text:span text:style-name="T225">' + str(</text:span>%s<text:span text:style-name="T237">)</text:span> <text:span text:style-name="T225">+ '</text:span><text:span text:style-name="T227">"</text:span></text:p>
<text:p text:style-name="P156">#%# joe1234.job.tmpl</text:p>
- <text:p text:style-name="P168"><text:soft-page-break/>#! /usr/bin/env python </text:p>
+ <text:p text:style-name="P168">#! /usr/bin/env python </text:p>
<text:p text:style-name="Preformatted_20_Text">NAME = '%{NAME}' </text:p>
- <text:p text:style-name="Preformatted_20_Text">print<text:span text:style-name="T272">(</text:span>'%{MESSAGE}'<text:span text:style-name="T272">)</text:span> </text:p>
+ <text:p text:style-name="Preformatted_20_Text">print<text:span text:style-name="T274">(</text:span>'%{MESSAGE}'<text:span text:style-name="T274">)</text:span> </text:p>
<text:p text:style-name="P62">This setup will expand to</text:p>
<text:p text:style-name="P168">#! /usr/bin/env python </text:p>
- <text:p text:style-name="P168">NAME = '<text:span text:style-name="T235">Joe User</text:span>' </text:p>
- <text:p text:style-name="P169">print<text:span text:style-name="T272">(</text:span>'<text:span text:style-name="T134">This experiment was generated by </text:span><text:span text:style-name="T143">' + str(</text:span><text:span text:style-name="T134">NAME) </text:span><text:span text:style-name="T143">+ '</text:span>'<text:span text:style-name="T272">)</text:span></text:p>
+ <text:p text:style-name="P168">NAME = '<text:span text:style-name="T237">Joe User</text:span>' </text:p>
+ <text:p text:style-name="P169">print<text:span text:style-name="T274">(</text:span>'<text:span text:style-name="T134">This experiment was generated by </text:span><text:span text:style-name="T143">' + str(</text:span><text:span text:style-name="T134">NAME) </text:span><text:span text:style-name="T143">+ '</text:span>'<text:span text:style-name="T274">)</text:span></text:p>
<text:h text:style-name="P330" 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="T239">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="T240">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="T240"> maintains the special variable VARIABLES_. When generating output for</text:span></text:p>
+ <text:p text:style-name="P64">In the previous section, the native variables were initialized by an addition<text:span text:style-name="T241">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="T242">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="T242"> 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="P158">EMAIL = joe@domain.tld</text:p>
<text:p text:style-name="P170"><text:span text:style-name="T134">MESSAGE = This experiment was generated by $${NAME} </text:span><text:span text:style-name="T145"><$${EMAIL}></text:span></text:p>
<text:p text:style-name="P65"><text:span text:style-name="T46">mkexp</text:span><text:span text:style-name="T134"> will parse all values, recognize 'NAME' and 'EMAIL' as native variables, and </text:span><text:span text:style-name="T146">will </text:span><text:span text:style-name="T134">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="T46">mkexp</text:span><text:span text:style-name="T134"> provides the 'context' function, such that the template</text:span></text:p>
<text:p text:style-name="P157">#! /bin/sh</text:p>
- <text:p text:style-name="P158">#%# for <text:span text:style-name="T168">variable</text:span> in <text:span text:style-name="T168">VARIABLES_</text:span>:</text:p>
- <text:p text:style-name="P158">%{<text:span text:style-name="T168">variable</text:span>}='%{<text:span text:style-name="T168">context(variable)</text:span>}'</text:p>
+ <text:p text:style-name="P158">#%# for <text:span text:style-name="T170">variable</text:span> in <text:span text:style-name="T170">VARIABLES_</text:span>:</text:p>
+ <text:p text:style-name="P158">%{<text:span text:style-name="T170">variable</text:span>}='%{<text:span text:style-name="T170">context(variable)</text:span>}'</text:p>
<text:p text:style-name="P158">#%# endfor</text:p>
- <text:p text:style-name="P158">echo <text:span text:style-name="T224">"</text:span>%{MESSAGE}<text:span text:style-name="T224">"</text:span></text:p>
+ <text:p text:style-name="P158">echo <text:span text:style-name="T226">"</text:span>%{MESSAGE}<text:span text:style-name="T226">"</text:span></text:p>
<text:p text:style-name="P54">eventually yields</text:p>
<text:p text:style-name="P157">#! /bin/sh</text:p>
- <text:p text:style-name="P170"><text:span text:style-name="T153">EMAIL</text:span><text:span text:style-name="T157">='</text:span><text:span text:style-name="T153">joe@domain.tld</text:span><text:span text:style-name="T157">'</text:span></text:p>
- <text:p text:style-name="P170"><text:span text:style-name="T152">NAME</text:span><text:span text:style-name="T156">=</text:span><text:span text:style-name="T157">'</text:span><text:span text:style-name="T152">Joe User</text:span><text:span text:style-name="T157">'</text:span></text:p>
- <text:p text:style-name="P170"><text:span text:style-name="T145">echo </text:span><text:span text:style-name="T226">"This experiment was generated by ${NAME} <${EMAIL}>"</text:span></text:p>
+ <text:p text:style-name="P170"><text:span text:style-name="T155">EMAIL</text:span><text:span text:style-name="T159">='</text:span><text:span text:style-name="T155">joe@domain.tld</text:span><text:span text:style-name="T159">'</text:span></text:p>
+ <text:p text:style-name="P170"><text:span text:style-name="T154">NAME</text:span><text:span text:style-name="T158">=</text:span><text:span text:style-name="T159">'</text:span><text:span text:style-name="T154">Joe User</text:span><text:span text:style-name="T159">'</text:span></text:p>
+ <text:p text:style-name="P170"><text:span text:style-name="T145">echo </text:span><text:span text:style-name="T228">"This experiment was generated by ${NAME} <${EMAIL}>"</text:span></text:p>
<text:p text:style-name="P67">Note that the order of variable names is not necessarily the order in which they were defined in the .config file.</text:p>
- <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2576_1114405012"/>Re-generation of <text:span text:style-name="T238">s</text:span>cripts and <text:span text:style-name="T238">b</text:span>ackup<text:bookmark-end text:name="__RefHeading__2576_1114405012"/></text:h>
+ <text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2576_1114405012"/><text:soft-page-break/>Re-generation of <text:span text:style-name="T240">s</text:span>cripts and <text:span text:style-name="T240">b</text:span>ackup<text:bookmark-end text:name="__RefHeading__2576_1114405012"/></text:h>
<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="T56"> 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:soft-page-break/><text:span text:style-name="T66">A</text:span><text:span text:style-name="T56">s a convenient short-cut, </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T56"> 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="T56">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="T56"> so that './update' reg</text:span><text:span text:style-name="T101">e</text:span><text:span text:style-name="T56">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="P91"><text:span text:style-name="T66">A</text:span><text:span text:style-name="T56">s a convenient short-cut, </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T56"> 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="T56">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="T56"> so that './update' reg</text:span><text:span text:style-name="T101">e</text:span><text:span text:style-name="T56">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">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="T56">Of course, there is also the possibility to </text:span><text:span text:style-name="T66">change</text:span><text:span text:style-name="T56"> the </text:span><text:span text:style-name="T19">generated</text:span><text:span text:style-name="T65"> </text:span><text:span text:style-name="T56">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="T67">facing</text:span><text:span text:style-name="T56"> the next </text:span><text:span text:style-name="T67">change,</text:span><text:span text:style-name="T56"> this might not be the case, so eventually you </text:span><text:span text:style-name="T65">may</text:span><text:span text:style-name="T56"> 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="T56">Whenever </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T56"> 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="T65">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="T66">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="T101">after a necessary regeneration</text:span><text:span text:style-name="T66">.</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="T167">of job descriptions, namely the system or machine dependent set up. Different computing centers use different job control software and naming conventions, might provide different versions of the same software at differing locations. This needs to be handled in a way that is independent of the other configuration as far as possible.</text:span></text:p>
+ <text:p text:style-name="P12">The above examples neglect an important feature <text:span text:style-name="T169">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>
- <text:p text:style-name="P13">The actual job control headers needed to run a certain job step are saved as <text:span text:style-name="T9">environmentname</text:span>.tmpl. This template will be filled using configuration information from both experiment, options, and environment. <text:span text:style-name="T185">The resulting job header</text:span> is usually included at the beginning of the experiment's job script templates.</text:p>
- <text:p text:style-name="P9">An experiment configuration <text:span text:style-name="T241">may</text:span> <text:span text:style-name="T241">set</text:span> the special variable E<text:span text:style-name="T241">NVIRONMENT</text:span> to the name of <text:span text:style-name="T241">the host </text:span>e<text:span text:style-name="T241">nvironment</text:span> to use. <text:span text:style-name="T241">If it is not set, or empty, the 'DEFAULT' environment settings will be used.</text:span></text:p>
- <text:h text:style-name="P344" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1883_1672291846"/><text:soft-page-break/>Defining namelists and other configuration files<text:bookmark-end text:name="__RefHeading__1883_1672291846"/></text:h>
+ <text:p text:style-name="P13">The actual job control headers needed to run a certain job step are saved as <text:span text:style-name="T9">environmentname</text:span>.tmpl. This template will be filled using configuration information from both experiment, options, and environment. <text:span text:style-name="T187">The resulting job header</text:span> is usually included at the beginning of the experiment's job script templates.</text:p>
+ <text:p text:style-name="P9"><text:soft-page-break/>An experiment configuration <text:span text:style-name="T243">may</text:span> <text:span text:style-name="T243">set</text:span> the special variable E<text:span text:style-name="T243">NVIRONMENT</text:span> to the name of <text:span text:style-name="T243">the host </text:span>e<text:span text:style-name="T243">nvironment</text:span> to use. <text:span text:style-name="T243">If it is not set, or empty, the 'DEFAULT' environment settings will be used.</text:span></text:p>
+ <text:h text:style-name="P344" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1883_1672291846"/>Defining namelists and other configuration files<text:bookmark-end text:name="__RefHeading__1883_1672291846"/></text:h>
<text:p text:style-name="P72"><text:span text:style-name="T78">Most models need at least one Fortran namelist file or another form of configuration file to run. </text:span><text:span text:style-name="T79">The special section [namelists] </text:span><text:span text:style-name="T78">is designed to </text:span><text:span text:style-name="T79">contain all information that goes into </text:span><text:span text:style-name="T78">these</text:span><text:span text:style-name="T79"> files. Each </text:span><text:span text:style-name="T76">immediate </text:span><text:span text:style-name="T79">subsection defines settings for a single file that will </text:span><text:span text:style-name="T78">by default be </text:span><text:span text:style-name="T79">formatted as a Fortran namelist. </text:span><text:span text:style-name="T78">For </text:span><text:span text:style-name="T79">example,</text:span></text:p>
<text:p text:style-name="P171">[namelists]</text:p>
<text:p text:style-name="P183"/>
- <text:p text:style-name="P171"><text:s text:c="2"/>[[<text:span text:style-name="T253">namelist.echam</text:span>]] </text:p>
+ <text:p text:style-name="P171"><text:s text:c="2"/>[[<text:span text:style-name="T255">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:s text:c="6"/>lamip = true</text:p>
- <text:p text:style-name="P171"><text:s text:c="6"/><text:span text:style-name="T262">nproma = 48</text:span></text:p>
+ <text:p text:style-name="P171"><text:s text:c="6"/><text:span text:style-name="T264">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="T254">dt_stop = 2009, 1, 1, 0, 0, 0</text:span></text:p>
+ <text:p text:style-name="P175"><text:s text:c="6"/><text:span text:style-name="T256">dt_stop = 2009, 1, 1, 0, 0, 0</text:span></text:p>
<text:p text:style-name="P69"><text:span text:style-name="T56">defines </text:span><text:span text:style-name="T77">a single </text:span><text:span text:style-name="T56">namelist file, </text:span><text:span text:style-name="T80">'namelist.echam'</text:span><text:span text:style-name="T56">, </text:span><text:span text:style-name="T78">containing a single namelist group with four variables of different types. Note </text:span><text:span text:style-name="T97">that you do not </text:span><text:span text:style-name="T78">need to use quotes for strings nor periods for logical values.</text:span></text:p>
<text:h text:style-name="P326" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2578_1114405012"/>Formatting the namelist information<text:bookmark-end text:name="__RefHeading__2578_1114405012"/></text:h>
- <text:p text:style-name="P101"><text:span text:style-name="T76">The </text:span><text:span text:style-name="T77">names of the </text:span><text:span text:style-name="T76">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="T77">name</text:span><text:span text:style-name="T76">s, and their variables are formatted as fields of this namelist </text:span><text:span text:style-name="T77">group</text:span><text:span text:style-name="T76">. </text:span><text:span text:style-name="T77">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="T253">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="T273">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="T80"> 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="P101"><text:span text:style-name="T76">The </text:span><text:span text:style-name="T77">names of the </text:span><text:span text:style-name="T76">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="T77">name</text:span><text:span text:style-name="T76">s, and their variables are formatted as fields of this namelist </text:span><text:span text:style-name="T77">group</text:span><text:span text:style-name="T76">. </text:span><text:span text:style-name="T77">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="T255">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="T275">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="T80"> 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>
- <text:p text:style-name="P177"><text:s text:c="4"/>lamip = <text:span text:style-name="T168">.true.</text:span></text:p>
- <text:p text:style-name="P177"><text:s text:c="4"/><text:span text:style-name="T253">nproma = </text:span><text:span text:style-name="T173">48</text:span></text:p>
- <text:p text:style-name="P176"><text:s text:c="4"/>earth_angular_velocity = <text:span text:style-name="T168">7.3e-5</text:span></text:p>
- <text:p text:style-name="P176"><text:s text:c="4"/>out_expname = <text:span text:style-name="T174">'</text:span><text:span text:style-name="T168">joe1234</text:span><text:span text:style-name="T174">'</text:span></text:p>
- <text:p text:style-name="P176"><text:span text:style-name="T80"><text:s text:c="4"/>dt_stop = </text:span><text:span text:style-name="T159">2009, 1, 1, 0, 0, 0</text:span></text:p>
+ <text:p text:style-name="P177"><text:s text:c="4"/>lamip = <text:span text:style-name="T170">.true.</text:span></text:p>
+ <text:p text:style-name="P177"><text:s text:c="4"/><text:span text:style-name="T255">nproma = </text:span><text:span text:style-name="T175">48</text:span></text:p>
+ <text:p text:style-name="P176"><text:s text:c="4"/>earth_angular_velocity = <text:span text:style-name="T170">7.3e-5</text:span></text:p>
+ <text:p text:style-name="P176"><text:s text:c="4"/>out_expname = <text:span text:style-name="T176">'</text:span><text:span text:style-name="T170">joe1234</text:span><text:span text:style-name="T176">'</text:span></text:p>
+ <text:p text:style-name="P176"><text:span text:style-name="T80"><text:s text:c="4"/>dt_stop = </text:span><text:span text:style-name="T161">2009, 1, 1, 0, 0, 0</text:span></text:p>
<text:p text:style-name="P159">/</text:p>
<text:p text:style-name="P102">Please note that both group and field names are converted to lower case! Two fields named 'key' and 'Key' will result in two 'key = …' lines, and will cause trouble. We recommend using lower case for all group and field names.</text:p>
- <text:h text:style-name="P335" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2580_1114405012"/><text:span text:style-name="T78">S</text:span><text:span text:style-name="T56">uppressing namelist </text:span><text:span text:style-name="T132">files, </text:span><text:span text:style-name="T56">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="T56">If you want to </text:span><text:span text:style-name="T120">disable</text:span><text:span text:style-name="T56"> a namelist group </text:span><text:span text:style-name="T132">or a whole namelist file </text:span><text:span text:style-name="T56">defined on a higher setup level, you may </text:span><text:span text:style-name="T132">set a</text:span><text:span text:style-name="T56"> special</text:span><text:span text:style-name="T132"> v</text:span><text:span text:style-name="T56">ariable '.hide' to </text:span><text:span text:style-name="T120">'</text:span><text:span text:style-name="T56">true</text:span><text:span text:style-name="T120">' </text:span><text:span text:style-name="T132">in the corresponding section</text:span><text:span text:style-name="T56">. </text:span><text:soft-page-break/><text:span text:style-name="T120">As you may suspect, setting '.hide' to 'false' for </text:span><text:span text:style-name="T133">elements</text:span><text:span text:style-name="T120"> that were hidden on a higher setup level will re-enable the</text:span><text:span text:style-name="T121">m</text:span><text:span text:style-name="T120">.</text:span></text:p>
- <text:p text:style-name="P112"><text:span text:style-name="T120">T</text:span><text:span text:style-name="T127">o disable a </text:span><text:span text:style-name="T128">single </text:span><text:span text:style-name="T127">namelist variable, simply </text:span><text:span text:style-name="T334">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="T335">to the namelist file</text:span><text:span text:style-name="T334">, so the default value is used instead. </text:span><text:span text:style-name="T335">Setting the variable to a non-empty value i</text:span><text:span text:style-name="T336">n a higher </text:span><text:span text:style-name="T335">level</text:span><text:span text:style-name="T336"> .</text:span><text:span text:style-name="T335">config file will re-enable it.</text:span></text:p>
- <text:p text:style-name="P110"><text:span text:style-name="T334">If the empty string is a valid value in </text:span><text:span text:style-name="T335">your namelist</text:span><text:span text:style-name="T334">, 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:h text:style-name="P335" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2580_1114405012"/><text:soft-page-break/><text:span text:style-name="T78">S</text:span><text:span text:style-name="T56">uppressing namelist </text:span><text:span text:style-name="T132">files, </text:span><text:span text:style-name="T56">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="T56">If you want to </text:span><text:span text:style-name="T120">disable</text:span><text:span text:style-name="T56"> a namelist group </text:span><text:span text:style-name="T132">or a whole namelist file </text:span><text:span text:style-name="T56">defined on a higher setup level, you may </text:span><text:span text:style-name="T132">set a</text:span><text:span text:style-name="T56"> special</text:span><text:span text:style-name="T132"> v</text:span><text:span text:style-name="T56">ariable '.hide' to </text:span><text:span text:style-name="T120">'</text:span><text:span text:style-name="T56">true</text:span><text:span text:style-name="T120">' </text:span><text:span text:style-name="T132">in the corresponding section</text:span><text:span text:style-name="T56">. </text:span><text:span text:style-name="T120">As you may suspect, setting '.hide' to 'false' for </text:span><text:span text:style-name="T133">elements</text:span><text:span text:style-name="T120"> that were hidden on a higher setup level will re-enable the</text:span><text:span text:style-name="T121">m</text:span><text:span text:style-name="T120">.</text:span></text:p>
+ <text:p text:style-name="P112"><text:span text:style-name="T120">T</text:span><text:span text:style-name="T127">o disable a </text:span><text:span text:style-name="T128">single </text:span><text:span text:style-name="T127">namelist variable, simply </text:span><text:span text:style-name="T336">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="T337">to the namelist file</text:span><text:span text:style-name="T336">, so the default value is used instead. </text:span><text:span text:style-name="T337">Setting the variable to a non-empty value i</text:span><text:span text:style-name="T338">n a higher </text:span><text:span text:style-name="T337">level</text:span><text:span text:style-name="T338"> .</text:span><text:span text:style-name="T337">config file will re-enable it.</text:span></text:p>
+ <text:p text:style-name="P110"><text:span text:style-name="T336">If the empty string is a valid value in </text:span><text:span text:style-name="T337">your namelist</text:span><text:span text:style-name="T336">, 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="T128">As a legacy, t</text:span><text:span text:style-name="T56">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="T128">Note that, w</text:span><text:span text:style-name="T129">hile '.remove' is useful to </text:span><text:span text:style-name="T87">suppress</text:span><text:span text:style-name="T129"> 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="T88">Therefore, its use in model setups is strongly discouraged.</text:span></text:p>
<text:h text:style-name="P336" 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:p text:style-name="P107">In general, <text:span text:style-name="T325">'#' </text:span>comments in namelist or group sections will by converted to Fortran 90 <text:span text:style-name="T325">'!' </text:span>comments. In-line comments for <text:span text:style-name="T325">individual</text:span> settings are also recognized.</text:p>
+ <text:p text:style-name="P107">In general, <text:span text:style-name="T327">'#' </text:span>comments in namelist or group sections will by converted to Fortran 90 <text:span text:style-name="T327">'!' </text:span>comments. In-line comments for <text:span text:style-name="T327">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>
- <text:p text:style-name="P193"><text:s text:c="4"/>lamip = true <text:span text:style-name="T179"># Use AMIP conventions</text:span></text:p>
+ <text:p text:style-name="P193"><text:s text:c="4"/>lamip = true <text:span text:style-name="T181"># Use AMIP conventions</text:span></text:p>
<text:p text:style-name="P139"><text:s text:c="4"/># Block size for optimization</text:p>
- <text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="4"/><text:span text:style-name="T262">nproma = 48</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="4"/><text:span text:style-name="T264">nproma = 48</text:span></text:p>
<text:p text:style-name="P139">! Run time settings</text:p>
<text:p text:style-name="P194">&runctl</text:p>
- <text:p text:style-name="P194"><text:s text:c="4"/>lamip = .true. <text:span text:style-name="T179">! Use AMIP conventions</text:span></text:p>
+ <text:p text:style-name="P194"><text:s text:c="4"/>lamip = .true. <text:span text:style-name="T181">! Use AMIP conventions</text:span></text:p>
<text:p text:style-name="P139"><text:s text:c="4"/>! Block size for optimization</text:p>
- <text:p text:style-name="P194"><text:s text:c="4"/><text:span text:style-name="T253">nproma = 48</text:span></text:p>
+ <text:p text:style-name="P194"><text:s text:c="4"/><text:span text:style-name="T255">nproma = 48</text:span></text:p>
<text:p text:style-name="P108">In addition, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T56"> </text:span><text:span text:style-name="T125">recognises namelist settings </text:span><text:span text:style-name="T56">that were commented out. </text:span><text:span text:style-name="T125">For these, the formatting of values as described before is also carried out within the comment.</text:span></text:p>
- <text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="4"/><text:span text:style-name="T179"># </text:span>lamip = true <text:span text:style-name="T207"># Use AMIP conventions</text:span></text:p>
- <text:p text:style-name="P194"><text:s text:c="4"/><text:span text:style-name="T168">!</text:span> lamip = <text:span text:style-name="T168">.true.</text:span> <text:span text:style-name="T179">! </text:span><text:span text:style-name="T326">Use AMIP conventions</text:span></text:p>
- <text:p text:style-name="P109">There is one hitch: if the last setting in a group is commented, the <text:span text:style-name="T44">configobj </text:span>library <text:span text:style-name="T327">will take this line to be a group comment for the following group. To work around this, </text:span><text:span text:style-name="T44">mkexp</text:span><text:span text:style-name="T126"> recognises a special namelist variable '.end' to keep the commented setting with the first group.</text:span></text:p>
- <text:p text:style-name="P200">[[[parctl]]]</text:p>
- <text:p text:style-name="P199"><text:s text:c="4"/><text:span text:style-name="T327"># nprocb = 48 </text:span><text:span text:style-name="T208"># </text:span><text:span text:style-name="T209">E</text:span><text:span text:style-name="T208">nd</text:span><text:span text:style-name="T209">s</text:span><text:span text:style-name="T208"> up with 'runctl' </text:span><text:span text:style-name="T209">instead</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="4"/><text:span text:style-name="T181"># </text:span>lamip = true <text:span text:style-name="T209"># Use AMIP conventions</text:span></text:p>
+ <text:p text:style-name="P194"><text:s text:c="4"/><text:span text:style-name="T170">!</text:span> lamip = <text:span text:style-name="T170">.true.</text:span> <text:span text:style-name="T181">! </text:span><text:span text:style-name="T328">Use AMIP conventions</text:span></text:p>
+ <text:p text:style-name="P109">There is one hitch: if the last setting in a group is commented, the <text:span text:style-name="T44">configobj </text:span>library <text:span text:style-name="T329">will take this line to be a group comment for the following group. To work around this, </text:span><text:span text:style-name="T44">mkexp</text:span><text:span text:style-name="T126"> recognises a special namelist variable '.end' to keep the commented setting with the first group.</text:span></text:p>
+ <text:p text:style-name="P200"><text:soft-page-break/>[[[parctl]]]</text:p>
+ <text:p text:style-name="P199"><text:s text:c="4"/><text:span text:style-name="T329"># nprocb = 48 </text:span><text:span text:style-name="T210"># </text:span><text:span text:style-name="T211">E</text:span><text:span text:style-name="T210">nd</text:span><text:span text:style-name="T211">s</text:span><text:span text:style-name="T210"> up with 'runctl' </text:span><text:span text:style-name="T211">instead</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text">[[[runctl]]]</text:p>
- <text:p text:style-name="P195"><text:soft-page-break/><text:s text:c="4"/><text:span text:style-name="T328"># </text:span>lamip = true <text:span text:style-name="T328"># Stays with 'runctl'</text:span></text:p>
- <text:p text:style-name="P195"><text:s text:c="4"/><text:span text:style-name="T168">.</text:span><text:span text:style-name="T181">end = </text:span></text:p>
+ <text:p text:style-name="P195"><text:s text:c="4"/><text:span text:style-name="T330"># </text:span>lamip = true <text:span text:style-name="T330"># Stays with 'runctl'</text:span></text:p>
+ <text:p text:style-name="P195"><text:s text:c="4"/><text:span text:style-name="T170">.</text:span><text:span text:style-name="T183">end = </text:span></text:p>
<text:p text:style-name="Preformatted_20_Text_20_Interrupt">[[[dynctl]]]</text:p>
- <text:p text:style-name="P199"><text:span text:style-name="T202">&</text:span><text:span text:style-name="T209">parctl</text:span></text:p>
+ <text:p text:style-name="P199"><text:span text:style-name="T204">&</text:span><text:span text:style-name="T211">parctl</text:span></text:p>
<text:p text:style-name="P197">/</text:p>
- <text:p text:style-name="P199"><text:span text:style-name="T209">! </text:span><text:span text:style-name="T208">nprocb = 48 ! </text:span><text:span text:style-name="T209">E</text:span><text:span text:style-name="T208">nd</text:span><text:span text:style-name="T209">s</text:span><text:span text:style-name="T208"> up with 'runctl' </text:span><text:span text:style-name="T209">instead</text:span></text:p>
+ <text:p text:style-name="P199"><text:span text:style-name="T211">! </text:span><text:span text:style-name="T210">nprocb = 48 ! </text:span><text:span text:style-name="T211">E</text:span><text:span text:style-name="T210">nd</text:span><text:span text:style-name="T211">s</text:span><text:span text:style-name="T210"> up with 'runctl' </text:span><text:span text:style-name="T211">instead</text:span></text:p>
<text:p text:style-name="P196">&runctl</text:p>
<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>
@@ -3385,7 +3447,7 @@
<text:p text:style-name="P72"><text:span text:style-name="T69">The name of </text:span><text:span text:style-name="T80">this </text:span><text:span text:style-name="T69">variable</text:span><text:span text:style-name="T70"> </text:span><text:span text:style-name="T80">is</text:span><text:span text:style-name="T69"> generated from </text:span><text:span text:style-name="T80">its</text:span><text:span text:style-name="T69"> </text:span><text:span text:style-name="T70">respective</text:span><text:span text:style-name="T69"> file name, </text:span><text:span text:style-name="T80">like</text:span><text:span text:style-name="T69"> 'namelist.echam', by </text:span><text:span text:style-name="T79">converting all letters to upper case </text:span><text:span text:style-name="T69">(</text:span><text:span text:style-name="T79">namelist.echam →</text:span><text:span text:style-name="T69"> </text:span><text:span text:style-name="T79">NAMELIST.ECHAM</text:span><text:span text:style-name="T69">) </text:span><text:span text:style-name="T70">and </text:span><text:span text:style-name="T69">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="T168">[[namelist.echam]]</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text"><text:s text:c="2"/><text:span text:style-name="T170">[[namelist.echam]]</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="4"/>[[[runctl]]]</text:p>
<text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="6"/>out_expname = $${EXP_ID}</text:p>
<text:p text:style-name="P172">#! /bin/sh</text:p>
@@ -3403,26 +3465,26 @@
<text:p text:style-name="P123">EOF</text:p>
<text:p text:style-name="P73"><text:span text:style-name="T80">Note how this setup uses the native script variable 'EXP_ID' to set the </text:span><text:span text:style-name="T76">namelist contents.</text:span></text:p>
<text:p text:style-name="P103"><text:span text:style-name="T56">As an option, the namelist text may be formatted using the global function 'format_namelist', </text:span><text:span text:style-name="T119">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"><text:soft-page-break/>EXP_ID=%{EXP_ID}</text:p>
+ <text:p text:style-name="P173"><text:soft-page-break/>#! /bin/sh</text:p>
+ <text:p text:style-name="P191">EXP_ID=%{EXP_ID}</text:p>
<text:p text:style-name="P125">cat > namelist.echam << EOF</text:p>
- <text:p text:style-name="P134">%{<text:span text:style-name="T318">format_namelist(namelists['namelist.echam'])</text:span>}</text:p>
+ <text:p text:style-name="P134">%{<text:span text:style-name="T320">format_namelist(namelists['namelist.echam'])</text:span>}</text:p>
<text:p text:style-name="P148">EOF</text:p>
<text:p text:style-name="P104"><text:span text:style-name="T119">T</text:span><text:span text:style-name="T56">he result will be the same as </text:span><text:span text:style-name="T119">in the original example</text:span><text:span text:style-name="T56">.</text:span></text:p>
<text:p text:style-name="P104"><text:span text:style-name="T119">Additionally, </text:span><text:span text:style-name="T118">'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">cat > namelist.echam << EOF</text:p>
- <text:p text:style-name="P135">%<text:span text:style-name="T202">{</text:span><text:span text:style-name="T206">format_namelist(namelists['namelist.echam']</text:span><text:span text:style-name="T318">, 'runctl'</text:span><text:span text:style-name="T206">)</text:span><text:span text:style-name="T202">}</text:span></text:p>
+ <text:p text:style-name="P135">%<text:span text:style-name="T204">{</text:span><text:span text:style-name="T208">format_namelist(namelists['namelist.echam']</text:span><text:span text:style-name="T320">, 'runctl'</text:span><text:span text:style-name="T208">)</text:span><text:span text:style-name="T204">}</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="T81">As </text:span><text:span text:style-name="T117">shown </text:span><text:span text:style-name="T81">in the example</text:span><text:span text:style-name="T117">s</text:span><text:span text:style-name="T81"> above, the script template is responsible for writing the namelist text to an actual file. </text:span><text:span text:style-name="T80">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="T80"> </text:span><text:span text:style-name="T117">will not</text:span><text:span text:style-name="T80"> enforce this. The template needs to be set up accordingly.</text:span></text:p>
<text:h text:style-name="P332" 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>
- <text:p text:style-name="P186"><text:s text:c="2"/><text:span text:style-name="T278">[[namelist.echam]]</text:span></text:p>
- <text:p text:style-name="P186"><text:s text:c="4"/><text:span text:style-name="T278">[[[runctl]]]</text:span></text:p>
- <text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="6"/><text:span text:style-name="T278">dt_stop = $$final_date</text:span></text:p>
+ <text:p text:style-name="P186"><text:s text:c="2"/><text:span text:style-name="T280">[[namelist.echam]]</text:span></text:p>
+ <text:p text:style-name="P186"><text:s text:c="4"/><text:span text:style-name="T280">[[[runctl]]]</text:span></text:p>
+ <text:p text:style-name="Preformatted_20_Text_20_Interrupt"><text:s text:c="6"/><text:span text:style-name="T280">dt_stop = $$final_date</text:span></text:p>
<text:p text:style-name="P160">final_date='2015, 12, 31, 23, 52, 30'</text:p>
<text:p text:style-name="P124">cat > namelist.echam << EOF</text:p>
<text:p text:style-name="P133">%{NAMELIST_ECHAM}</text:p>
@@ -3440,24 +3502,24 @@
<text:p text:style-name="List_20_Heading"><text:span text:style-name="T56">.</text:span><text:span text:style-name="T107">sub_dir</text:span></text:p>
<text:p text:style-name="P260"><text:span text:style-name="T108">file names are taken to be relative to this subdirectory of </text:span><text:span text:style-name="T56">'.base_dir'</text:span></text:p>
<text:p text:style-name="P66"><text:span text:style-name="T150">For expanding the resulting file path</text:span><text:span text:style-name="T134">, </text:span><text:span text:style-name="T46">mkexp</text:span><text:span text:style-name="T134"> provides </text:span><text:span text:style-name="T151">two</text:span><text:span text:style-name="T150"> global function</text:span><text:span text:style-name="T151">s</text:span><text:span text:style-name="T150">:</text:span></text:p>
- <text:p text:style-name="P288"><text:span text:style-name="T134">get_file</text:span><text:span text:style-name="T156">(</text:span><text:span text:style-name="T48">section</text:span><text:span text:style-name="T156">, </text:span><text:span text:style-name="T48">name</text:span><text:span text:style-name="T156">)</text:span></text:p>
- <text:p text:style-name="P236">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="T317">If the value of </text:span><text:span text:style-name="Variable"><text:span text:style-name="T317">name</text:span></text:span><text:span text:style-name="T317"> 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="P296"><text:span text:style-name="T168">get_dir</text:span>(<text:span text:style-name="T9">section</text:span><text:span text:style-name="T56">)</text:span></text:p>
- <text:p text:style-name="P236"><text:span text:style-name="T56">returns the </text:span><text:span text:style-name="T317">directory for the </text:span><text:span text:style-name="T56">given </text:span><text:span text:style-name="T9">section</text:span><text:span text:style-name="T56"> object</text:span></text:p>
+ <text:p text:style-name="P288"><text:span text:style-name="T134">get_file</text:span><text:span text:style-name="T158">(</text:span><text:span text:style-name="T48">section</text:span><text:span text:style-name="T158">, </text:span><text:span text:style-name="T48">name</text:span><text:span text:style-name="T158">)</text:span></text:p>
+ <text:p text:style-name="P236">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="T319">If the value of </text:span><text:span text:style-name="Variable"><text:span text:style-name="T319">name</text:span></text:span><text:span text:style-name="T319"> 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="P296"><text:span text:style-name="T170">get_dir</text:span>(<text:span text:style-name="T9">section</text:span><text:span text:style-name="T56">)</text:span></text:p>
+ <text:p text:style-name="P236"><text:span text:style-name="T56">returns the </text:span><text:span text:style-name="T319">directory for the </text:span><text:span text:style-name="T56">given </text:span><text:span text:style-name="T9">section</text:span><text:span text:style-name="T56"> object</text:span></text:p>
<text:p text:style-name="P89"><text:span text:style-name="T107">Other than that, t</text:span><text:span text:style-name="T100">here are no restrictions on the content structure of this section, and the job script templates are responsible for converting this content into a suitable script text.</text:span></text:p>
- <text:h text:style-name="P325" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2833_1132221942"/>Overriding <text:span text:style-name="T276">input file</text:span>s <text:span text:style-name="T276">for certain</text:span> jobs<text:bookmark-end text:name="__RefHeading__2833_1132221942"/></text:h>
- <text:p text:style-name="P51"><text:span text:style-name="T277">As for namelists, t</text:span>here is special provision to change <text:span text:style-name="T276">the [</text:span>files<text:span text:style-name="T276">]</text:span> settings for a specific job. <text:span text:style-name="T276">Let us assume</text:span> <text:span text:style-name="T276">that a model run continues a previous run and reads that run's state from a restart file that may be defined like this:</text:span></text:p>
- <text:p text:style-name="P166">[<text:span text:style-name="T276">files</text:span>]</text:p>
- <text:p text:style-name="P119"><text:s text:c="2"/>[[<text:span text:style-name="T276">echam</text:span>]]</text:p>
- <text:p text:style-name="P119"><text:s text:c="4"/>[[[<text:span text:style-name="T276">restart</text:span>]]]</text:p>
- <text:p text:style-name="P119"><text:s text:c="6"/><text:span text:style-name="T276">restart_myexp_echam.nc = restart_myexp_echam_18491231.nc</text:span></text:p>
- <text:p text:style-name="P90"><text:soft-page-break/>The first run <text:span text:style-name="T277">will instead pick up its state from another experiment. This is done with </text:span><text:span text:style-name="T140"><text:s/>a job specific </text:span><text:span text:style-name="T149">'file</text:span><text:span text:style-name="T140">s</text:span><text:span text:style-name="T149">'</text:span><text:span text:style-name="T140"> subsection that – apart from the addition</text:span><text:span text:style-name="T142">al</text:span><text:span text:style-name="T140"> brackets – has the same structure as</text:span><text:span text:style-name="T139"> </text:span><text:span text:style-name="T140">the global </text:span><text:span text:style-name="T149">'files'</text:span><text:span text:style-name="T140"> section.</text:span></text:p>
+ <text:h text:style-name="P325" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2833_1132221942"/>Overriding <text:span text:style-name="T278">input file</text:span>s <text:span text:style-name="T278">for certain</text:span> jobs<text:bookmark-end text:name="__RefHeading__2833_1132221942"/></text:h>
+ <text:p text:style-name="P51"><text:span text:style-name="T279">As for namelists, t</text:span>here is special provision to change <text:span text:style-name="T278">the [</text:span>files<text:span text:style-name="T278">]</text:span> settings for a specific job. <text:span text:style-name="T278">Let us assume</text:span> <text:span text:style-name="T278">that a model run continues a previous run and reads that run's state from a restart file that may be defined like this:</text:span></text:p>
+ <text:p text:style-name="P166">[<text:span text:style-name="T278">files</text:span>]</text:p>
+ <text:p text:style-name="P119"><text:s text:c="2"/>[[<text:span text:style-name="T278">echam</text:span>]]</text:p>
+ <text:p text:style-name="P119"><text:s text:c="4"/>[[[<text:span text:style-name="T278">restart</text:span>]]]</text:p>
+ <text:p text:style-name="P119"><text:s text:c="6"/><text:span text:style-name="T278">restart_myexp_echam.nc = restart_myexp_echam_18491231.nc</text:span></text:p>
+ <text:p text:style-name="P90"><text:soft-page-break/>The first run <text:span text:style-name="T279">will instead pick up its state from another experiment. This is done with </text:span><text:span text:style-name="T140"><text:s/>a job specific </text:span><text:span text:style-name="T149">'file</text:span><text:span text:style-name="T140">s</text:span><text:span text:style-name="T149">'</text:span><text:span text:style-name="T140"> subsection that – apart from the addition</text:span><text:span text:style-name="T142">al</text:span><text:span text:style-name="T140"> brackets – has the same structure as</text:span><text:span text:style-name="T139"> </text:span><text:span text:style-name="T140">the global </text:span><text:span text:style-name="T149">'files'</text:span><text:span text:style-name="T140"> section.</text:span></text:p>
<text:p text:style-name="P166">[jobs]</text:p>
<text:p text:style-name="P166"><text:s text:c="2"/>[[run_first]]</text:p>
- <text:p text:style-name="P166"><text:s text:c="4"/><text:span text:style-name="T168">[[[</text:span><text:span text:style-name="T177">file</text:span><text:span text:style-name="T168">s]</text:span><text:span text:style-name="T177">]</text:span><text:span text:style-name="T168">]</text:span></text:p>
- <text:p text:style-name="P119"><text:s text:c="6"/><text:span text:style-name="T220">[[</text:span>[[<text:span text:style-name="T277">echam</text:span>]]<text:span text:style-name="T220">]]</text:span></text:p>
- <text:p text:style-name="P119"><text:s text:c="8"/><text:span text:style-name="T220">[[</text:span>[[[<text:span text:style-name="T277">restart</text:span>]]]<text:span text:style-name="T220">]]</text:span></text:p>
- <text:p text:style-name="P120"><text:span text:style-name="T134"><text:s text:c="10"/></text:span><text:span text:style-name="T148">restart_myexp_echam.nc = restart_</text:span><text:span text:style-name="T154">another</text:span><text:span text:style-name="T155">exp</text:span><text:span text:style-name="T148">_echam_18491231.nc</text:span></text:p>
+ <text:p text:style-name="P166"><text:s text:c="4"/><text:span text:style-name="T170">[[[</text:span><text:span text:style-name="T179">file</text:span><text:span text:style-name="T170">s]</text:span><text:span text:style-name="T179">]</text:span><text:span text:style-name="T170">]</text:span></text:p>
+ <text:p text:style-name="P119"><text:s text:c="6"/><text:span text:style-name="T222">[[</text:span>[[<text:span text:style-name="T279">echam</text:span>]]<text:span text:style-name="T222">]]</text:span></text:p>
+ <text:p text:style-name="P119"><text:s text:c="8"/><text:span text:style-name="T222">[[</text:span>[[[<text:span text:style-name="T279">restart</text:span>]]]<text:span text:style-name="T222">]]</text:span></text:p>
+ <text:p text:style-name="P120"><text:span text:style-name="T134"><text:s text:c="10"/></text:span><text:span text:style-name="T148">restart_myexp_echam.nc = restart_</text:span><text:span text:style-name="T156">another</text:span><text:span text:style-name="T157">exp</text:span><text:span text:style-name="T148">_echam_18491231.nc</text:span></text:p>
<text:p text:style-name="P47"><text:span text:style-name="T140">This</text:span><text:span text:style-name="T148"> will result in a '.run_first' </text:span><text:span text:style-name="T149">script</text:span><text:span text:style-name="T148"> tha</text:span><text:span text:style-name="T149">t gets the model state from 'anotherexp', while the '.run' script</text:span><text:span text:style-name="T148"> </text:span><text:span text:style-name="T149">uses 'myexp'.</text:span></text:p>
</office:text>
</office:body>
diff --git a/doc/mkexp.pdf b/doc/mkexp.pdf
index 04665a4f01b613d75ca9e4b2146379470588dc72..4ba242f2f64703489642e5caacfb7db34538d720 100644
Binary files a/doc/mkexp.pdf and b/doc/mkexp.pdf differ
diff --git a/expconfig.py b/expconfig.py
index 0c34c31c7ebe2a36ff9fc6d563273e1a795f6e08..cfe3d7a753ea57f6ffee61e200d17ce2da41b3ae 100644
--- a/expconfig.py
+++ b/expconfig.py
@@ -49,29 +49,37 @@ class ConfigObj(configobj.ConfigObj):
else:
return [_f for _f in [x.rstrip() for x in arg] if _f]
- def merge_comments(this, indict):
- '''Merge comments from indict into current configuration.
+ def merge_structure(this, indict, main=None, parent=None, depth=0):
+ '''Merge structure from indict into current configuration.
Requires indict to be merged before being called.
'''
+ if not main: main = this
+ if not parent: parent = this
+
+ this.main = main
+ this.parent = parent
+ this.depth = depth
+
if isinstance(indict, configobj.ConfigObj):
if is_not_empty(indict.initial_comment):
this.initial_comment = indict.initial_comment
if is_not_empty(indict.final_comment):
this.final_comment = indict.final_comment
- for key in indict.scalars:
- if is_not_empty(indict.comments[key]):
- this.comments[key] = indict.comments[key]
- if is_not_empty(indict.inline_comments[key]):
- this.inline_comments[key] = indict.inline_comments[key]
-
- for key in indict.sections:
- merge_comments(this[key], indict[key])
+ if isinstance(indict, configobj.Section):
+ for key in indict.scalars:
+ if is_not_empty(indict.comments[key]):
+ this.comments[key] = indict.comments[key]
+ if is_not_empty(indict.inline_comments[key]):
+ this.inline_comments[key] = indict.inline_comments[key]
+
+ for key, value in indict.items():
+ if isinstance(value, dict):
+ merge_structure(this[key], value, main, this, depth+1)
configobj.ConfigObj.merge(self, indict)
- if isinstance(indict, configobj.Section):
- merge_comments(self, indict)
+ merge_structure(self, indict)
class ExpConfigError(InterpolationError):
diff --git a/mkexp b/mkexp
index de30beeffa8b88d8b1e506eff72e2270234e60c0..e1fe32a13d2785dc16be48c3aefdd6f1e124ace4 100755
--- a/mkexp
+++ b/mkexp
@@ -5,8 +5,9 @@
# $Id$
#
-import copy
+from copy import deepcopy
import io
+import numbers
import os
import re
import stat
@@ -234,7 +235,7 @@ def format_vars(section, key, log, fmt):
value = section[key]
newkey = transform(key)
section.rename(key, newkey)
- if not isinstance(value, (list, tuple, dict)):
+ if not isinstance(value, (list, tuple, dict, numbers.Number)):
# Format string variables
section[newkey] = transform(value)
elif isinstance(value, (list, tuple)):
@@ -346,7 +347,7 @@ def list_singleton(eval_ctx, x, keep_empty=False, *args, **kwargs):
if getattr(list_original, 'evalcontextfilter', False):
return list_original(eval_ctx, x, *args, **kwargs)
return list_original(x, *args, **kwargs)
- if not keep_empty and x == '':
+ if not keep_empty and not x:
return []
return [x]
template_env.filters['list'] = list_singleton
@@ -449,16 +450,12 @@ dump_file.close()
# Process scripts for each job
# Cut queue specific settings
-job_dict = {}
remove_list = get_remove_list(config['jobs'], '.remove')
remove_list += get_remove_list(config['jobs'], 'remove')
-for key, value in config['jobs'].items():
- if not isinstance(value, dict):
- job_dict[key] = value
- del config['jobs'][key]
# Extend the given subjob config recursively
-def extend(subjob, jobs_config, extended_jobs):
+def extend(subjob, config, extended_jobs):
+ jobs_config = config['jobs']
if subjob not in extended_jobs:
subconfig = jobs_config[subjob]
@@ -472,117 +469,111 @@ def extend(subjob, jobs_config, extended_jobs):
extended_job = subconfig['extends']
subconfig.rename('extends', '.extends')
if extended_job:
- extend(extended_job, jobs_config, extended_jobs)
+ extend(extended_job, config, extended_jobs)
- # Add global job settings
- pre_config = ConfigObj(interpolation=False)
- pre_config.merge(job_dict)
+ # Collect all inherited data
- # Add parent config
+ pre_config = ConfigObj(interpolation=False)
if extended_job:
- pre_config.merge(copy.deepcopy(jobs_config[extended_job]))
-
+ # Add parent config
+ pre_config.merge(deepcopy(jobs_config[extended_job]))
+ else:
+ # Add global job settings
+ pre_config.merge(deepcopy({s: config[s] for s in config.keys()
+ if s not in ('jobs', 'DEFAULT')}))
+ pre_config.merge({s: jobs_config[s] for s in jobs_config.scalars
+ if s not in ('.remove', 'remove')})
# Add actual subjob config
- pre_config.merge(subconfig)
+ pre_config.merge(deepcopy(subconfig))
# Replace subjob config by extended config
- jobs_config[subjob] = {}
- jobs_config[subjob].merge(pre_config)
+ config.merge({'jobs': {subjob: pre_config}})
del pre_config
# Tick off extended jobs
extended_jobs.add(subjob)
-# Extend all subjobs
+# Remove or extend subjobs
jobs_config = config['jobs']
extended_jobs = set()
-for subjob in jobs_config:
- if not subjob in remove_list:
+removed_jobs = set()
+for subjob in jobs_config.sections:
+ if subjob in remove_list:
+ removed_jobs.add(subjob)
+ else:
# Extend subjob config
- extend(subjob, jobs_config, extended_jobs)
+ extend(subjob, config, extended_jobs)
# Add useful settings
subconfig = jobs_config[subjob]
- subconfig['id'] = subjob
+ subconfig[u'id'] = subjob
if not 'tasks' in subconfig:
- subconfig['tasks'] = str(int(subconfig.get('nodes', 1)) *
- int(subconfig.get('tasks_per_node', 1)))
+ subconfig[u'tasks'] = (int(subconfig.get('nodes', 1)) *
+ int(subconfig.get('tasks_per_node', 1)))
+for subjob in removed_jobs:
+ del jobs_config[subjob]
# Paste them into each job
-for subjob, subconfig in jobs_config.items():
- if not subjob in remove_list:
-
- # Copy current config settings to job
- config_lines = io.BytesIO()
- config.write(config_lines)
- config_lines.seek(0)
- job_config = ConfigObj(io.TextIOWrapper(config_lines),
- interpolation=False)
-
- # Check namelist override
- if 'namelists' in subconfig:
- job_config['namelists'].merge(subconfig['namelists'])
- del subconfig['namelists']
-
- # Check files override
- if 'files' in subconfig:
- job_config['files'].merge(subconfig['files'])
- del subconfig['files']
-
- # Paste pre config into job config
- job_config[u'JOB'] = subconfig
- del subconfig
-
- # Prepare namelists for inclusion in scripts
- var_format = job_config['JOB'].get('.var_format', '${%s}')
- var_list = set()
- del job_config['jobs']
- job_config['jobs'] = copy.deepcopy(jobs_config)
- job_config.walk(format_vars, log=var_list, fmt=var_format)
- job_config['VARIABLES_'] = var_list
- for namelist, groups in job_config['namelists'].items():
- if isinstance(groups, dict):
- # Skip hidden namelists
- if is_set(groups.get('.hide')):
- continue
- # Support deprecated keyword 'use_template' but warn user
- if groups.get('use_template'):
- keyword_warning('use_template')
-
- namelist_name = re.sub(r'\W', '_', namelist.upper())
- use_template = (groups.get('.use_template') or
- groups.get('use_template') or '')
- if use_template.lower() == 'true':
- job_config[namelist_name] = \
- expand_template(groups, get_template_name(namelist))
- elif use_template:
- job_config[namelist_name] = \
- expand_template(groups, get_template_name(use_template))
- else:
- job_config[namelist_name] = \
- format_namelist(groups)
-
- # Generate job script
- template_search_list = (
- get_exp_template_name(experiment_config_id, subjob, ''),
- get_exp_template_name(config.experiment_id, subjob, ''),
- get_exp_template_name(config.experiment_kind, subjob),
- get_exp_template_name(ExpConfig.default_name, subjob)
+for subjob in jobs_config.sections:
+ subconfig = jobs_config[subjob]
+
+ # Copy current config settings to job
+ job_config = ConfigObj(interpolation=False)
+ job_config.merge(subconfig)
+
+ # Paste pre config into job config
+ job_config.merge({u'DEFAULT': config[u'DEFAULT']})
+ job_config.merge({u'jobs': deepcopy(jobs_config)})
+ job_config.merge({u'JOB': deepcopy(subconfig)})
+
+ # Prepare namelists for inclusion in scripts
+ var_format = subconfig.get('.var_format', '${%s}')
+ var_list = set()
+ job_config.walk(format_vars, log=var_list, fmt=var_format)
+ job_config[u'VARIABLES_'] = var_list
+ for namelist, groups in job_config['namelists'].items():
+ if isinstance(groups, dict):
+ # Skip hidden namelists
+ if is_set(groups.get('.hide')):
+ continue
+ # Support deprecated keyword 'use_template' but warn user
+ if groups.get('use_template'):
+ keyword_warning('use_template')
+
+ namelist_name = re.sub(r'\W', '_', namelist.upper())
+ use_template = (groups.get('.use_template') or
+ groups.get('use_template') or '')
+ if use_template.lower() == 'true':
+ job_config[namelist_name] = \
+ expand_template(groups, get_template_name(namelist))
+ elif use_template:
+ job_config[namelist_name] = \
+ expand_template(groups, get_template_name(use_template))
+ else:
+ job_config[namelist_name] = \
+ format_namelist(groups)
+
+ # Generate job script
+ template_search_list = (
+ get_exp_template_name(experiment_config_id, subjob, ''),
+ get_exp_template_name(config.experiment_id, subjob, ''),
+ get_exp_template_name(config.experiment_kind, subjob),
+ get_exp_template_name(ExpConfig.default_name, subjob)
+ )
+ extended_job = jobs_config[subjob].get('.extends')
+ while extended_job:
+ template_search_list += (
+ get_exp_template_name(experiment_config_id, extended_job, ''),
+ get_exp_template_name(config.experiment_id, extended_job, ''),
+ get_exp_template_name(config.experiment_kind, extended_job),
+ get_exp_template_name(ExpConfig.default_name, extended_job)
)
- extended_job = jobs_config[subjob].get('.extends')
- while extended_job:
- template_search_list += (
- get_exp_template_name(experiment_config_id, extended_job, ''),
- get_exp_template_name(config.experiment_id, extended_job, ''),
- get_exp_template_name(config.experiment_kind, extended_job),
- get_exp_template_name(ExpConfig.default_name, extended_job)
- )
- extended_job = jobs_config[extended_job].get('.extends')
-
- expand_template_file(job_config, template_search_list,
- get_exp_script_name(config.experiment_id, subjob),
- os.path.join(backup_dir,
- config.experiment_id+'.'+subjob))
+ extended_job = jobs_config[extended_job].get('.extends')
+
+ expand_template_file(job_config, template_search_list,
+ get_exp_script_name(config.experiment_id, subjob),
+ os.path.join(backup_dir,
+ config.experiment_id+'.'+subjob))
# Create README file from experiment description
diff --git a/package_info.py b/package_info.py
index cf42aeabb6eb74ad1a87b1c529615763bf56d209..5e31345b417144481d8241dd1f200655ba728e0d 100644
--- a/package_info.py
+++ b/package_info.py
@@ -4,4 +4,4 @@ Information on package name and version
full_name = 'Make Experiments!'
name = 'mkexp'
-version = '1.1.2'
+version = '1.2.0dev'
diff --git a/test.py b/test.py
index 4988533034500b9ef300a1750a9615045e2a4187..f8c04ac54decb681da285983eb2f1f3498043221 100644
--- a/test.py
+++ b/test.py
@@ -1272,6 +1272,38 @@ class InheritanceTestCase(MkexpSimpleTestCase):
result = align(result)
self.assertMultiLineEqual(expecteds[i], result)
+ def test_global_override(self):
+ writeconfig(self.exp_id, u"""
+ EXP_TYPE =
+ INITIAL_DATE = 12-34-5678
+ FINAL_DATE = 87-65-4321
+ [jobs]
+ [[job]]
+ [[job1]]
+ .extends = job
+ INITIAL_DATE = $FINAL_DATE
+ """)
+ writetemplate(self.exp_id, 'job', u"""
+ %{INITIAL_DATE}
+ %{FINAL_DATE}
+ """)
+ expecteds = {
+ 'job': align(u"""
+ 12-34-5678
+ 87-65-4321
+ """),
+ 'job1': align(u"""
+ 87-65-4321
+ 87-65-4321
+ """),
+ }
+ ignore = output(script("mkexp "+self.exp_id+".config"))
+ for i in ('job', 'job1'):
+ result = readfile(join("test", "experiments", self.exp_id,
+ self.exp_id+"."+i))
+ result = align(result)
+ self.assertMultiLineEqual(expecteds[i], result)
+
class JobSiblingsTestCase(MkexpSimpleTestCase):
def test_sibling_lookup(self):