From a5cfe7c6e48ba25f7b1decf82860ed6d4358ade2 Mon Sep 17 00:00:00 2001
From: Karl-Hermann Wieners <karl-hermann.wieners@mpimet.mpg.de>
Date: Thu, 10 Dec 2015 22:50:26 +0000
Subject: [PATCH] Added new features (expr-only-file, quiet options)
* Added -q (quiet) option to mkexp to suppress info messages
* Fixed diffpath to also compare two files (used to expect directories)
* Incremented version info in setup, changes and documentation
---
CHANGES.txt | 9 +
diffpath | 23 +-
doc/mkexp.fodt | 1093 ++++++++++++++++++++++++------------------------
doc/mkexp.pdf | Bin 387806 -> 387869 bytes
mkexp | 6 +
setup.py | 2 +-
6 files changed, 584 insertions(+), 549 deletions(-)
diff --git a/CHANGES.txt b/CHANGES.txt
index e42f98c..a98585d 100644
--- a/CHANGES.txt
+++ b/CHANGES.txt
@@ -6,6 +6,15 @@ Make Experiments!
Release Changes
---------------
+Release 0.3.5
+=============
+
+Global
+------
+
+* Added -q (quiet) option to mkexp to suppress info messages
+* Fixed diffpath to also compare two files (used to expect directories)
+
Release 0.3.4
=============
diff --git a/diffpath b/diffpath
index c88b40d..e16ddb8 100755
--- a/diffpath
+++ b/diffpath
@@ -49,10 +49,27 @@ PATH_B=${4:-`echo "$PATH_A" | sed "s,$EXP_A,$EXP_B,g"`}
trap 'rm -r $DIFF_FILE' 0
DIFF_FILE=`mktemp`
+if [ -d "$PATH_A" ]
+then :
+else
+ FIND_A="-name $(basename $PATH_A)"
+ PATH_A=$(dirname $PATH_A)
+fi
+
+if [ -d "$PATH_B" ]
+then :
+else
+ FIND_B="-name $(basename $PATH_B)"
+ PATH_B=$(dirname $PATH_B)
+fi
+
for FILE_A in $(
- {
- (cd "$PATH_A" && find . ! -type d ! -name '*.log' ! -path '*/backup/*' )
- (cd "$PATH_B" && find . ! -type d ! -name '*.log' ! -path '*/backup/*' | sed "s,$EXP_B,$EXP_A,g")
+ {
+ ( cd "$PATH_A" &&
+ find . ! -type d ! -name '*.log' ! -path '*/backup/*' $FIND_A )
+ ( cd "$PATH_B" &&
+ find . ! -type d ! -name '*.log' ! -path '*/backup/*' $FIND_B |
+ sed "s,$EXP_B,$EXP_A,g" )
} | sed 's,^\./,,' | sort -u
)
do
diff --git a/doc/mkexp.fodt b/doc/mkexp.fodt
index 8c094dc..be0f2ca 100644
--- a/doc/mkexp.fodt
+++ b/doc/mkexp.fodt
@@ -1,24 +1,24 @@
<?xml version="1.0" encoding="UTF-8"?>
<office:document xmlns:office="urn:oasis:names:tc:opendocument:xmlns:office:1.0" xmlns:style="urn:oasis:names:tc:opendocument:xmlns:style:1.0" xmlns:text="urn:oasis:names:tc:opendocument:xmlns:text:1.0" xmlns:table="urn:oasis:names:tc:opendocument:xmlns:table:1.0" xmlns:draw="urn:oasis:names:tc:opendocument:xmlns:drawing:1.0" xmlns:fo="urn:oasis:names:tc:opendocument:xmlns:xsl-fo-compatible:1.0" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:meta="urn:oasis:names:tc:opendocument:xmlns:meta:1.0" xmlns:number="urn:oasis:names:tc:opendocument:xmlns:datastyle:1.0" xmlns:svg="urn:oasis:names:tc:opendocument:xmlns:svg-compatible:1.0" xmlns:chart="urn:oasis:names:tc:opendocument:xmlns:chart:1.0" xmlns:dr3d="urn:oasis:names:tc:opendocument:xmlns:dr3d: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:config="urn:oasis:names:tc:opendocument:xmlns:config:1.0" xmlns:ooo="http://openoffice.org/2004/office" xmlns:ooow="http://openoffice.org/2004/writer" xmlns:oooc="http://openoffice.org/2004/calc" xmlns:dom="http://www.w3.org/2001/xml-events" xmlns:xforms="http://www.w3.org/2002/xforms" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:rpt="http://openoffice.org/2005/report" xmlns:of="urn:oasis:names:tc:opendocument:xmlns:of:1.2" xmlns:xhtml="http://www.w3.org/1999/xhtml" xmlns:grddl="http://www.w3.org/2003/g/data-view#" xmlns:officeooo="http://openoffice.org/2009/office" xmlns:tableooo="http://openoffice.org/2009/table" xmlns:drawooo="http://openoffice.org/2010/draw" xmlns:calcext="urn:org:documentfoundation:names:experimental:calc:xmlns:calcext:1.0" xmlns:loext="urn:org:documentfoundation:names:experimental:office:xmlns:loext:1.0" xmlns:field="urn:openoffice:names:experimental:ooo-ms-interop:xmlns:field:1.0" xmlns:formx="urn:openoffice:names:experimental:ooxml-odf-interop:xmlns:form:1.0" xmlns:css3t="http://www.w3.org/TR/css3-text/" 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>P11DT23H4M5S</meta:editing-duration><meta:editing-cycles>99</meta:editing-cycles><meta:generator>LibreOffice/4.2.8.2$Linux_X86_64 LibreOffice_project/420m0$Build-2</meta:generator><meta:initial-creator>Karl-Hermann Wieners</meta:initial-creator><dc:date>2015-11-05T23:10:43.863488180</dc:date><dc:creator>Karl-Hermann Wieners</dc:creator><meta:printed-by>Karl-Hermann Wieners</meta:printed-by><meta:print-date>2015-01-20T10:55:48.576690105</meta:print-date><dc:subject>Run-script generation for earth system models</dc:subject><meta:document-statistic meta:table-count="0" meta:image-count="0" meta:object-count="0" meta:page-count="26" meta:paragraph-count="523" meta:word-count="7155" meta:character-count="45703" meta:non-whitespace-character-count="38695"/><meta:template xlink:type="simple" xlink:actuate="onRequest" xlink:title="A4" xlink:href="../../../../../../../../../../home/m221078/.config/libreoffice/4/user/template/A4.ott" meta:date="2015-01-05T17:44:27.463210655"/></office:meta>
+ <office:meta><meta:creation-date>2015-01-05T17:44:27.618344249</meta:creation-date><dc:title>Make Experiments!</dc:title><meta:editing-duration>P11DT23H4M5S</meta:editing-duration><meta:editing-cycles>100</meta:editing-cycles><meta:generator>LibreOffice/4.2.8.2$Linux_X86_64 LibreOffice_project/420m0$Build-2</meta:generator><meta:initial-creator>Karl-Hermann Wieners</meta:initial-creator><dc:date>2015-12-10T23:45:42.562162112</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="26" meta:paragraph-count="523" meta:word-count="7155" meta:character-count="45706" meta:non-whitespace-character-count="38698"/><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">267626</config:config-item>
+ <config:config-item config:name="ViewAreaTop" config:type="long">6703</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">32731</config:config-item>
- <config:config-item config:name="ViewAreaHeight" config:type="long">21407</config:config-item>
+ <config:config-item config:name="ViewAreaWidth" config:type="long">24608</config:config-item>
+ <config:config-item config:name="ViewAreaHeight" config:type="long">22438</config:config-item>
<config:config-item config:name="ShowRedlineChanges" config:type="boolean">true</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">16540</config:config-item>
- <config:config-item config:name="ViewTop" config:type="long">279996</config:config-item>
+ <config:config-item config:name="ViewLeft" config:type="long">11164</config:config-item>
+ <config:config-item config:name="ViewTop" config:type="long">15314</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">267626</config:config-item>
- <config:config-item config:name="VisibleRight" config:type="long">32729</config:config-item>
- <config:config-item config:name="VisibleBottom" config:type="long">289031</config:config-item>
+ <config:config-item config:name="VisibleTop" config:type="long">6703</config:config-item>
+ <config:config-item config:name="VisibleRight" config:type="long">24606</config:config-item>
+ <config:config-item config:name="VisibleBottom" config:type="long">29139</config:config-item>
<config:config-item config:name="ZoomType" config:type="short">0</config:config-item>
<config:config-item config:name="ViewLayoutColumns" config:type="short">0</config:config-item>
<config:config-item config:name="ViewLayoutBookMode" config:type="boolean">false</config:config-item>
@@ -81,9 +81,9 @@
<config:config-item config:name="ConsiderTextWrapOnObjPos" config:type="boolean">false</config:config-item>
<config:config-item config:name="CurrentDatabaseCommandType" config:type="int">0</config:config-item>
<config:config-item config:name="RedlineProtectionKey" config:type="base64Binary"/>
- <config:config-item config:name="Rsid" config:type="int">13178698</config:config-item>
+ <config:config-item config:name="Rsid" config:type="int">13248803</config:config-item>
<config:config-item config:name="PrintProspectRTL" config:type="boolean">false</config:config-item>
- <config:config-item config:name="PrinterSetup" config:type="base64Binary">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</config:config-item>
+ <config:config-item config:name="PrinterSetup" config:type="base64Binary">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</config:config-item>
<config:config-item config:name="AlignTabStopPosition" config:type="boolean">true</config:config-item>
<config:config-item config:name="ProtectForm" config:type="boolean">false</config:config-item>
<config:config-item config:name="InvertBorderSpacing" config:type="boolean">false</config:config-item>
@@ -546,548 +546,548 @@
<style:text-properties fo:font-style="normal" officeooo:rsid="00931d47" officeooo:paragraph-rsid="00931d47" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
<style:style style:name="P57" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="005a5c62" officeooo:paragraph-rsid="005a5c62"/>
+ <style:text-properties fo:font-style="normal" officeooo:rsid="00c85300" officeooo:paragraph-rsid="00c85300" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
<style:style style:name="P58" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="005b6c85" officeooo:paragraph-rsid="005b6c85"/>
+ <style:text-properties officeooo:rsid="005a5c62" officeooo:paragraph-rsid="005a5c62"/>
</style:style>
<style:style style:name="P59" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="00617108" officeooo:paragraph-rsid="00617108"/>
+ <style:text-properties officeooo:rsid="005b6c85" officeooo:paragraph-rsid="005b6c85"/>
</style:style>
<style:style style:name="P60" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="0063d022" officeooo:paragraph-rsid="006727cc"/>
+ <style:text-properties officeooo:rsid="00617108" officeooo:paragraph-rsid="00617108"/>
</style:style>
<style:style style:name="P61" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="00657146" officeooo:paragraph-rsid="00657146"/>
+ <style:text-properties officeooo:rsid="0063d022" officeooo:paragraph-rsid="006727cc"/>
</style:style>
<style:style style:name="P62" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="006727cc" officeooo:paragraph-rsid="006727cc"/>
+ <style:text-properties officeooo:rsid="00657146" officeooo:paragraph-rsid="00657146"/>
</style:style>
<style:style style:name="P63" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="006e58f1" officeooo:paragraph-rsid="006e58f1"/>
+ <style:text-properties officeooo:rsid="006727cc" officeooo:paragraph-rsid="006727cc"/>
</style:style>
<style:style style:name="P64" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="006e58f1" officeooo:paragraph-rsid="0086f697"/>
+ <style:text-properties officeooo:rsid="006e58f1" officeooo:paragraph-rsid="006e58f1"/>
</style:style>
<style:style style:name="P65" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="006e58f1" officeooo:paragraph-rsid="00881a06"/>
+ <style:text-properties officeooo:rsid="006e58f1" officeooo:paragraph-rsid="0086f697"/>
</style:style>
<style:style style:name="P66" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="00823929" officeooo:paragraph-rsid="00823929"/>
+ <style:text-properties officeooo:rsid="006e58f1" officeooo:paragraph-rsid="00881a06"/>
</style:style>
<style:style style:name="P67" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:paragraph-rsid="0086f697"/>
+ <style:text-properties officeooo:rsid="00823929" officeooo:paragraph-rsid="00823929"/>
</style:style>
<style:style style:name="P68" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="0081efeb" officeooo:paragraph-rsid="00881a06"/>
+ <style:text-properties officeooo:paragraph-rsid="0086f697"/>
</style:style>
<style:style style:name="P69" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:paragraph-rsid="00881a06"/>
+ <style:text-properties officeooo:rsid="0081efeb" officeooo:paragraph-rsid="00881a06"/>
</style:style>
<style:style style:name="P70" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="00895410" officeooo:paragraph-rsid="0089d9b6"/>
+ <style:text-properties officeooo:paragraph-rsid="00881a06"/>
</style:style>
<style:style style:name="P71" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="0089d9b6" officeooo:paragraph-rsid="0089d9b6"/>
+ <style:text-properties officeooo:rsid="00895410" officeooo:paragraph-rsid="0089d9b6"/>
</style:style>
<style:style style:name="P72" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="0089d9b6" officeooo:paragraph-rsid="008a0101"/>
+ <style:text-properties officeooo:rsid="0089d9b6" officeooo:paragraph-rsid="0089d9b6"/>
</style:style>
<style:style style:name="P73" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="008a0101" officeooo:paragraph-rsid="008a0101"/>
+ <style:text-properties officeooo:rsid="0089d9b6" officeooo:paragraph-rsid="008a0101"/>
</style:style>
<style:style style:name="P74" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="008b134d" officeooo:paragraph-rsid="008b134d"/>
+ <style:text-properties officeooo:rsid="008a0101" officeooo:paragraph-rsid="008a0101"/>
</style:style>
<style:style style:name="P75" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="008c2cba" officeooo:paragraph-rsid="008c2cba"/>
+ <style:text-properties officeooo:rsid="008b134d" officeooo:paragraph-rsid="008b134d"/>
</style:style>
<style:style style:name="P76" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="008e158e" officeooo:paragraph-rsid="008e158e"/>
+ <style:text-properties officeooo:rsid="008c2cba" officeooo:paragraph-rsid="008c2cba"/>
</style:style>
<style:style style:name="P77" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="008e53fe" officeooo:paragraph-rsid="008e53fe"/>
+ <style:text-properties officeooo:rsid="008e158e" officeooo:paragraph-rsid="008e158e"/>
</style:style>
<style:style style:name="P78" style:family="paragraph" style:parent-style-name="Text_20_body">
- <style:text-properties officeooo:rsid="00931d47" officeooo:paragraph-rsid="009475bb"/>
+ <style:text-properties officeooo:rsid="008e53fe" officeooo:paragraph-rsid="008e53fe"/>
</style:style>
<style:style style:name="P79" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:text-properties officeooo:rsid="00931d47" officeooo:paragraph-rsid="009475bb"/>
+ </style:style>
+ <style:style style:name="P80" style:family="paragraph" style:parent-style-name="Text_20_body">
<style:paragraph-properties fo:text-align="start" style:justify-single-word="false"/>
<style:text-properties officeooo:rsid="00973c25" officeooo:paragraph-rsid="009acc7d"/>
</style:style>
- <style:style style:name="P80" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:style style:name="P81" style:family="paragraph" style:parent-style-name="Text_20_body">
<style:text-properties officeooo:paragraph-rsid="000a3505"/>
</style:style>
- <style:style style:name="P81" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:style style:name="P82" style:family="paragraph" style:parent-style-name="Text_20_body">
<style:text-properties officeooo:paragraph-rsid="00423119"/>
</style:style>
- <style:style style:name="P82" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:style style:name="P83" style:family="paragraph" style:parent-style-name="Text_20_body">
<style:text-properties officeooo:rsid="00c20e43" officeooo:paragraph-rsid="00c20e43"/>
</style:style>
- <style:style style:name="P83" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:style style:name="P84" style:family="paragraph" style:parent-style-name="Text_20_body">
<style:text-properties officeooo:rsid="00c2926f" officeooo:paragraph-rsid="00c2926f"/>
</style:style>
- <style:style style:name="P84" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:style style:name="P85" style:family="paragraph" style:parent-style-name="Text_20_body">
<style:text-properties officeooo:rsid="00c4ca99" officeooo:paragraph-rsid="00c4ca99"/>
</style:style>
- <style:style style:name="P85" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:style style:name="P86" style:family="paragraph" style:parent-style-name="Text_20_body">
<style:text-properties officeooo:rsid="00c6886f" officeooo:paragraph-rsid="00c6886f"/>
</style:style>
- <style:style style:name="P86" style:family="paragraph" style:parent-style-name="Text_20_body">
+ <style:style style:name="P87" style:family="paragraph" style:parent-style-name="Text_20_body">
<style:text-properties officeooo:rsid="00c85300" officeooo:paragraph-rsid="00c85300"/>
</style:style>
- <style:style style:name="P87" style:family="paragraph" style:parent-style-name="Preformatted_20_Text">
+ <style:style style:name="P88" style:family="paragraph" style:parent-style-name="Preformatted_20_Text">
<style:text-properties officeooo:paragraph-rsid="000ef722"/>
</style:style>
- <style:style style:name="P88" style:family="paragraph" style:parent-style-name="Preformatted_20_Text">
+ <style:style style:name="P89" style:family="paragraph" style:parent-style-name="Preformatted_20_Text">
<style:text-properties officeooo:rsid="000ef722" officeooo:paragraph-rsid="000ef722"/>
</style:style>
- <style:style style:name="P89" style:family="paragraph" style:parent-style-name="Preformatted_20_Text">
+ <style:style style:name="P90" style:family="paragraph" style:parent-style-name="Preformatted_20_Text">
<style:text-properties officeooo:rsid="0010c1fe" officeooo:paragraph-rsid="0010c1fe"/>
</style:style>
- <style:style style:name="P90" style:family="paragraph" style:parent-style-name="Preformatted_20_Text">
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<style:text-properties officeooo:rsid="000a3505" officeooo:paragraph-rsid="00beeeb9"/>
</style:style>
- <style:style style:name="P226" style:family="paragraph" style:parent-style-name="Subtitle">
+ <style:style style:name="P227" style:family="paragraph" style:parent-style-name="Subtitle">
<style:text-properties officeooo:rsid="00beeeb9" officeooo:paragraph-rsid="00beeeb9"/>
</style:style>
- <style:style style:name="P227" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P228" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="00b17591"/>
</style:style>
- <style:style style:name="P228" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P229" 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="P229" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P230" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="00423119"/>
</style:style>
- <style:style style:name="P230" style:family="paragraph" style:parent-style-name="Heading_20_2">
+ <style:style style:name="P231" style:family="paragraph" style:parent-style-name="Heading_20_2">
<style:text-properties officeooo:paragraph-rsid="0063d022"/>
</style:style>
- <style:style style:name="P231" style:family="paragraph" style:parent-style-name="Heading_20_2">
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<style:text-properties fo:font-style="normal" officeooo:paragraph-rsid="0086f697" style:font-style-asian="normal" style:font-style-complex="normal"/>
</style:style>
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<style:style style:name="P233" style:family="paragraph" style:parent-style-name="Title" style:master-page-name="First_20_Page">
<style:paragraph-properties style:page-number="auto"/>
<style:text-properties officeooo:rsid="000a3505" officeooo:paragraph-rsid="000a3505"/>
@@ -1753,6 +1753,9 @@
<style:style style:name="T202" style:family="text">
<style:text-properties officeooo:rsid="00c9174a"/>
</style:style>
+ <style:style style:name="T203" style:family="text">
+ <style:text-properties officeooo:rsid="00ca2923"/>
+ </style:style>
<style:style style:name="Sect1" style:family="section">
<style:section-properties fo:background-color="transparent" style:editable="false">
<style:columns fo:column-count="1" fo:column-gap="0cm"/>
@@ -1807,7 +1810,7 @@
<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">10</text:page-number><text:tab/><text:tab/><text:modification-date style:data-style-name="N84">2015-11-05</text:modification-date>, <text:modification-time style:data-style-name="N41">23:10:44</text:modification-time></text:p>
+ <text:p text:style-name="Footer"><text:page-number text:select-page="current">2</text:page-number><text:tab/><text:tab/><text:modification-date style:data-style-name="N84">2015-12-10</text:modification-date>, <text:modification-time style:data-style-name="N41">23:45:43</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"/>
@@ -1822,9 +1825,9 @@
<text:sequence-decl text:display-outline-level="0" text:name="Drawing"/>
</text:sequence-decls>
<text:p text:style-name="P233">Make Experiments!</text:p>
- <text:p text:style-name="P225">Run-script generation for earth system models</text:p>
- <text:p text:style-name="P226">Release 0.3.<text:span text:style-name="T202">4</text:span></text:p>
- <text:p text:style-name="P204">Karl-Hermann Wieners<text:line-break/><text:span text:style-name="T196">Max-Planck-Institut für Meteorologie<text:line-break/>Hamburg</text:span></text:p>
+ <text:p text:style-name="P226">Run-script generation for earth system models</text:p>
+ <text:p text:style-name="P227">Release 0.3.<text:span text:style-name="T203">5dev</text:span></text:p>
+ <text:p text:style-name="P205">Karl-Hermann Wieners<text:line-break/><text:span text:style-name="T196">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>
@@ -1911,172 +1914,172 @@
</text:table-of-content-source>
<text:index-body>
<text:index-title text:style-name="Sect2" text:name="Table of Contents1_Head">
- <text:p text:style-name="P205">Table of Contents</text:p>
+ <text:p text:style-name="P206">Table of Contents</text:p>
</text:index-title>
- <text:p text:style-name="P207"><text:a xlink:type="simple" xlink:href="#__RefHeading__2518_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1 Introduction<text:tab/>3</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2520_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1 Example: ECHAM experiment setup<text:tab/>3</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2522_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.1 Experiments are defined by custom and default settings<text:tab/>3</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2524_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.2 Job templates are completed by settings to create scripts<text:tab/>4</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2526_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.3 Generating scripts only refers to the custom settings' file<text:tab/>6</text:a></text:p>
- <text:p text:style-name="P207"><text:a xlink:type="simple" xlink:href="#__RefHeading__2528_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2 Details on experiment definition<text:tab/>6</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2530_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.1 Design<text:tab/>7</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2532_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.2 Tools<text:tab/>7</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2534_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3 Format of .config files<text:tab/>8</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__1669_1438093122" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.1 Variables<text:tab/>8</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2536_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.2 Sections<text:tab/>9</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2538_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.3 Special variables and sections<text:tab/>9</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2540_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.4 Variable interpolation<text:tab/>11</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2542_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.5 Evaluation of interpolation<text:tab/>12</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2544_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.6 Special expressions<text:tab/>13</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2546_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4 Format of .tmpl files<text:tab/>14</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2548_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.1 Placeholders<text:tab/>14</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2550_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.2 Variables in sections<text:tab/>14</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2552_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.3 Expressions<text:tab/>15</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2554_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.4 Loops<text:tab/>15</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2556_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.5 Conditions<text:tab/>16</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2558_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.6 Comments<text:tab/>16</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2560_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.5 Standard experiments<text:tab/>17</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2562_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.6 Standard options<text:tab/>17</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2564_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7 Standard environments<text:tab/>18</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__1508_1711940803" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8 Generating jobs<text:tab/>18</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.1 Changing the model job list<text:tab/>19</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2568_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.2 Pre-defined job variables<text:tab/>19</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.3 Overriding namelist settings in derived jobs<text:tab/>20</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2572_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.4 Native script variables<text:tab/>20</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2574_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.5 Initializing native script variables<text:tab/>21</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2576_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.6 Re-generation of scripts and backup<text:tab/>22</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__1883_1672291846" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9 Defining namelists and other configuration files<text:tab/>22</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2578_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.1 Formatting the namelist information<text:tab/>23</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.2 Suppressing namelist groups or variables<text:tab/>23</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2714_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.3 Using the namelist text<text:tab/>24</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2584_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.4 Non-namelist configuration files<text:tab/>24</text:a></text:p>
- <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10 Defining input files for an experiment<text:tab/>25</text:a></text:p>
- <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2833_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10.1 Overriding input files for certain jobs<text:tab/>25</text:a></text:p>
+ <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2518_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1 Introduction<text:tab/>3</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2520_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1 Example: ECHAM experiment setup<text:tab/>3</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2522_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.1 Experiments are defined by custom and default settings<text:tab/>3</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2524_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.2 Job templates are completed by settings to create scripts<text:tab/>4</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2526_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">1.1.3 Generating scripts only refers to the custom settings' file<text:tab/>6</text:a></text:p>
+ <text:p text:style-name="P208"><text:a xlink:type="simple" xlink:href="#__RefHeading__2528_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2 Details on experiment definition<text:tab/>6</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2530_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.1 Design<text:tab/>7</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2532_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.2 Tools<text:tab/>7</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2534_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3 Format of .config files<text:tab/>8</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__1669_1438093122" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.1 Variables<text:tab/>8</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2536_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.2 Sections<text:tab/>9</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2538_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.3 Special variables and sections<text:tab/>9</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2540_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.4 Variable interpolation<text:tab/>11</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2542_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.5 Evaluation of interpolation<text:tab/>12</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2544_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.3.6 Special expressions<text:tab/>13</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2546_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4 Format of .tmpl files<text:tab/>14</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2548_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.1 Placeholders<text:tab/>14</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2550_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.2 Variables in sections<text:tab/>14</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2552_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.3 Expressions<text:tab/>15</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2554_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.4 Loops<text:tab/>15</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2556_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.5 Conditions<text:tab/>16</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2558_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.4.6 Comments<text:tab/>16</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2560_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.5 Standard experiments<text:tab/>17</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2562_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.6 Standard options<text:tab/>17</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2564_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.7 Standard environments<text:tab/>18</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__1508_1711940803" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8 Generating jobs<text:tab/>18</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2566_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.1 Changing the model job list<text:tab/>19</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2568_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.2 Pre-defined job variables<text:tab/>19</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2570_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.3 Overriding namelist settings in derived jobs<text:tab/>20</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2572_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.4 Native script variables<text:tab/>20</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2574_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.5 Initializing native script variables<text:tab/>21</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2576_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.8.6 Re-generation of scripts and backup<text:tab/>22</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__1883_1672291846" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9 Defining namelists and other configuration files<text:tab/>22</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2578_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.1 Formatting the namelist information<text:tab/>23</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2580_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.2 Suppressing namelist groups or variables<text:tab/>23</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2714_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.3 Using the namelist text<text:tab/>24</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2584_1114405012" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.9.4 Non-namelist configuration files<text:tab/>24</text:a></text:p>
+ <text:p text:style-name="P209"><text:a xlink:type="simple" xlink:href="#__RefHeading__2831_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10 Defining input files for an experiment<text:tab/>25</text:a></text:p>
+ <text:p text:style-name="P210"><text:a xlink:type="simple" xlink:href="#__RefHeading__2833_1132221942" text:style-name="Index_20_Link" text:visited-style-name="Index_20_Link">2.10.1 Overriding input files for certain jobs<text:tab/>25</text:a></text:p>
</text:index-body>
</text:table-of-content>
- <text:p text:style-name="P80"/>
- <text:h text:style-name="P206" 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="P81"/>
+ <text:h text:style-name="P207" 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="T124">Make Experiments! (</text:span>mkexp<text:span text:style-name="T124">)</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="P212" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2522_1114405012"/>Experiments are defined by custom and default settings<text:bookmark-end text:name="__RefHeading__2522_1114405012"/></text:h>
+ <text:h text:style-name="P213" 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="T166">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="P89"><text:soft-page-break/># Standard AMIP experiment as baseline for further experiments (LR)</text:p>
- <text:p text:style-name="P89"/>
- <text:p text:style-name="P89">EXP_TYPE = amip-LR</text:p>
+ <text:p text:style-name="P90"><text:soft-page-break/># Standard AMIP experiment as baseline for further experiments (LR)</text:p>
+ <text:p text:style-name="P90"/>
+ <text:p text:style-name="P90">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="T165">'</text:span>amip-LR.config<text:span text:style-name="T165">'</text:span> includes these settings</text:p>
- <text:p text:style-name="P88"># Default definitions for amip-LR experiments </text:p>
- <text:p text:style-name="P87"/>
- <text:p text:style-name="P87">RES = 63 </text:p>
+ <text:p text:style-name="P89"># Default definitions for amip-LR experiments </text:p>
+ <text:p text:style-name="P88"/>
+ <text:p text:style-name="P88">RES = 63 </text:p>
<text:p text:style-name="Preformatted_20_Text"/>
<text:p text:style-name="Preformatted_20_Text">[namelists] </text:p>
- <text:p text:style-name="P87"/>
- <text:p text:style-name="P87"><text:s text:c="2"/>[[namelist.echam]] </text:p>
+ <text:p text:style-name="P88"/>
+ <text:p text:style-name="P88"><text:s text:c="2"/>[[namelist.echam]] </text:p>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="3"/>[[[runctl]]] </text:p>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="6"/>lamip = true</text:p>
- <text:p text:style-name="P90"/>
- <text:p text:style-name="P90"><text:s text:c="2"/>[[namelist.jsbach]] </text:p>
- <text:p text:style-name="P90"><text:s text:c="4"/>[[[jsbach_ctl]]] </text:p>
- <text:p text:style-name="P90"><text:s text:c="6"/>use_dynveg <text:s/>= false </text:p>
+ <text:p text:style-name="P91"/>
+ <text:p text:style-name="P91"><text:s text:c="2"/>[[namelist.jsbach]] </text:p>
+ <text:p text:style-name="P91"><text:s text:c="4"/>[[[jsbach_ctl]]] </text:p>
+ <text:p text:style-name="P91"><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="T122">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="T165">Some s</text:span>ettings apply to all <text:span text:style-name="T165">ECHAM </text:span>experiment types. <text:span text:style-name="T165">They</text:span> go into a file named <text:span text:style-name="T165">'</text:span>DEFAULT.config<text:span text:style-name="T165">'</text:span>. <text:span text:style-name="T9">mkexp</text:span> will <text:span text:style-name="T165">always </text:span>read this file <text:span text:style-name="T165">first, </text:span>before applying <text:span text:style-name="T165">any </text:span>settings from <text:span text:style-name="T165">a specific experiment type like 'amip-LR.config'.</text:span> <text:span text:style-name="T165">Such settings might be default paths for input data, as in</text:span></text:p>
- <text:p text:style-name="P94"># <text:span text:style-name="T165">Default definitions for all </text:span>ECHAM experiment<text:span text:style-name="T165">s</text:span></text:p>
- <text:p text:style-name="P94"/>
- <text:p text:style-name="P94">ATMO_INPUT_ROOT = /pool/data/ECHAM6/input/r0004 </text:p>
- <text:p text:style-name="P94">LAND_INPUT_ROOT = /pool/data/JSBACH/input/r0004 </text:p>
+ <text:p text:style-name="P95"># <text:span text:style-name="T165">Default definitions for all </text:span>ECHAM experiment<text:span text:style-name="T165">s</text:span></text:p>
+ <text:p text:style-name="P95"/>
+ <text:p text:style-name="P95">ATMO_INPUT_ROOT = /pool/data/ECHAM6/input/r0004 </text:p>
+ <text:p text:style-name="P95">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="T35">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="P213" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2524_1114405012"/>Job templates are completed by settings to create scripts<text:bookmark-end text:name="__RefHeading__2524_1114405012"/></text:h>
+ <text:h text:style-name="P214" 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="T165">Now the experiment configuration is finalized, the </text:span>settings are used to fill in <text:span text:style-name="T165">a kind of job description forms, so called </text:span><text:span text:style-name="T9">templates</text:span><text:span text:style-name="T165">, </text:span>from which eventually the <text:span text:style-name="T165">actual </text:span>job description files are created. As the structure of<text:span text:style-name="T165"> </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="T186">'</text:span>amip.run.tmpl<text:span text:style-name="T186">'</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="T123">placeholders</text:span> that are filled using the .config file information:</text:p>
- <text:p text:style-name="P94"><text:soft-page-break/>#! /bin/bash</text:p>
- <text:p text:style-name="P94"/>
- <text:p text:style-name="P94"># Job file to run ECHAM 6 </text:p>
- <text:p text:style-name="P94"/>
- <text:p text:style-name="P98">EXP=<text:span text:style-name="T112">%{EXP_ID}</text:span> # experiment identifier </text:p>
- <text:p text:style-name="P94"/>
- <text:p text:style-name="P94">RES=<text:span text:style-name="T112">%{RES}</text:span> <text:span text:style-name="T123"># experiment truncation</text:span></text:p>
- <text:p text:style-name="P94"/>
- <text:p text:style-name="P98"># absolute paths to directories with initial data: </text:p>
- <text:p text:style-name="P98">ATMO_DATA=<text:span text:style-name="T112">%{ATMO_INPUT_ROOT}</text:span> </text:p>
- <text:p text:style-name="P98">ATMO_MAP_DATA=$ATMO_DATA/T${RES} </text:p>
- <text:p text:style-name="P98"/>
- <text:p text:style-name="P98"># absolute path to directory with initial data for JSBACH: </text:p>
- <text:p text:style-name="P98">LAND_MAP_DATA=<text:span text:style-name="T112">%{LAND_INPUT_ROOT}</text:span>/T${RES} </text:p>
- <text:p text:style-name="P95"/>
- <text:p text:style-name="P95"># </text:p>
- <text:p text:style-name="P94"># ECHAM6 namelist </text:p>
- <text:p text:style-name="P94"># </text:p>
- <text:p text:style-name="P94">cat > namelist.echam << EOF </text:p>
- <text:p text:style-name="P94"><text:span text:style-name="T112">%{NAMELIST_ECHAM}</text:span> </text:p>
- <text:p text:style-name="P94">EOF </text:p>
- <text:p text:style-name="P94"/>
- <text:p text:style-name="P94"># </text:p>
- <text:p text:style-name="P94"># JSBACH namelist</text:p>
- <text:p text:style-name="P94"># </text:p>
- <text:p text:style-name="P94">cat > namelist.jsbach << EOF </text:p>
- <text:p text:style-name="P94"><text:span text:style-name="T112">%{NAMELIST_JSBACH}</text:span> </text:p>
- <text:p text:style-name="P94">EOF </text:p>
- <text:p text:style-name="P7"><text:span text:style-name="T166">T</text:span>h<text:span text:style-name="T166">e</text:span>se <text:span text:style-name="T166">'</text:span>%{...}<text:span text:style-name="T166">'</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="T186">the setting </text:span>given <text:span text:style-name="T166">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="T166">'</text:span>joe1234.run<text:span text:style-name="T166">'</text:span>:</text:p>
<text:p text:style-name="P95"><text:soft-page-break/>#! /bin/bash</text:p>
<text:p text:style-name="P95"/>
<text:p text:style-name="P95"># Job file to run ECHAM 6 </text:p>
<text:p text:style-name="P95"/>
- <text:p text:style-name="P98">EXP=<text:span text:style-name="T112">joe1234</text:span> # experiment identifier </text:p>
+ <text:p text:style-name="P99">EXP=<text:span text:style-name="T112">%{EXP_ID}</text:span> # experiment identifier </text:p>
<text:p text:style-name="P95"/>
- <text:p text:style-name="P95">RES=<text:span text:style-name="T113">63</text:span><text:span text:style-name="T6"> # experiment truncation</text:span></text:p>
+ <text:p text:style-name="P95">RES=<text:span text:style-name="T112">%{RES}</text:span> <text:span text:style-name="T123"># experiment truncation</text:span></text:p>
<text:p text:style-name="P95"/>
- <text:p text:style-name="P95">#<text:span text:style-name="T6"> absolute paths to directories with initial data: </text:span></text:p>
- <text:p text:style-name="P98">ATMO_DATA=<text:span text:style-name="T114">/pool/data/ECHAM6/input/r0004</text:span><text:span text:style-name="T5"> </text:span></text:p>
- <text:p text:style-name="P98">ATMO_MAP_DATA=$ATMO_DATA/T${RES} </text:p>
- <text:p text:style-name="P98"/>
- <text:p text:style-name="P98"># absolute path to directory with initial data for JSBACH: </text:p>
- <text:p text:style-name="P98">LAND_MAP_DATA=<text:span text:style-name="T114">/pool/data/JSBACH/input/r0004</text:span>/T${RES} </text:p>
- <text:p text:style-name="P98"/>
- <text:p text:style-name="P98">#</text:p>
+ <text:p text:style-name="P99"># absolute paths to directories with initial data: </text:p>
+ <text:p text:style-name="P99">ATMO_DATA=<text:span text:style-name="T112">%{ATMO_INPUT_ROOT}</text:span> </text:p>
+ <text:p text:style-name="P99">ATMO_MAP_DATA=$ATMO_DATA/T${RES} </text:p>
+ <text:p text:style-name="P99"/>
+ <text:p text:style-name="P99"># absolute path to directory with initial data for JSBACH: </text:p>
+ <text:p text:style-name="P99">LAND_MAP_DATA=<text:span text:style-name="T112">%{LAND_INPUT_ROOT}</text:span>/T${RES} </text:p>
+ <text:p text:style-name="P96"/>
+ <text:p text:style-name="P96"># </text:p>
<text:p text:style-name="P95"># ECHAM6 namelist </text:p>
<text:p text:style-name="P95"># </text:p>
<text:p text:style-name="P95">cat > namelist.echam << EOF </text:p>
- <text:p text:style-name="P100"><text:span text:style-name="T6">&</text:span>runctl </text:p>
- <text:p text:style-name="P100"><text:s text:c="4"/>lamip = .true.</text:p>
- <text:p text:style-name="P101">/</text:p>
+ <text:p text:style-name="P95"><text:span text:style-name="T112">%{NAMELIST_ECHAM}</text:span> </text:p>
<text:p text:style-name="P95">EOF </text:p>
<text:p text:style-name="P95"/>
<text:p text:style-name="P95"># </text:p>
<text:p text:style-name="P95"># JSBACH namelist</text:p>
<text:p text:style-name="P95"># </text:p>
<text:p text:style-name="P95">cat > namelist.jsbach << EOF </text:p>
- <text:p text:style-name="P101"><text:span text:style-name="T6">&</text:span>jsbach_ctl </text:p>
- <text:p text:style-name="P101"><text:s text:c="4"/>use_dynveg = .false.</text:p>
- <text:p text:style-name="P101">/</text:p>
+ <text:p text:style-name="P95"><text:span text:style-name="T112">%{NAMELIST_JSBACH}</text:span> </text:p>
<text:p text:style-name="P95">EOF </text:p>
+ <text:p text:style-name="P7"><text:span text:style-name="T166">T</text:span>h<text:span text:style-name="T166">e</text:span>se <text:span text:style-name="T166">'</text:span>%{...}<text:span text:style-name="T166">'</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="T186">the setting </text:span>given <text:span text:style-name="T166">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="T166">'</text:span>joe1234.run<text:span text:style-name="T166">'</text:span>:</text:p>
+ <text:p text:style-name="P96"><text:soft-page-break/>#! /bin/bash</text:p>
+ <text:p text:style-name="P96"/>
+ <text:p text:style-name="P96"># Job file to run ECHAM 6 </text:p>
+ <text:p text:style-name="P96"/>
+ <text:p text:style-name="P99">EXP=<text:span text:style-name="T112">joe1234</text:span> # experiment identifier </text:p>
+ <text:p text:style-name="P96"/>
+ <text:p text:style-name="P96">RES=<text:span text:style-name="T113">63</text:span><text:span text:style-name="T6"> # experiment truncation</text:span></text:p>
+ <text:p text:style-name="P96"/>
+ <text:p text:style-name="P96">#<text:span text:style-name="T6"> absolute paths to directories with initial data: </text:span></text:p>
+ <text:p text:style-name="P99">ATMO_DATA=<text:span text:style-name="T114">/pool/data/ECHAM6/input/r0004</text:span><text:span text:style-name="T5"> </text:span></text:p>
+ <text:p text:style-name="P99">ATMO_MAP_DATA=$ATMO_DATA/T${RES} </text:p>
+ <text:p text:style-name="P99"/>
+ <text:p text:style-name="P99"># absolute path to directory with initial data for JSBACH: </text:p>
+ <text:p text:style-name="P99">LAND_MAP_DATA=<text:span text:style-name="T114">/pool/data/JSBACH/input/r0004</text:span>/T${RES} </text:p>
+ <text:p text:style-name="P99"/>
+ <text:p text:style-name="P99">#</text:p>
+ <text:p text:style-name="P96"># ECHAM6 namelist </text:p>
+ <text:p text:style-name="P96"># </text:p>
+ <text:p text:style-name="P96">cat > namelist.echam << EOF </text:p>
+ <text:p text:style-name="P101"><text:span text:style-name="T6">&</text:span>runctl </text:p>
+ <text:p text:style-name="P101"><text:s text:c="4"/>lamip = .true.</text:p>
+ <text:p text:style-name="P102">/</text:p>
+ <text:p text:style-name="P96">EOF </text:p>
+ <text:p text:style-name="P96"/>
+ <text:p text:style-name="P96"># </text:p>
+ <text:p text:style-name="P96"># JSBACH namelist</text:p>
+ <text:p text:style-name="P96"># </text:p>
+ <text:p text:style-name="P96">cat > namelist.jsbach << EOF </text:p>
+ <text:p text:style-name="P102"><text:span text:style-name="T6">&</text:span>jsbach_ctl </text:p>
+ <text:p text:style-name="P102"><text:s text:c="4"/>use_dynveg = .false.</text:p>
+ <text:p text:style-name="P102">/</text:p>
+ <text:p text:style-name="P96">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="T166">G</text:span>enerat<text:span text:style-name="T166">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="T165">So, as soon as</text:span> <text:span text:style-name="T165">you have set up '</text:span>joe1234.config<text:span text:style-name="T165">'</text:span>, you may create the job scripts that are needed to run your experiment. Still within ECHAM's <text:span text:style-name="T167">'</text:span>run<text:span text:style-name="T167">'</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="T124">read all configuration information and </text:span>create all job scripts that are defined within your experiment's setup, <text:span text:style-name="T124">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="T124">scripts </text:span>in <text:span text:style-name="T124">a common</text:span> directory defined by the .config variable <text:span text:style-name="T167">'</text:span>SCRIPT_DIR<text:span text:style-name="T167">'</text:span>, and <text:span text:style-name="T167">print</text:span> the name of this directory on your terminal.</text:p>
- <text:h text:style-name="P210" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2528_1114405012"/>Details on <text:span text:style-name="T185">experiment</text:span> <text:span text:style-name="T185">definition</text:span><text:bookmark-end text:name="__RefHeading__2528_1114405012"/></text:h>
+ <text:h text:style-name="P211" text:outline-level="1"><text:bookmark-start text:name="__RefHeading__2528_1114405012"/>Details on <text:span text:style-name="T185">experiment</text:span> <text:span text:style-name="T185">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="T38">.</text:span></text:p>
- <text:h text:style-name="P227" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2530_1114405012"/><text:soft-page-break/>Design<text:bookmark-end text:name="__RefHeading__2530_1114405012"/></text:h>
+ <text:h text:style-name="P228" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2530_1114405012"/><text:soft-page-break/>Design<text:bookmark-end text:name="__RefHeading__2530_1114405012"/></text:h>
<text:p text:style-name="P34">Experiment definition with <text:span text:style-name="T9">mkexp</text:span> <text:span text:style-name="T147">is organized</text:span> <text:span text:style-name="T147">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="T146">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="T44">, it refers to this system level.</text:span></text:p>
<text:p text:style-name="P34"><text:span text:style-name="T146">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="T146">: 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="T43">. 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="T43">.</text:span></text:p>
<text:p text:style-name="P35"><text:span text:style-name="T38">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="T75">defines</text:span><text:span text:style-name="T38"> 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="T38">.</text:span></text:p>
<text:p text:style-name="P36"><text:span text:style-name="T38">All levels should make a clear distinction </text:span><text:span text:style-name="T45">between </text:span><text:span text:style-name="T38">the .config files, containing the experiment's configuration information, </text:span><text:span text:style-name="T45">and </text:span><text:span text:style-name="T38">the .tmpl files, containing the actual job description and job control syntax.</text:span></text:p>
- <text:h text:style-name="P228" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2532_1114405012"/>Tools<text:bookmark-end text:name="__RefHeading__2532_1114405012"/></text:h>
- <text:p text:style-name="P81"><text:span text:style-name="T124">The </text:span><text:span text:style-name="T32">mkexp</text:span><text:span text:style-name="T124"> package provides a number of tools for working with script configurations and setups.</text:span></text:p>
+ <text:h text:style-name="P229" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2532_1114405012"/>Tools<text:bookmark-end text:name="__RefHeading__2532_1114405012"/></text:h>
+ <text:p text:style-name="P82"><text:span text:style-name="T124">The </text:span><text:span text:style-name="T32">mkexp</text:span><text:span text:style-name="T124"> package provides a number of tools for working with script configurations and setups.</text:span></text:p>
<text:p text:style-name="Preformatted_20_List_20_Heading">mkexp <text:span text:style-name="T23">file</text:span><text:span text:style-name="T56">.</text:span><text:span text:style-name="T38">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="P181"><text:span text:style-name="T124">This is the main tool for generating an experiment setup. It </text:span>takes <text:span text:style-name="T168">the given</text:span> <text:span text:style-name="T168">user setup</text:span> and <text:span text:style-name="T187">the model setup that is referenced by the user setup </text:span>to generate <text:span text:style-name="T168">the</text:span> <text:span text:style-name="T168">job description files or</text:span> scripts that <text:span text:style-name="T187">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="T56">config</text:span><text:span text:style-name="T168">.</text:span></text:p>
- <text:p text:style-name="P185">When running, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> 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="P184">mkexp<text:span text:style-name="T38"> allows to override </text:span><text:span text:style-name="T54">or amend </text:span><text:span text:style-name="T38">the .config file settings on the command line </text:span><text:span text:style-name="T54">by defining or re-defining a variable </text:span><text:span text:style-name="T169">name</text:span><text:span text:style-name="T54"> set to </text:span><text:span text:style-name="T169">value</text:span><text:span text:style-name="T54">. Section variables are referenced as </text:span><text:span text:style-name="T169">sectionname</text:span><text:span text:style-name="T54">.</text:span><text:span text:style-name="T169">variablename</text:span><text:span text:style-name="T54">. 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 </text:span><text:soft-page-break/><text:span text:style-name="T54">'..', thus it is not possible to use variable names th</text:span><text:span text:style-name="T76">at</text:span><text:span text:style-name="T54"> </text:span><text:span text:style-name="T169">end</text:span><text:span text:style-name="T54"> </text:span><text:span text:style-name="T76">i</text:span><text:span text:style-name="T54">n a period.</text:span></text:p>
- <text:p text:style-name="P194"><text:span text:style-name="T54">g</text:span><text:span text:style-name="T38">etexp [-v] </text:span><text:span text:style-name="T9">file</text:span><text:span text:style-name="T38">.config [</text:span><text:span text:style-name="T9">name</text:span><text:span text:style-name="T38">=</text:span><text:span text:style-name="T9">value ...</text:span><text:span text:style-name="T38">]</text:span></text:p>
- <text:p text:style-name="P182">getexp<text:span text:style-name="T38"> reads the experiment setup the same way </text:span><text:span text:style-name="T76">as</text:span><text:span text:style-name="T38"> </text:span>mkexp<text:span text:style-name="T38">, but does not generate job scripts. Instead it prints the experiment name and directories to be generated in a shell-readable form. It is intended for debugging or passing setup information to utility scripts.</text:span></text:p>
- <text:p text:style-name="P186"><text:span text:style-name="T38">When given the '-v' (verbose) option, </text:span><text:span text:style-name="T9">all</text:span><text:span text:style-name="T38"> global configuration variables and their values are printed in alphabetical order.</text:span></text:p>
- <text:p text:style-name="P193">diffexp <text:span text:style-name="T22">file</text:span><text:span text:style-name="T23">1</text:span><text:span text:style-name="T170">.config </text:span><text:span text:style-name="T22">file2</text:span><text:span text:style-name="T55">.</text:span><text:span text:style-name="T56">config</text:span></text:p>
- <text:p text:style-name="P174">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="P195">rmexp <text:span text:style-name="T24">file</text:span><text:span text:style-name="T171">.config</text:span><text:span text:style-name="T57"> [</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T57">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T57">]</text:span></text:p>
- <text:p text:style-name="P187">This allows <text:span text:style-name="T174">interactive </text:span>remov<text:span text:style-name="T174">al for </text:span>all scripting and run-time data of an experiment without having to deal with path names, as these are read from the configuration.</text:p>
- <text:h text:style-name="P229" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2534_1114405012"/><text:span text:style-name="T130">F</text:span>ormat of .config files<text:bookmark-end text:name="__RefHeading__2534_1114405012"/></text:h>
+ <text:p text:style-name="P182"><text:span text:style-name="T124">This is the main tool for generating an experiment setup. It </text:span>takes <text:span text:style-name="T168">the given</text:span> <text:span text:style-name="T168">user setup</text:span> and <text:span text:style-name="T187">the model setup that is referenced by the user setup </text:span>to generate <text:span text:style-name="T168">the</text:span> <text:span text:style-name="T168">job description files or</text:span> scripts that <text:span text:style-name="T187">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="T56">config</text:span><text:span text:style-name="T168">.</text:span></text:p>
+ <text:p text:style-name="P186">When running, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> 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="P185">mkexp<text:span text:style-name="T38"> allows to override </text:span><text:span text:style-name="T54">or amend </text:span><text:span text:style-name="T38">the .config file settings on the command line </text:span><text:span text:style-name="T54">by defining or re-defining a variable </text:span><text:span text:style-name="T169">name</text:span><text:span text:style-name="T54"> set to </text:span><text:span text:style-name="T169">value</text:span><text:span text:style-name="T54">. Section variables are referenced as </text:span><text:span text:style-name="T169">sectionname</text:span><text:span text:style-name="T54">.</text:span><text:span text:style-name="T169">variablename</text:span><text:span text:style-name="T54">. 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 </text:span><text:soft-page-break/><text:span text:style-name="T54">'..', thus it is not possible to use variable names th</text:span><text:span text:style-name="T76">at</text:span><text:span text:style-name="T54"> </text:span><text:span text:style-name="T169">end</text:span><text:span text:style-name="T54"> </text:span><text:span text:style-name="T76">i</text:span><text:span text:style-name="T54">n a period.</text:span></text:p>
+ <text:p text:style-name="P195"><text:span text:style-name="T54">g</text:span><text:span text:style-name="T38">etexp [-v] </text:span><text:span text:style-name="T9">file</text:span><text:span text:style-name="T38">.config [</text:span><text:span text:style-name="T9">name</text:span><text:span text:style-name="T38">=</text:span><text:span text:style-name="T9">value ...</text:span><text:span text:style-name="T38">]</text:span></text:p>
+ <text:p text:style-name="P183">getexp<text:span text:style-name="T38"> reads the experiment setup the same way </text:span><text:span text:style-name="T76">as</text:span><text:span text:style-name="T38"> </text:span>mkexp<text:span text:style-name="T38">, but does not generate job scripts. Instead it prints the experiment name and directories to be generated in a shell-readable form. It is intended for debugging or passing setup information to utility scripts.</text:span></text:p>
+ <text:p text:style-name="P187"><text:span text:style-name="T38">When given the '-v' (verbose) option, </text:span><text:span text:style-name="T9">all</text:span><text:span text:style-name="T38"> global configuration variables and their values are printed in alphabetical order.</text:span></text:p>
+ <text:p text:style-name="P194">diffexp <text:span text:style-name="T22">file</text:span><text:span text:style-name="T23">1</text:span><text:span text:style-name="T170">.config </text:span><text:span text:style-name="T22">file2</text:span><text:span text:style-name="T55">.</text:span><text:span text:style-name="T56">config</text:span></text:p>
+ <text:p text:style-name="P175">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="P196">rmexp <text:span text:style-name="T24">file</text:span><text:span text:style-name="T171">.config</text:span><text:span text:style-name="T57"> [</text:span><text:span text:style-name="T24">name</text:span><text:span text:style-name="T57">=</text:span><text:span text:style-name="T24">value ...</text:span><text:span text:style-name="T57">]</text:span></text:p>
+ <text:p text:style-name="P188">This allows <text:span text:style-name="T174">interactive </text:span>remov<text:span text:style-name="T174">al for </text:span>all scripting and run-time data of an experiment without having to deal with path names, as these are read from the configuration.</text:p>
+ <text:h text:style-name="P230" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2534_1114405012"/><text:span text:style-name="T130">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="T125">For reading these files, </text:span><text:span text:style-name="T12">mkexp</text:span><text:span text:style-name="T125"> uses the </text:span><text:span text:style-name="T12">configobj</text:span><text:span text:style-name="T125"> 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="T126">configuration variable is set by simply assigning a text value to a name, as in</text:span></text:p>
@@ -2088,112 +2091,112 @@
<text:p text:style-name="P21">will set PATH to ['/bin', '/usr/bin', '/usr/local/bin'].</text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2536_1114405012"/>Sections<text:bookmark-end text:name="__RefHeading__2536_1114405012"/></text:h>
<text:p text:style-name="P22">Variable assignments may be contained in <text:span text:style-name="T9">sections</text:span><text:span text:style-name="T38">. They </text:span><text:span text:style-name="T40">group</text:span><text:span text:style-name="T38"> a set of variables that may be treated </text:span><text:span text:style-name="T77">in a way </text:span><text:span text:style-name="T38">different fro</text:span><text:span text:style-name="T77">m</text:span><text:span text:style-name="T38"> the global variables. Sections are created by a section name on a line by itself, enclosed by brackets. Any variables defined later in the .config file belong to this section:</text:span></text:p>
- <text:p text:style-name="P113">[section1]</text:p>
- <text:p text:style-name="P113"><text:s text:c="4"/>description = This is the first section</text:p>
+ <text:p text:style-name="P114">[section1]</text:p>
+ <text:p text:style-name="P114"><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="T128">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: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="P108"><text:s text:c="4"/>[[subsection1<text:span text:style-name="T128">b</text:span>]]</text:p>
- <text:p text:style-name="P108"><text:s text:c="8"/>description = This is the <text:span text:style-name="T128">second</text:span> sub section of the first section</text:p>
- <text:p text:style-name="P107">[section2]</text:p>
- <text:p text:style-name="P107"><text:s text:c="4"/>description = This is the second section </text:p>
+ <text:p text:style-name="P109"><text:s text:c="4"/>[[subsection1<text:span text:style-name="T128">b</text:span>]]</text:p>
+ <text:p text:style-name="P109"><text:s text:c="8"/>description = This is the <text:span text:style-name="T128">second</text:span> sub section of the first section</text:p>
+ <text:p text:style-name="P108">[section2]</text:p>
+ <text:p text:style-name="P108"><text:s text:c="4"/>description = This is the second section </text:p>
<text:p text:style-name="P23"><text:span text:style-name="T172">A s</text:span>ection <text:span text:style-name="T172">is</text:span> closed by the beginning of a new section of the same level, by a section <text:span text:style-name="T172">of </text:span>l<text:span text:style-name="T172">ower</text:span> <text:span text:style-name="T172">nesting </text:span>depth, <text:span text:style-name="T172">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="T129">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="T164">v</text:span>ariables <text:span text:style-name="T164">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="T38">There are a number of special variables that influence the way </text:span>mkexp<text:span text:style-name="T38"> works. They must be present in one of the .config files, unless noted otherwise below. </text:span><text:span text:style-name="T42">They are </text:span><text:soft-page-break/><text:span text:style-name="T42">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="T42">T</text:span><text:span text:style-name="T38">he first set of variables is usually defined in the model setup:</text:span></text:p>
- <text:p text:style-name="P153">SCRIPT_DIR</text:p>
- <text:p text:style-name="P166"><text:span text:style-name="T41">D</text:span><text:span text:style-name="T38">irectory where the generated job descriptions are stored. This directory and its parents are created by </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> if they do not exist.</text:span></text:p>
- <text:p text:style-name="P154">WORK_DIR</text:p>
- <text:p text:style-name="P169">Directory where the experiment is run. The jobs will use this for providing input data and configuration files needed for model execution. This directory and its parents are created if they do not exist.</text:p>
- <text:p text:style-name="P155">DATA_DIR</text:p>
- <text:p text:style-name="P169">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="P159">VERSION_</text:p>
- <text:p text:style-name="P175">Each .config file in the model setup <text:span text:style-name="T202">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="P154">SCRIPT_DIR</text:p>
+ <text:p text:style-name="P167"><text:span text:style-name="T41">D</text:span><text:span text:style-name="T38">irectory where the generated job descriptions are stored. This directory and its parents are created by </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> if they do not exist.</text:span></text:p>
+ <text:p text:style-name="P155">WORK_DIR</text:p>
+ <text:p text:style-name="P170">Directory where the experiment is run. The jobs will use this for providing input data and configuration files needed for model execution. This directory and its parents are created if they do not exist.</text:p>
+ <text:p text:style-name="P156">DATA_DIR</text:p>
+ <text:p text:style-name="P170">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="P160">VERSION_</text:p>
+ <text:p text:style-name="P176">Each .config file in the model setup <text:span text:style-name="T202">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="P41">There is a second set of variables that belongs in the user setup:</text:p>
- <text:p text:style-name="P157">EXP_TYPE</text:p>
- <text:p text:style-name="P171">Selects one of the standard experiments that are pre-defined in the model setup as basis of the current experiment definition.</text:p>
- <text:p text:style-name="P158">ENVIRONMENT</text:p>
- <text:p text:style-name="P168">Selects one of the standard host environments that are available for the model.</text:p>
- <text:p text:style-name="P162"><text:span text:style-name="T38">EXP_OPTIONS (</text:span><text:span text:style-name="T9">optional</text:span><text:span text:style-name="T38">)</text:span></text:p>
- <text:p text:style-name="P172">Subset of the model's standard options that should be applied to the current experiment definition.</text:p>
- <text:p text:style-name="P163">EXP_ID (<text:span text:style-name="T9">optional</text:span>)</text:p>
- <text:p text:style-name="P179">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="P152">EXP_DESCRIPTION <text:span text:style-name="T145">(</text:span><text:span text:style-name="T16">optional</text:span><text:span text:style-name="T145">)</text:span></text:p>
- <text:p text:style-name="P170">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 and leading and trailing empty lines are removed. Note that <text:span text:style-name="T188">both header comment and </text:span>EXP_DESCRIPTION may reference any other global variable defined in the experiment configuration <text:span text:style-name="T188">(see section </text:span><text:span text:style-name="T188"><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="T188">)</text:span>.</text:p>
- <text:p text:style-name="P170">The contents of this variable is written to a 'README' file in SCRIPT_DIR.</text:p>
+ <text:p text:style-name="P158">EXP_TYPE</text:p>
+ <text:p text:style-name="P172">Selects one of the standard experiments that are pre-defined in the model setup as basis of the current experiment definition.</text:p>
+ <text:p text:style-name="P159">ENVIRONMENT</text:p>
+ <text:p text:style-name="P169">Selects one of the standard host environments that are available for the model.</text:p>
+ <text:p text:style-name="P163"><text:span text:style-name="T38">EXP_OPTIONS (</text:span><text:span text:style-name="T9">optional</text:span><text:span text:style-name="T38">)</text:span></text:p>
+ <text:p text:style-name="P173">Subset of the model's standard options that should be applied to the current experiment definition.</text:p>
+ <text:p text:style-name="P164">EXP_ID (<text:span text:style-name="T9">optional</text:span>)</text:p>
+ <text:p text:style-name="P180">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="P153">EXP_DESCRIPTION <text:span text:style-name="T145">(</text:span><text:span text:style-name="T16">optional</text:span><text:span text:style-name="T145">)</text:span></text:p>
+ <text:p text:style-name="P171">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 and leading and trailing empty lines are removed. Note that <text:span text:style-name="T188">both header comment and </text:span>EXP_DESCRIPTION may reference any other global variable defined in the experiment configuration <text:span text:style-name="T188">(see section </text:span><text:span text:style-name="T188"><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="T188">)</text:span>.</text:p>
+ <text:p text:style-name="P171">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="T38">Another set of variables is automatically added to the job specific experiment configuration. </text:span><text:span text:style-name="T53">These are considered read-only</text:span><text:span text:style-name="T38"> </text:span><text:span text:style-name="T46">and may not be altered</text:span><text:span text:style-name="T38">.</text:span></text:p>
- <text:p text:style-name="P151"><text:soft-page-break/>JOB</text:p>
- <text:p text:style-name="P167">A dictionary of system settings pertaining to the current job.</text:p>
- <text:p text:style-name="P156">VARIABLES_</text:p>
- <text:p text:style-name="P173">List of all names that were recognized as native variables of the current job. May be used to maintain a variable definition list in the generated script.</text:p>
- <text:p text:style-name="P164"><text:span text:style-name="T50">m</text:span><text:span text:style-name="T38">kexp_input</text:span></text:p>
- <text:p text:style-name="P176">Descriptive string for script headers. It is set to 'Generated by … mkexp …' where the ellipses are filled with version information.</text:p>
- <text:p text:style-name="P159">VERSIONS_</text:p>
- <text:p text:style-name="P175">List of all 'VERSION_' strings that were found in the different .config files.</text:p>
- <text:p text:style-name="P63">These special sections are usually pre-defined in the model setup, but are commonly altered by the user.</text:p>
+ <text:p text:style-name="P152"><text:soft-page-break/>JOB</text:p>
+ <text:p text:style-name="P168">A dictionary of system settings pertaining to the current job.</text:p>
+ <text:p text:style-name="P157">VARIABLES_</text:p>
+ <text:p text:style-name="P174">List of all names that were recognized as native variables of the current job. May be used to maintain a variable definition list in the generated script.</text:p>
+ <text:p text:style-name="P165"><text:span text:style-name="T50">m</text:span><text:span text:style-name="T38">kexp_input</text:span></text:p>
+ <text:p text:style-name="P177">Descriptive string for script headers. It is set to 'Generated by … mkexp …' where the ellipses are filled with version information.</text:p>
+ <text:p text:style-name="P160">VERSIONS_</text:p>
+ <text:p text:style-name="P176">List of all 'VERSION_' strings that were found in the different .config files.</text:p>
+ <text:p text:style-name="P64">These special sections are usually pre-defined in the model setup, but are commonly altered by the user.</text:p>
<text:p text:style-name="List_20_Heading">[jobs]</text:p>
- <text:p text:style-name="P180">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">2.8</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="P181">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">2.8</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="P180">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="T177">'</text:span><text:span text:style-name="T177"><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="T177">'.</text:span></text:p>
- <text:p text:style-name="P165">[files]</text:p>
- <text:p text:style-name="P192">All input files that are needed for an experiment and <text:span text:style-name="T199">information</text:span> to provide them go into this section. <text:span text:style-name="T199">See section </text:span><text:span text:style-name="T199"><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="T199">, '</text:span><text:span text:style-name="T199"><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="T199">'.</text:span></text:p>
+ <text:p text:style-name="P181">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="T177">'</text:span><text:span text:style-name="T177"><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="T177">'.</text:span></text:p>
+ <text:p text:style-name="P166">[files]</text:p>
+ <text:p text:style-name="P193">All input files that are needed for an experiment and <text:span text:style-name="T199">information</text:span> to provide them go into this section. <text:span text:style-name="T199">See section </text:span><text:span text:style-name="T199"><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="T199">, '</text:span><text:span text:style-name="T199"><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="T199">'.</text:span></text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2540_1114405012"/>Variable interpolation<text:bookmark-end text:name="__RefHeading__2540_1114405012"/></text:h>
- <text:p text:style-name="P70">The value of a .config variable may reference the value of another variable by prefixing its name with <text:span text:style-name="T178">a </text:span>dollar sign. <text:span text:style-name="T178">This is called </text:span><text:span text:style-name="T26">interpolation</text:span><text:span text:style-name="T64"> of variables. E.g.</text:span></text:p>
- <text:p text:style-name="P141"># joe1234.config</text:p>
- <text:p text:style-name="P147">WORK_ROOT = /scratch/joe</text:p>
+ <text:p text:style-name="P71">The value of a .config variable may reference the value of another variable by prefixing its name with <text:span text:style-name="T178">a </text:span>dollar sign. <text:span text:style-name="T178">This is called </text:span><text:span text:style-name="T26">interpolation</text:span><text:span text:style-name="T64"> of variables. E.g.</text:span></text:p>
+ <text:p text:style-name="P142"># joe1234.config</text:p>
+ <text:p text:style-name="P148">WORK_ROOT = /scratch/joe</text:p>
<text:p text:style-name="Preformatted_20_Text">WORK_DIR = $WORK_ROOT/experiments/<text:span text:style-name="T179">$EXP_ID</text:span></text:p>
- <text:p text:style-name="P72">will set 'WORK_DIR' to '/scratch/joe/experiments/joe1234'.</text:p>
- <text:p text:style-name="P71">Interpolation only works for variables of the current section or its ancestor sections.</text:p>
+ <text:p text:style-name="P73">will set 'WORK_DIR' to '/scratch/joe/experiments/joe1234'.</text:p>
+ <text:p text:style-name="P72">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>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="2"/>size = 42 </text:p>
<text:p text:style-name="Preformatted_20_Text">[jobs] </text:p>
<text:p text:style-name="Preformatted_20_Text"><text:s text:c="2"/>ensemble_size = $size </text:p>
- <text:p text:style-name="P71">will fail with</text:p>
+ <text:p text:style-name="P72">will fail with</text:p>
<text:p text:style-name="Preformatted_20_Text">Oops: missing option "size" in interpolation while reading key 'ensemble_size'</text:p>
- <text:p text:style-name="P71">because 'size' is not defined in 'jobs', nor on the global level.</text:p>
- <text:p text:style-name="P73"><text:soft-page-break/>As in shell scripts, the variable name must be enclosed in braces if the interpolation continues with a word character (alphanumerical or underscore), or if the variable name contains a space (which is perfectly legal):</text:p>
+ <text:p text:style-name="P72">because 'size' is not defined in 'jobs', nor on the global level.</text:p>
+ <text:p text:style-name="P74"><text:soft-page-break/>As in shell scripts, the variable name must be enclosed in braces if the interpolation continues with a word character (alphanumerical or underscore), or if the variable name contains a space (which is perfectly legal):</text:p>
<text:p text:style-name="Preformatted_20_Text">WORK_DIR = /tmp/$EXP_ID_test <text:s text:c="3"/><text:span text:style-name="T179"># ERROR: missing option "EXP_ID_test"</text:span></text:p>
- <text:p text:style-name="P142"><text:span text:style-name="T179">WORK_DIR = /tmp/</text:span><text:span text:style-name="T119">${EXP_ID}_test</text:span><text:span text:style-name="T179"> <text:s/># OK</text:span></text:p>
- <text:p text:style-name="P141"/>
- <text:p text:style-name="P141">SPACY <text:span text:style-name="T180">VAR</text:span> = Whew! </text:p>
- <text:p text:style-name="P141"><text:span text:style-name="T180">MESSAGE</text:span> = He said: $SPACY VAR <text:s text:c="2"/><text:span text:style-name="T180"># ERROR: missing option </text:span>"<text:span text:style-name="T180">SPACY</text:span>"</text:p>
- <text:p text:style-name="P143">MESSAGE = <text:span text:style-name="T179">He said: </text:span><text:span text:style-name="T119">$</text:span><text:span text:style-name="T112">{</text:span><text:span text:style-name="T119">SPACY VAR</text:span><text:span text:style-name="T112">}</text:span> # OK</text:p>
- <text:p text:style-name="P73">The user<text:span text:style-name="T189">'</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="P143"><text:span text:style-name="T179">WORK_DIR = /tmp/</text:span><text:span text:style-name="T119">${EXP_ID}_test</text:span><text:span text:style-name="T179"> <text:s/># OK</text:span></text:p>
+ <text:p text:style-name="P142"/>
+ <text:p text:style-name="P142">SPACY <text:span text:style-name="T180">VAR</text:span> = Whew! </text:p>
+ <text:p text:style-name="P142"><text:span text:style-name="T180">MESSAGE</text:span> = He said: $SPACY VAR <text:s text:c="2"/><text:span text:style-name="T180"># ERROR: missing option </text:span>"<text:span text:style-name="T180">SPACY</text:span>"</text:p>
+ <text:p text:style-name="P144">MESSAGE = <text:span text:style-name="T179">He said: </text:span><text:span text:style-name="T119">$</text:span><text:span text:style-name="T112">{</text:span><text:span text:style-name="T119">SPACY VAR</text:span><text:span text:style-name="T112">}</text:span> # OK</text:p>
+ <text:p text:style-name="P74">The user<text:span text:style-name="T189">'</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="P73">setting 'SCRIPT_ROOT' to a subdirectory of the user's home directory.</text:p>
+ <text:p text:style-name="P74">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="P74">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="P144"># model setup</text:p>
- <text:p text:style-name="P202"><text:span text:style-name="T181">MODEL</text:span>_<text:span text:style-name="T181">DIR</text:span> = $HOME/<text:span text:style-name="T181">$MODEL_SUBDIR</text:span></text:p>
- <text:p text:style-name="P145"># user setup</text:p>
- <text:p text:style-name="P145">MODEL_SUBDIR = echam</text:p>
- <text:p text:style-name="P75">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="T182">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="P75">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="P75">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="P145"># model setup</text:p>
+ <text:p text:style-name="P203"><text:span text:style-name="T181">MODEL</text:span>_<text:span text:style-name="T181">DIR</text:span> = $HOME/<text:span text:style-name="T181">$MODEL_SUBDIR</text:span></text:p>
+ <text:p text:style-name="P146"># user setup</text:p>
+ <text:p text:style-name="P146">MODEL_SUBDIR = echam</text:p>
+ <text:p text:style-name="P76">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="T182">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="P76">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="P76">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="P77">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="Preformatted_20_Text"><text:soft-page-break/>Oops: interpolation loop detected in value "SUBMODELS" while reading key 'SUBMODELS'</text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2544_1114405012"/>Special expressions<text:bookmark-end text:name="__RefHeading__2544_1114405012"/></text:h>
- <text:p text:style-name="P77">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="T38"> includes some special expressions, that are evaluated when interpolation occurs.</text:span></text:p>
- <text:p text:style-name="P196"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T38"> = </text:span><text:span text:style-name="T108">eval(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T108">)</text:span><text:span text:style-name="T38"><text:line-break/></text:span><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T38"> = </text:span><text:span text:style-name="T108">evals(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T108">)</text:span></text:p>
- <text:p text:style-name="P188"><text:span text:style-name="T68">I</text:span><text:span text:style-name="T38">nterpret </text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T38"> as a valid Python expression and assign the result to </text:span><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T38"> as a string. When the result is a list, </text:span><text:span text:style-name="T9">eval</text:span><text:span text:style-name="T38"> will return a list of strings, while </text:span><text:span text:style-name="T9">evals</text:span><text:span text:style-name="T38"> will return a single string, where elements are joined by a comma and a space.</text:span></text:p>
- <text:p text:style-name="P188"><text:span text:style-name="T38">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="T65">to a string containing a Python list expression</text:span><text:span text:style-name="T38">, and </text:span><text:span text:style-name="T65">then </text:span><text:span text:style-name="T38">use </text:span><text:span text:style-name="T9">eval</text:span><text:span text:style-name="T38"> </text:span><text:span text:style-name="T78">a</text:span><text:span text:style-name="T38">round the interpolation expression:</text:span></text:p>
- <text:p text:style-name="P203">DATE_<text:span text:style-name="T190">STRING</text:span> = '[2010, 10, 20]' # need quotes here!</text:p>
- <text:p text:style-name="P203">DATE_<text:span text:style-name="T190">LIST</text:span> = eval($DATE_<text:span text:style-name="T191">STRING</text:span>) # becomes a 3 element list</text:p>
- <text:p text:style-name="P197">variable<text:span text:style-name="T38"> = </text:span><text:span text:style-name="T108">read(</text:span>file_name<text:span text:style-name="T108">)</text:span></text:p>
- <text:p text:style-name="P183"><text:span text:style-name="T38">Read the contents of the file </text:span>file_name<text:span text:style-name="T38"> and assign its contents to </text:span>variable<text:span text:style-name="T38"> as a string.</text:span></text:p>
- <text:p text:style-name="P198"><text:span text:style-name="T27">variable</text:span><text:span text:style-name="T66"> = </text:span><text:span text:style-name="T110">split_date(</text:span><text:span text:style-name="T27">timestamp</text:span><text:span text:style-name="T110">)</text:span></text:p>
- <text:p text:style-name="P189"><text:span text:style-name="T183">T</text:span>ake <text:span text:style-name="T9">timestamp</text:span><text:span text:style-name="T38"> and split it into a list of numerical date/time elements. </text:span><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="T38"> </text:span><text:span text:style-name="T67">must have </text:span><text:span text:style-name="T38">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="T67">'; </text:span><text:span text:style-name="T38">trailing time elements </text:span><text:span text:style-name="T68">and their separators </text:span><text:span text:style-name="T67">are optional</text:span><text:span text:style-name="T38">; time zone indicator is not supported). </text:span><text:span text:style-name="T80">Unlike ISO, </text:span><text:span text:style-name="T31">split_date</text:span><text:span text:style-name="T80"> also</text:span><text:span text:style-name="T38"> </text:span><text:span text:style-name="T80">allows the date to be in the form YYYYMMDD</text:span><text:span text:style-name="T38">. </text:span><text:span text:style-name="T68">Unset fields default to zero.</text:span></text:p>
- <text:p text:style-name="P199"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T38"> = </text:span><text:span text:style-name="T108">sec2time(</text:span><text:span text:style-name="T9">second_of_day</text:span><text:span text:style-name="T108">)</text:span></text:p>
- <text:p text:style-name="P177">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="P200"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T112">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="P190">Take integer <text:span text:style-name="T9">offset</text:span><text:span text:style-name="T38"> (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="T38"> and return the resulting date string.</text:span></text:p>
- <text:p text:style-name="P201"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T112">add_</text:span><text:span text:style-name="T120">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="P191"><text:span text:style-name="T38">Take integer </text:span><text:span text:style-name="T9">offset</text:span><text:span text:style-name="T38"> (may be negative), add it to the </text:span><text:span text:style-name="T81">day</text:span><text:span text:style-name="T38"> portion of </text:span><text:span text:style-name="T9">datestamp</text:span><text:span text:style-name="T38"> and return the resulting date string. </text:span><text:span text:style-name="T81">Year and month portions will be set as </text:span><text:soft-page-break/><text:span text:style-name="T81">appropriate, assuming a Proleptic Gregorian calendar with year 0.</text:span></text:p>
+ <text:p text:style-name="P78">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="T38"> includes some special expressions, that are evaluated when interpolation occurs.</text:span></text:p>
+ <text:p text:style-name="P197"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T38"> = </text:span><text:span text:style-name="T108">eval(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T108">)</text:span><text:span text:style-name="T38"><text:line-break/></text:span><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T38"> = </text:span><text:span text:style-name="T108">evals(</text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T108">)</text:span></text:p>
+ <text:p text:style-name="P189"><text:span text:style-name="T68">I</text:span><text:span text:style-name="T38">nterpret </text:span><text:span text:style-name="T9">expression</text:span><text:span text:style-name="T38"> as a valid Python expression and assign the result to </text:span><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T38"> as a string. When the result is a list, </text:span><text:span text:style-name="T9">eval</text:span><text:span text:style-name="T38"> will return a list of strings, while </text:span><text:span text:style-name="T9">evals</text:span><text:span text:style-name="T38"> will return a single string, where elements are joined by a comma and a space.</text:span></text:p>
+ <text:p text:style-name="P189"><text:span text:style-name="T38">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="T65">to a string containing a Python list expression</text:span><text:span text:style-name="T38">, and </text:span><text:span text:style-name="T65">then </text:span><text:span text:style-name="T38">use </text:span><text:span text:style-name="T9">eval</text:span><text:span text:style-name="T38"> </text:span><text:span text:style-name="T78">a</text:span><text:span text:style-name="T38">round the interpolation expression:</text:span></text:p>
+ <text:p text:style-name="P204">DATE_<text:span text:style-name="T190">STRING</text:span> = '[2010, 10, 20]' # need quotes here!</text:p>
+ <text:p text:style-name="P204">DATE_<text:span text:style-name="T190">LIST</text:span> = eval($DATE_<text:span text:style-name="T191">STRING</text:span>) # becomes a 3 element list</text:p>
+ <text:p text:style-name="P198">variable<text:span text:style-name="T38"> = </text:span><text:span text:style-name="T108">read(</text:span>file_name<text:span text:style-name="T108">)</text:span></text:p>
+ <text:p text:style-name="P184"><text:span text:style-name="T38">Read the contents of the file </text:span>file_name<text:span text:style-name="T38"> and assign its contents to </text:span>variable<text:span text:style-name="T38"> as a string.</text:span></text:p>
+ <text:p text:style-name="P199"><text:span text:style-name="T27">variable</text:span><text:span text:style-name="T66"> = </text:span><text:span text:style-name="T110">split_date(</text:span><text:span text:style-name="T27">timestamp</text:span><text:span text:style-name="T110">)</text:span></text:p>
+ <text:p text:style-name="P190"><text:span text:style-name="T183">T</text:span>ake <text:span text:style-name="T9">timestamp</text:span><text:span text:style-name="T38"> and split it into a list of numerical date/time elements. </text:span><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="T38"> </text:span><text:span text:style-name="T67">must have </text:span><text:span text:style-name="T38">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="T67">'; </text:span><text:span text:style-name="T38">trailing time elements </text:span><text:span text:style-name="T68">and their separators </text:span><text:span text:style-name="T67">are optional</text:span><text:span text:style-name="T38">; time zone indicator is not supported). </text:span><text:span text:style-name="T80">Unlike ISO, </text:span><text:span text:style-name="T31">split_date</text:span><text:span text:style-name="T80"> also</text:span><text:span text:style-name="T38"> </text:span><text:span text:style-name="T80">allows the date to be in the form YYYYMMDD</text:span><text:span text:style-name="T38">. </text:span><text:span text:style-name="T68">Unset fields default to zero.</text:span></text:p>
+ <text:p text:style-name="P200"><text:span text:style-name="T9">variable</text:span><text:span text:style-name="T38"> = </text:span><text:span text:style-name="T108">sec2time(</text:span><text:span text:style-name="T9">second_of_day</text:span><text:span text:style-name="T108">)</text:span></text:p>
+ <text:p text:style-name="P178">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="P201"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T112">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="P191">Take integer <text:span text:style-name="T9">offset</text:span><text:span text:style-name="T38"> (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="T38"> and return the resulting date string.</text:span></text:p>
+ <text:p text:style-name="P202"><text:span text:style-name="T9">variable</text:span> = '<text:span text:style-name="T112">add_</text:span><text:span text:style-name="T120">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="P192"><text:span text:style-name="T38">Take integer </text:span><text:span text:style-name="T9">offset</text:span><text:span text:style-name="T38"> (may be negative), add it to the </text:span><text:span text:style-name="T81">day</text:span><text:span text:style-name="T38"> portion of </text:span><text:span text:style-name="T9">datestamp</text:span><text:span text:style-name="T38"> and return the resulting date string. </text:span><text:span text:style-name="T81">Year and month portions will be set as </text:span><text:soft-page-break/><text:span text:style-name="T81">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>
@@ -2202,8 +2205,8 @@
<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="T132">#</text:span> This script was <text:span text:style-name="T132">crea</text:span>ted by %{NAME}</text:p>
<text:p text:style-name="P33">Here, the placehol<text:span text:style-name="T173">d</text:span>er requests the 'NAME' variable which was set to 'Joe User' in the example .config file <text:span text:style-name="T173">of section </text:span><text:span text:style-name="T173"><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="T173">configuration</text:span> and used to textually replace the placeholder expression, yield<text:span text:style-name="T173">ing</text:span> the final text:</text:p>
- <text:p text:style-name="P110">#! /bin/ksh</text:p>
- <text:p text:style-name="P109"><text:span text:style-name="T133"># </text:span>This script was <text:span text:style-name="T133">crea</text:span>ted by <text:span text:style-name="T131">Joe User</text:span></text:p>
+ <text:p text:style-name="P111">#! /bin/ksh</text:p>
+ <text:p text:style-name="P110"><text:span text:style-name="T133"># </text:span>This script was <text:span text:style-name="T133">crea</text:span>ted by <text:span text:style-name="T131">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:span text:style-name="T135">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>
@@ -2220,8 +2223,8 @@
<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="T135">42</text:span> to string</text:p>
- <text:p text:style-name="P112">LIST_ELEMENT=%{PATH[0]} <text:s/># indices start with 0</text:p>
- <text:p text:style-name="P112">LIST_SUBLIST=%{PATH[1:3]}</text:p>
+ <text:p text:style-name="P113">LIST_ELEMENT=%{PATH[0]} <text:s/># indices start with 0</text:p>
+ <text:p text:style-name="P113">LIST_SUBLIST=%{PATH[1:3]}</text:p>
<text:p text:style-name="Preformatted_20_Text">FILTERED_STRING=%{NAME | <text:span text:style-name="T135">lower()} <text:s/># is 'joe user'</text:span></text:p>
<text:p text:style-name="Text_20_body">The last example allows for <text:span text:style-name="T144">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="T9">mkexp</text:span> defines two additional filters, 'split' for cutting a string into a list of substrings, and 'filter' for removing (empty) ele<text:span text:style-name="T200">s</text:span>ments from a list:</text:p>
<text:p text:style-name="Preformatted_20_Text">SPLIT_EXAMPLE=%{'A B C' | split(' ')} <text:s/># is ['A', 'B', 'C']</text:p>
@@ -2230,14 +2233,14 @@
<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="T192">i.e. lines </text:span>beginning with '#%'. <text:span text:style-name="T192">They </text:span>start with '#% for … <text:span text:style-name="T138">in …:</text:span>' and end in '#% endfor':</text:p>
<text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T112">#% for</text:span> countdown <text:span text:style-name="T112">in</text:span> [3, 2, 1, '<text:span text:style-name="T192">liftoff</text:span>']<text:span text:style-name="T112">:</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text">echo %{countdown}</text:p>
- <text:p text:style-name="P99">#% endfor</text:p>
+ <text:p text:style-name="P100">#% endfor</text:p>
<text:p text:style-name="P28">will <text:span text:style-name="T136">be expanded by </text:span><text:span text:style-name="T30">mkexp</text:span><text:span text:style-name="T136"> 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="T192">liftoff</text:span></text:p>
<text:p text:style-name="P31"><text:span text:style-name="T138">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="T138">and the size of a list is queried with the 'length' filter</text:span>.</text:p>
- <text:p text:style-name="P111"><text:soft-page-break/>#% for index in <text:span text:style-name="T112">range(1, </text:span><text:span text:style-name="T115">PATH|length()</text:span><text:span text:style-name="T112">)</text:span> <text:s/><text:span text:style-name="T138"># PATH was defined in </text:span><text:span text:style-name="T138"><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="P112"><text:soft-page-break/>#% for index in <text:span text:style-name="T112">range(1, </text:span><text:span text:style-name="T115">PATH|length()</text:span><text:span text:style-name="T112">)</text:span> <text:s/><text:span text:style-name="T138"># PATH was defined in </text:span><text:span text:style-name="T138"><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="T138">echo</text:span> %<text:span text:style-name="T139">{index}: </text:span>%{<text:span text:style-name="T138">PATH[</text:span>index<text:span text:style-name="T138">]</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="T137">indexing of lists starts at 0,</text:span> <text:span text:style-name="T137">i.e. the first element of the PATH list is skipped. Besides, </text:span>the stop index <text:span text:style-name="T139">is</text:span> not included, i.e. <text:span text:style-name="T138">as PATH has a length of 3, </text:span>the last looping has index <text:span text:style-name="T137">2</text:span>:</text:p>
@@ -2247,17 +2250,17 @@
<text:p text:style-name="P29">A template may contain alternative parts <text:span text:style-name="T139">that are selected depending on the .config data</text:span>, <text:span text:style-name="T139">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="T139">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="T139"> 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="T112">#% if </text:span><text:span text:style-name="T141">PATH|length()</text:span><text:span text:style-name="T140"> </text:span><text:span text:style-name="T116">is divisibleby 3:</text:span></text:p>
- <text:p text:style-name="P127">diff3 %{PATH[:3]|join(' ')}</text:p>
- <text:p text:style-name="P102">#% elif <text:span text:style-name="T141">PATH|length()</text:span> is even:</text:p>
- <text:p text:style-name="P112">diff %{PATH[:2]|join(' ')}</text:p>
- <text:p text:style-name="P99">#% else:</text:p>
+ <text:p text:style-name="P128">diff3 %{PATH[:3]|join(' ')}</text:p>
+ <text:p text:style-name="P103">#% elif <text:span text:style-name="T141">PATH|length()</text:span> is even:</text:p>
+ <text:p text:style-name="P113">diff %{PATH[:2]|join(' ')}</text:p>
+ <text:p text:style-name="P100">#% else:</text:p>
<text:p text:style-name="Preformatted_20_Text">echo <text:span text:style-name="T142">cannot handle PATH</text:span></text:p>
- <text:p text:style-name="P99">#% endif</text:p>
+ <text:p text:style-name="P100">#% 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="P30"><text:span text:style-name="T139"><text:s/>For a list of available tests, see the </text:span><text:span text:style-name="T15">Jinja</text:span><text:span text:style-name="T143"> documentation.</text:span></text:p>
<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="P57"><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="T193">'#%</text:span>#':</text:p>
+ <text:p text:style-name="P58"><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="T193">'#%</text:span>#':</text:p>
<text:p text:style-name="Preformatted_20_Text"><text:soft-page-break/># 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="T152">and is for template documentation only</text:span></text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2560_1114405012"/>Standard experiment<text:span text:style-name="T36">s</text:span><text:bookmark-end text:name="__RefHeading__2560_1114405012"/></text:h>
@@ -2274,186 +2277,186 @@
<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="T124">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="T163">may</text:span> <text:span text:style-name="T163">set</text:span> the special variable E<text:span text:style-name="T163">NVIRONMENT</text:span> to the name of <text:span text:style-name="T163">the host </text:span>e<text:span text:style-name="T163">nvironment</text:span> to use. <text:span text:style-name="T163">If it is not set, the 'DEFAULT' environment settings will be used.</text:span></text:p>
- <text:h text:style-name="P230" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1508_1711940803"/>Generating <text:span text:style-name="T160">j</text:span>obs<text:bookmark-end text:name="__RefHeading__1508_1711940803"/></text:h>
+ <text:h text:style-name="P231" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__1508_1711940803"/>Generating <text:span text:style-name="T160">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="T148"> </text:span>running <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T86">, </text:span><text:span text:style-name="T87">the special configuration section [jobs]</text:span><text:span text:style-name="T34"> </text:span><text:span text:style-name="T87">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="P128"># <text:span text:style-name="T149">model setup: experiment type 'control'</text:span></text:p>
- <text:p text:style-name="P115">[jobs]</text:p>
- <text:p text:style-name="P115"><text:s text:c="2"/>[[pre]]</text:p>
- <text:p text:style-name="P115"><text:s text:c="2"/>[[run]]</text:p>
- <text:p text:style-name="P115"><text:s text:c="2"/>[[post]]</text:p>
+ <text:p text:style-name="P129"># <text:span text:style-name="T149">model setup: experiment type 'control'</text:span></text:p>
+ <text:p text:style-name="P116">[jobs]</text:p>
+ <text:p text:style-name="P116"><text:s text:c="2"/>[[pre]]</text:p>
+ <text:p text:style-name="P116"><text:s text:c="2"/>[[run]]</text:p>
+ <text:p text:style-name="P116"><text:s text:c="2"/>[[post]]</text:p>
<text:p text:style-name="P43"><text:span text:style-name="T87">For each of </text:span><text:span text:style-name="T89">the jobs defined in the model setup above</text:span><text:span text:style-name="T87">, there </text:span><text:span text:style-name="T89">must</text:span><text:span text:style-name="T87"> be a template file in the model setup, </text:span><text:span text:style-name="T89">e.g. for [[run]] </text:span><text:span text:style-name="T87">either as 'control.run.tmpl' or 'DEFAULT.run.tmpl'. </text:span><text:span text:style-name="T88">The corresponding</text:span><text:span text:style-name="T87"> file is expanded to its final form using the </text:span><text:span text:style-name="T88">full</text:span><text:span text:style-name="T87"> experiment configuration, </text:span><text:span text:style-name="T88">as described before</text:span><text:span text:style-name="T87">. Besides, the </text:span><text:span text:style-name="T88">job specific </text:span><text:span text:style-name="T87">variable</text:span><text:span text:style-name="T88">s</text:span><text:span text:style-name="T87"> </text:span><text:span text:style-name="T88">are set and passed according to their respective template</text:span><text:span text:style-name="T87">.</text:span></text:p>
<text:p text:style-name="P43"><text:span text:style-name="T90">The resulting job scripts are </text:span><text:span text:style-name="T89">written to the directory defined by SCRIPT_DIR, </text:span><text:span text:style-name="T90">e.g. </text:span><text:span text:style-name="T89">as 'joe1234.run', </text:span><text:span text:style-name="T90">and marked as being executable. </text:span><text:span text:style-name="T96">Besides, as mentioned before, the contents of the special variable EXP_DESCRIPTION is written to a README file in that same directory. </text:span><text:span text:style-name="T99">Also, an update script is created that allows to re-generate all output files with identical environment and command line settings by simply running './update' from the script directory.</text:span></text:p>
<text:h text:style-name="Heading_20_3" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2566_1114405012"/><text:soft-page-break/><text:span text:style-name="T90">C</text:span><text:span text:style-name="T86">hanging the model job list</text:span><text:bookmark-end text:name="__RefHeading__2566_1114405012"/></text:h>
<text:p text:style-name="P44"><text:span text:style-name="T87">U</text:span><text:span text:style-name="T86">sually, the job list is defined in the model setup. The user may chose to add </text:span><text:span text:style-name="T92">jobs </text:span><text:span text:style-name="T86">and delete jobs from this list as appropriate. While adding a job is straightforward, removing a job uses a special section variable '.remove' (note the leading period). It </text:span><text:span text:style-name="T92">is</text:span><text:span text:style-name="T86"> defined in the [jobs] section and contains a list of the jobs to be suppressed.</text:span></text:p>
- <text:p text:style-name="P115"># joe1234.config</text:p>
- <text:p text:style-name="P115">EXP_TYPE = control</text:p>
- <text:p text:style-name="P115">[jobs]</text:p>
- <text:p text:style-name="P115"><text:s text:c="2"/>.remove = post, pre</text:p>
- <text:p text:style-name="P115"><text:s text:c="2"/>[[my_pre]]</text:p>
- <text:p text:style-name="P115"><text:s text:c="2"/>[[my_post]]</text:p>
+ <text:p text:style-name="P116"># joe1234.config</text:p>
+ <text:p text:style-name="P116">EXP_TYPE = control</text:p>
+ <text:p text:style-name="P116">[jobs]</text:p>
+ <text:p text:style-name="P116"><text:s text:c="2"/>.remove = post, pre</text:p>
+ <text:p text:style-name="P116"><text:s text:c="2"/>[[my_pre]]</text:p>
+ <text:p text:style-name="P116"><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="T150">ost</text:span>' job, that is basically the same as the old 'p<text:span text:style-name="T150">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="P115">[jobs]</text:p>
- <text:p text:style-name="P129"><text:span text:style-name="T86"><text:s text:c="2"/>[[my_p</text:span><text:span text:style-name="T91">ost</text:span><text:span text:style-name="T86">]]</text:span></text:p>
- <text:p text:style-name="P129"><text:span text:style-name="T86"><text:s text:c="4"/>.</text:span><text:span text:style-name="T90">extends</text:span><text:span text:style-name="T86"> = p</text:span><text:span text:style-name="T91">ost</text:span></text:p>
- <text:p text:style-name="P116"><text:s text:c="4"/>command = $HOME/bin/my_special_command</text:p>
+ <text:p text:style-name="P116">[jobs]</text:p>
+ <text:p text:style-name="P130"><text:span text:style-name="T86"><text:s text:c="2"/>[[my_p</text:span><text:span text:style-name="T91">ost</text:span><text:span text:style-name="T86">]]</text:span></text:p>
+ <text:p text:style-name="P130"><text:span text:style-name="T86"><text:s text:c="4"/>.</text:span><text:span text:style-name="T90">extends</text:span><text:span text:style-name="T86"> = p</text:span><text:span text:style-name="T91">ost</text:span></text:p>
+ <text:p text:style-name="P117"><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="T151">made available </text:span>to <text:span text:style-name="T151">the template via the</text:span> 'JOB' dictionary.</text:p>
- <text:h text:style-name="P215" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2568_1114405012"/>Pre-defined job variables<text:bookmark-end text:name="__RefHeading__2568_1114405012"/></text:h>
+ <text:h text:style-name="P216" 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="P160">tasks</text:p>
- <text:p text:style-name="P178">The total number of parallel (MPI) tasks that will be started when running the model. If a job section does not define 'tasks', its value defaults to 'nodes' times 'tasks_per_node'. Some models require that 'tasks' may explicitly be set to some artificial value to trigger the testing mode.</text:p>
- <text:p text:style-name="P161">nodes</text:p>
- <text:p text:style-name="P178">Number of computing nodes required on the computing system. Needed if 'tasks' is not set.</text:p>
- <text:p text:style-name="P161">tasks_per_node</text:p>
- <text:p text:style-name="P178">Number of parallel (MPI) tasks on a single node. Needed if 'tasks' is not set.</text:p>
- <text:h text:style-name="P214" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2570_1114405012"/><text:soft-page-break/>Overriding namelist settings in derived jobs<text:bookmark-end text:name="__RefHeading__2570_1114405012"/></text:h>
+ <text:p text:style-name="P161">tasks</text:p>
+ <text:p text:style-name="P179">The total number of parallel (MPI) tasks that will be started when running the model. If a job section does not define 'tasks', its value defaults to 'nodes' times 'tasks_per_node'. Some models require that 'tasks' may explicitly be set to some artificial value to trigger the testing mode.</text:p>
+ <text:p text:style-name="P162">nodes</text:p>
+ <text:p text:style-name="P179">Number of computing nodes required on the computing system. Needed if 'tasks' is not set.</text:p>
+ <text:p text:style-name="P162">tasks_per_node</text:p>
+ <text:p text:style-name="P179">Number of parallel (MPI) tasks on a single node. Needed if 'tasks' is not set.</text:p>
+ <text:h text:style-name="P215" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2570_1114405012"/><text:soft-page-break/>Overriding namelist settings in derived jobs<text:bookmark-end text:name="__RefHeading__2570_1114405012"/></text:h>
<text:p text:style-name="P50">There is special provision to change namelist files settings for a specific job. Consider this setting from the introductory example.</text:p>
- <text:p text:style-name="P130">[namelists]</text:p>
- <text:p text:style-name="P91"><text:s text:c="2"/>[[namelist.jsbach]]</text:p>
- <text:p text:style-name="P91"><text:s text:c="4"/>[[[jsbach_ctl]]]</text:p>
- <text:p text:style-name="P91"><text:s text:c="6"/>use_dynveg = false</text:p>
+ <text:p text:style-name="P131">[namelists]</text:p>
+ <text:p text:style-name="P92"><text:s text:c="2"/>[[namelist.jsbach]]</text:p>
+ <text:p text:style-name="P92"><text:s text:c="4"/>[[[jsbach_ctl]]]</text:p>
+ <text:p text:style-name="P92"><text:s text:c="6"/>use_dynveg = false</text:p>
<text:p text:style-name="P46"><text:span text:style-name="T86">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="T92">with a job specific namelists subsection that – apart from the addition</text:span><text:span text:style-name="T94">al</text:span><text:span text:style-name="T92"> brackets – has the same structure as</text:span><text:span text:style-name="T86"> </text:span><text:span text:style-name="T92">the global namelists section.</text:span></text:p>
- <text:p text:style-name="P130">[jobs]</text:p>
- <text:p text:style-name="P130"><text:s text:c="2"/>[[run_first]]</text:p>
- <text:p text:style-name="P130"><text:s text:c="4"/>.extends = run</text:p>
- <text:p text:style-name="P130"><text:s text:c="4"/><text:span text:style-name="T112">[[[namelists]]</text:span><text:span text:style-name="T121">]</text:span></text:p>
- <text:p text:style-name="P91"><text:s text:c="6"/><text:span text:style-name="T150">[[</text:span>[[namelist.jsbach]]<text:span text:style-name="T150">]]</text:span></text:p>
- <text:p text:style-name="P91"><text:s text:c="8"/><text:span text:style-name="T150">[[</text:span>[[[jsbach_ctl]]]<text:span text:style-name="T150">]]</text:span></text:p>
- <text:p text:style-name="P91"><text:span text:style-name="T86"><text:s text:c="10"/>use_dynveg = </text:span><text:span text:style-name="T91">true</text:span></text:p>
+ <text:p text:style-name="P131">[jobs]</text:p>
+ <text:p text:style-name="P131"><text:s text:c="2"/>[[run_first]]</text:p>
+ <text:p text:style-name="P131"><text:s text:c="4"/>.extends = run</text:p>
+ <text:p text:style-name="P131"><text:s text:c="4"/><text:span text:style-name="T112">[[[namelists]]</text:span><text:span text:style-name="T121">]</text:span></text:p>
+ <text:p text:style-name="P92"><text:s text:c="6"/><text:span text:style-name="T150">[[</text:span>[[namelist.jsbach]]<text:span text:style-name="T150">]]</text:span></text:p>
+ <text:p text:style-name="P92"><text:s text:c="8"/><text:span text:style-name="T150">[[</text:span>[[[jsbach_ctl]]]<text:span text:style-name="T150">]]</text:span></text:p>
+ <text:p text:style-name="P92"><text:span text:style-name="T86"><text:s text:c="10"/>use_dynveg = </text:span><text:span text:style-name="T91">true</text:span></text:p>
<text:p text:style-name="P46"><text:span text:style-name="T92">This</text:span><text:span text:style-name="T86"> 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="P214" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2572_1114405012"/>Native script variables<text:bookmark-end text:name="__RefHeading__2572_1114405012"/></text:h>
+ <text:h text:style-name="P215" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2572_1114405012"/>Native script variables<text:bookmark-end text:name="__RefHeading__2572_1114405012"/></text:h>
<text:p text:style-name="P48"><text:span text:style-name="T86">While the definition of .config variables may use</text:span><text:span text:style-name="T93"> variable references like</text:span><text:span text:style-name="T86"> $NAME or ${NAME} to include the </text:span><text:span text:style-name="T93">verbatim </text:span><text:span text:style-name="T86">value of other .config variables, this may not always be what you want. If you want to create a job </text:span><text:span text:style-name="T93">script</text:span><text:span text:style-name="T86"> that is supposed to be 'user-serviceable' for certain applications, the users will not appreciate having to change the same value several times in the same script. </text:span><text:span text:style-name="T93">Instead they will want to have a single, native script variable that is used throughout the job script, and that may be re-defined on a single line.</text:span></text:p>
<text:p text:style-name="P52">To allow this, <text:span text:style-name="T9">mkexp</text:span> locates all expressions like $${NAME} in the configuration values, and re-formats them to the syntax of the current job script:</text:p>
- <text:p text:style-name="P115"># joe1234.config</text:p>
- <text:p text:style-name="P115">NAME = Joe User</text:p>
+ <text:p text:style-name="P116"># joe1234.config</text:p>
+ <text:p text:style-name="P116">NAME = Joe User</text:p>
<text:p text:style-name="Preformatted_20_Text_20_Interrupt">MESSAGE = This experiment was generated by $${NAME}</text:p>
- <text:p text:style-name="P121">#%# joe1234.job.tmpl</text:p>
- <text:p text:style-name="P115">#! /bin/sh</text:p>
- <text:p text:style-name="P119">NAME='%{NAME}'</text:p>
- <text:p text:style-name="P115">echo %{MESSAGE}</text:p>
+ <text:p text:style-name="P122">#%# joe1234.job.tmpl</text:p>
+ <text:p text:style-name="P116">#! /bin/sh</text:p>
+ <text:p text:style-name="P120">NAME='%{NAME}'</text:p>
+ <text:p text:style-name="P116">echo %{MESSAGE}</text:p>
<text:p text:style-name="P52">By default, <text:span text:style-name="T152">native variables are formatted as </text:span>shell script, namely ${NAME}:</text:p>
- <text:p text:style-name="P118"><text:soft-page-break/>#! /bin/sh</text:p>
- <text:p text:style-name="P121">NAME='Joe User'</text:p>
- <text:p text:style-name="P117">echo This experiment was generated by ${NAME}</text:p>
+ <text:p text:style-name="P119"><text:soft-page-break/>#! /bin/sh</text:p>
+ <text:p text:style-name="P122">NAME='Joe User'</text:p>
+ <text:p text:style-name="P118">echo This experiment was generated by ${NAME}</text:p>
<text:p text:style-name="P53"><text:span text:style-name="T159">T</text:span>o support variable reference<text:span text:style-name="T158">s for other script languages, a</text:span> job specific variable '.var_format' may be defined. <text:span text:style-name="T158">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="T152">this may look like:</text:span></text:p>
- <text:p text:style-name="P120"># joe1234.config</text:p>
- <text:p text:style-name="P120">NAME = Joe User</text:p>
- <text:p text:style-name="P120">MESSAGE = This experiment was generated by $${NAME}</text:p>
- <text:p text:style-name="P132">[jobs]</text:p>
+ <text:p text:style-name="P121"># joe1234.config</text:p>
+ <text:p text:style-name="P121">NAME = Joe User</text:p>
+ <text:p text:style-name="P121">MESSAGE = This experiment was generated by $${NAME}</text:p>
+ <text:p text:style-name="P133">[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="T155">"</text:span><text:span text:style-name="T153">' + str(</text:span>%s<text:span text:style-name="T157">)</text:span> <text:span text:style-name="T153">+ '</text:span><text:span text:style-name="T155">"</text:span></text:p>
- <text:p text:style-name="P121">#%# joe1234.job.tmpl</text:p>
- <text:p text:style-name="P133">#! /usr/bin/env python </text:p>
+ <text:p text:style-name="P122">#%# joe1234.job.tmpl</text:p>
+ <text:p text:style-name="P134">#! /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="T194">(</text:span>'%{MESSAGE}'<text:span text:style-name="T194">)</text:span> </text:p>
- <text:p text:style-name="P58">This setup will expand to</text:p>
- <text:p text:style-name="P133">#! /usr/bin/env python </text:p>
- <text:p text:style-name="P133">NAME = '<text:span text:style-name="T157">Joe User</text:span>' </text:p>
- <text:p text:style-name="P134">print<text:span text:style-name="T194">(</text:span>'<text:span text:style-name="T86">This experiment was generated by </text:span><text:span text:style-name="T95">' + str(</text:span><text:span text:style-name="T86">NAME) </text:span><text:span text:style-name="T95">+ '</text:span>'<text:span text:style-name="T194">)</text:span></text:p>
- <text:h text:style-name="P221" 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="P60">In the previous section, the native variables were initialized by an addition<text:span text:style-name="T161">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="P60"><text:span text:style-name="T162">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="T162"> maintains the special variable VARIABLES_. When generating output for</text:span></text:p>
- <text:p text:style-name="P122">NAME = Joe User</text:p>
- <text:p text:style-name="P123">EMAIL = joe@domain.tld</text:p>
- <text:p text:style-name="P135"><text:span text:style-name="T86">MESSAGE = This experiment was generated by $${NAME} </text:span><text:span text:style-name="T97"><$${EMAIL}></text:span></text:p>
- <text:p text:style-name="P61"><text:span text:style-name="T33">mkexp</text:span><text:span text:style-name="T86"> will parse all values, recognize 'NAME' and 'EMAIL' as native variables, and </text:span><text:span text:style-name="T98">will </text:span><text:span text:style-name="T86">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="T33">mkexp</text:span><text:span text:style-name="T86"> provides the 'context' function, such that the template</text:span></text:p>
- <text:p text:style-name="P122"><text:soft-page-break/>#! /bin/sh</text:p>
- <text:p text:style-name="P123">#%# for <text:span text:style-name="T112">variable</text:span> in <text:span text:style-name="T112">VARIABLES_</text:span>:</text:p>
- <text:p text:style-name="P123">%{<text:span text:style-name="T112">variable</text:span>}='%{<text:span text:style-name="T112">context(variable)</text:span>}'</text:p>
- <text:p text:style-name="P123">#%# endfor</text:p>
- <text:p text:style-name="P123">echo <text:span text:style-name="T154">"</text:span>%{MESSAGE}<text:span text:style-name="T154">"</text:span></text:p>
+ <text:p text:style-name="P59">This setup will expand to</text:p>
+ <text:p text:style-name="P134">#! /usr/bin/env python </text:p>
+ <text:p text:style-name="P134">NAME = '<text:span text:style-name="T157">Joe User</text:span>' </text:p>
+ <text:p text:style-name="P135">print<text:span text:style-name="T194">(</text:span>'<text:span text:style-name="T86">This experiment was generated by </text:span><text:span text:style-name="T95">' + str(</text:span><text:span text:style-name="T86">NAME) </text:span><text:span text:style-name="T95">+ '</text:span>'<text:span text:style-name="T194">)</text:span></text:p>
+ <text:h text:style-name="P222" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2574_1114405012"/>Initializing native script variables<text:bookmark-end text:name="__RefHeading__2574_1114405012"/></text:h>
+ <text:p text:style-name="P61">In the previous section, the native variables were initialized by an addition<text:span text:style-name="T161">al script line. While this is sufficient for a small number of variables, it may be difficult to maintain these initialization lines for a more complex setup with changing requirements.</text:span></text:p>
+ <text:p text:style-name="P61"><text:span text:style-name="T162">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="T162"> maintains the special variable VARIABLES_. When generating output for</text:span></text:p>
+ <text:p text:style-name="P123">NAME = Joe User</text:p>
+ <text:p text:style-name="P124">EMAIL = joe@domain.tld</text:p>
+ <text:p text:style-name="P136"><text:span text:style-name="T86">MESSAGE = This experiment was generated by $${NAME} </text:span><text:span text:style-name="T97"><$${EMAIL}></text:span></text:p>
+ <text:p text:style-name="P62"><text:span text:style-name="T33">mkexp</text:span><text:span text:style-name="T86"> will parse all values, recognize 'NAME' and 'EMAIL' as native variables, and </text:span><text:span text:style-name="T98">will </text:span><text:span text:style-name="T86">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="T33">mkexp</text:span><text:span text:style-name="T86"> provides the 'context' function, such that the template</text:span></text:p>
+ <text:p text:style-name="P123"><text:soft-page-break/>#! /bin/sh</text:p>
+ <text:p text:style-name="P124">#%# for <text:span text:style-name="T112">variable</text:span> in <text:span text:style-name="T112">VARIABLES_</text:span>:</text:p>
+ <text:p text:style-name="P124">%{<text:span text:style-name="T112">variable</text:span>}='%{<text:span text:style-name="T112">context(variable)</text:span>}'</text:p>
+ <text:p text:style-name="P124">#%# endfor</text:p>
+ <text:p text:style-name="P124">echo <text:span text:style-name="T154">"</text:span>%{MESSAGE}<text:span text:style-name="T154">"</text:span></text:p>
<text:p text:style-name="P54">eventually yields</text:p>
- <text:p text:style-name="P122">#! /bin/sh</text:p>
- <text:p text:style-name="P135"><text:span text:style-name="T103">EMAIL</text:span><text:span text:style-name="T107">='</text:span><text:span text:style-name="T103">joe@domain.tld</text:span><text:span text:style-name="T107">'</text:span></text:p>
- <text:p text:style-name="P135"><text:span text:style-name="T102">NAME</text:span><text:span text:style-name="T106">=</text:span><text:span text:style-name="T107">'</text:span><text:span text:style-name="T102">Joe User</text:span><text:span text:style-name="T107">'</text:span></text:p>
- <text:p text:style-name="P135"><text:span text:style-name="T97">echo </text:span><text:span text:style-name="T156">"This experiment was generated by ${NAME} <${EMAIL}>"</text:span></text:p>
- <text:p text:style-name="P62">Note that the order of variable names is not necessarily the order in which they were defined in the .config file.</text:p>
+ <text:p text:style-name="P123">#! /bin/sh</text:p>
+ <text:p text:style-name="P136"><text:span text:style-name="T103">EMAIL</text:span><text:span text:style-name="T107">='</text:span><text:span text:style-name="T103">joe@domain.tld</text:span><text:span text:style-name="T107">'</text:span></text:p>
+ <text:p text:style-name="P136"><text:span text:style-name="T102">NAME</text:span><text:span text:style-name="T106">=</text:span><text:span text:style-name="T107">'</text:span><text:span text:style-name="T102">Joe User</text:span><text:span text:style-name="T107">'</text:span></text:p>
+ <text:p text:style-name="P136"><text:span text:style-name="T97">echo </text:span><text:span text:style-name="T156">"This experiment was generated by ${NAME} <${EMAIL}>"</text:span></text:p>
+ <text:p text:style-name="P63">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="T160">s</text:span>cripts and <text:span text:style-name="T160">b</text:span>ackup<text:bookmark-end text:name="__RefHeading__2576_1114405012"/></text:h>
- <text:p text:style-name="P59">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="T38"> 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="P84"><text:span text:style-name="T48">A</text:span><text:span text:style-name="T38">s a convenient short-cut, </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> 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="T38">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="T38"> so that './update' reg</text:span><text:span text:style-name="T83">e</text:span><text:span text:style-name="T38">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="P114">./update FINAL_DATE=2015-12-31</text:p>
- <text:p text:style-name="P84">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="P59"><text:span text:style-name="T38">Of course, there is also the possibility to </text:span><text:span text:style-name="T48">change</text:span><text:span text:style-name="T38"> the </text:span><text:span text:style-name="T19">generated</text:span><text:span text:style-name="T47"> </text:span><text:span text:style-name="T38">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="T49">facing</text:span><text:span text:style-name="T38"> the next </text:span><text:span text:style-name="T49">change,</text:span><text:span text:style-name="T38"> this might not be the case, so eventually you </text:span><text:span text:style-name="T47">may</text:span><text:span text:style-name="T38"> 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="P59"><text:span text:style-name="T38">Whenever </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> 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="T47">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="T48">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="T83">after a necessary regeneration</text:span><text:span text:style-name="T48">.</text:span></text:p>
- <text:h text:style-name="P231" 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="P67"><text:span text:style-name="T60">Most models need at least one Fortran namelist file or another form of configuration file to run. </text:span><text:span text:style-name="T61">The special section [namelists] </text:span><text:span text:style-name="T60">is designed to </text:span><text:span text:style-name="T61">contain all information that goes into </text:span><text:span text:style-name="T60">these</text:span><text:span text:style-name="T61"> files. Each </text:span><text:span text:style-name="T58">immediate </text:span><text:span text:style-name="T61">subsection defines settings for a single file that will </text:span><text:span text:style-name="T60">by default be </text:span><text:span text:style-name="T61">formatted as a Fortran namelist. </text:span><text:span text:style-name="T60">For </text:span><text:span text:style-name="T61">example,</text:span></text:p>
- <text:p text:style-name="P136">[namelists]</text:p>
- <text:p text:style-name="P146"/>
- <text:p text:style-name="P136"><text:s text:c="2"/>[[<text:span text:style-name="T175">namelist.echam</text:span>]] </text:p>
- <text:p text:style-name="P136"><text:s text:c="4"/>[[[runctl]]] </text:p>
- <text:p text:style-name="P136"><text:s text:c="6"/>lamip = true</text:p>
- <text:p text:style-name="P136"><text:s text:c="6"/><text:span text:style-name="T184">nproma = 48</text:span></text:p>
- <text:p text:style-name="P138"><text:s text:c="6"/>earth_angular_velocity = 7.3e-5</text:p>
- <text:p text:style-name="P138"><text:s text:c="6"/>out_expname = joe1234</text:p>
- <text:p text:style-name="P138"><text:s text:c="6"/><text:span text:style-name="T176">dt_stop = 2009, 1, 1, 0, 0, 0</text:span></text:p>
- <text:p text:style-name="P64"><text:span text:style-name="T38">defines </text:span><text:span text:style-name="T59">a single </text:span><text:span text:style-name="T38">namelist file, </text:span><text:span text:style-name="T62">'namelist.echam'</text:span><text:span text:style-name="T38">, </text:span><text:span text:style-name="T60">containing a single namelist group with four variables of different types. Note </text:span><text:span text:style-name="T79">that you do not </text:span><text:span text:style-name="T60">need to use quotes for strings nor periods for logical values.</text:span></text:p>
- <text:h text:style-name="P217" 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="P69"><text:span text:style-name="T58">The </text:span><text:span text:style-name="T59">names of the </text:span><text:span text:style-name="T58">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="T59">name</text:span><text:span text:style-name="T58">s, and their variables are formatted as fields of this namelist </text:span><text:span text:style-name="T59">group</text:span><text:span text:style-name="T58">. </text:span><text:span text:style-name="T59">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="T175">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="P69"><text:span text:style-name="T195">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="T62"> 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="P106"><text:soft-page-break/>&runctl</text:p>
- <text:p text:style-name="P140"><text:s text:c="4"/>lamip = <text:span text:style-name="T112">.true.</text:span></text:p>
- <text:p text:style-name="P140"><text:s text:c="4"/><text:span text:style-name="T175">nproma = </text:span><text:span text:style-name="T117">48</text:span></text:p>
- <text:p text:style-name="P139"><text:s text:c="4"/>earth_angular_velocity = <text:span text:style-name="T112">7.3e-5</text:span></text:p>
- <text:p text:style-name="P139"><text:s text:c="4"/>out_expname = <text:span text:style-name="T118">'</text:span><text:span text:style-name="T112">joe1234</text:span><text:span text:style-name="T118">'</text:span></text:p>
- <text:p text:style-name="P139"><text:span text:style-name="T62"><text:s text:c="4"/>dt_stop = </text:span><text:span text:style-name="T109">2009, 1, 1, 0, 0, 0</text:span></text:p>
- <text:p text:style-name="P124">/</text:p>
- <text:h text:style-name="P222" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2580_1114405012"/><text:span text:style-name="T60">S</text:span><text:span text:style-name="T38">uppressing namelist groups or variables</text:span><text:bookmark-end text:name="__RefHeading__2580_1114405012"/></text:h>
+ <text:p text:style-name="P60">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="T38"> 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="P85"><text:span text:style-name="T48">A</text:span><text:span text:style-name="T38">s a convenient short-cut, </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> 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="T38">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="T38"> so that './update' reg</text:span><text:span text:style-name="T83">e</text:span><text:span text:style-name="T38">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="P115">./update FINAL_DATE=2015-12-31</text:p>
+ <text:p text:style-name="P85">may be used to regenerate scripts with a new final date. Note that these settings are also recorded, i.e. running just './update' the next time will again set FINAL_DATE.</text:p>
+ <text:p text:style-name="P60"><text:span text:style-name="T38">Of course, there is also the possibility to </text:span><text:span text:style-name="T48">change</text:span><text:span text:style-name="T38"> the </text:span><text:span text:style-name="T19">generated</text:span><text:span text:style-name="T47"> </text:span><text:span text:style-name="T38">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="T49">facing</text:span><text:span text:style-name="T38"> the next </text:span><text:span text:style-name="T49">change,</text:span><text:span text:style-name="T38"> this might not be the case, so eventually you </text:span><text:span text:style-name="T47">may</text:span><text:span text:style-name="T38"> need to re-generate the whole thing. What now about those manual changes to the job scripts?</text:span></text:p>
+ <text:p text:style-name="P60"><text:span text:style-name="T38">Whenever </text:span><text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> 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="T47">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="T48">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="T83">after a necessary regeneration</text:span><text:span text:style-name="T48">.</text:span></text:p>
+ <text:h text:style-name="P232" 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="P68"><text:span text:style-name="T60">Most models need at least one Fortran namelist file or another form of configuration file to run. </text:span><text:span text:style-name="T61">The special section [namelists] </text:span><text:span text:style-name="T60">is designed to </text:span><text:span text:style-name="T61">contain all information that goes into </text:span><text:span text:style-name="T60">these</text:span><text:span text:style-name="T61"> files. Each </text:span><text:span text:style-name="T58">immediate </text:span><text:span text:style-name="T61">subsection defines settings for a single file that will </text:span><text:span text:style-name="T60">by default be </text:span><text:span text:style-name="T61">formatted as a Fortran namelist. </text:span><text:span text:style-name="T60">For </text:span><text:span text:style-name="T61">example,</text:span></text:p>
+ <text:p text:style-name="P137">[namelists]</text:p>
+ <text:p text:style-name="P147"/>
+ <text:p text:style-name="P137"><text:s text:c="2"/>[[<text:span text:style-name="T175">namelist.echam</text:span>]] </text:p>
+ <text:p text:style-name="P137"><text:s text:c="4"/>[[[runctl]]] </text:p>
+ <text:p text:style-name="P137"><text:s text:c="6"/>lamip = true</text:p>
+ <text:p text:style-name="P137"><text:s text:c="6"/><text:span text:style-name="T184">nproma = 48</text:span></text:p>
+ <text:p text:style-name="P139"><text:s text:c="6"/>earth_angular_velocity = 7.3e-5</text:p>
+ <text:p text:style-name="P139"><text:s text:c="6"/>out_expname = joe1234</text:p>
+ <text:p text:style-name="P139"><text:s text:c="6"/><text:span text:style-name="T176">dt_stop = 2009, 1, 1, 0, 0, 0</text:span></text:p>
+ <text:p text:style-name="P65"><text:span text:style-name="T38">defines </text:span><text:span text:style-name="T59">a single </text:span><text:span text:style-name="T38">namelist file, </text:span><text:span text:style-name="T62">'namelist.echam'</text:span><text:span text:style-name="T38">, </text:span><text:span text:style-name="T60">containing a single namelist group with four variables of different types. Note </text:span><text:span text:style-name="T79">that you do not </text:span><text:span text:style-name="T60">need to use quotes for strings nor periods for logical values.</text:span></text:p>
+ <text:h text:style-name="P218" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2578_1114405012"/>Formatting the namelist information<text:bookmark-end text:name="__RefHeading__2578_1114405012"/></text:h>
+ <text:p text:style-name="P70"><text:span text:style-name="T58">The </text:span><text:span text:style-name="T59">names of the </text:span><text:span text:style-name="T58">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="T59">name</text:span><text:span text:style-name="T58">s, and their variables are formatted as fields of this namelist </text:span><text:span text:style-name="T59">group</text:span><text:span text:style-name="T58">. </text:span><text:span text:style-name="T59">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="T175">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="P70"><text:span text:style-name="T195">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="T62"> 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="P107"><text:soft-page-break/>&runctl</text:p>
+ <text:p text:style-name="P141"><text:s text:c="4"/>lamip = <text:span text:style-name="T112">.true.</text:span></text:p>
+ <text:p text:style-name="P141"><text:s text:c="4"/><text:span text:style-name="T175">nproma = </text:span><text:span text:style-name="T117">48</text:span></text:p>
+ <text:p text:style-name="P140"><text:s text:c="4"/>earth_angular_velocity = <text:span text:style-name="T112">7.3e-5</text:span></text:p>
+ <text:p text:style-name="P140"><text:s text:c="4"/>out_expname = <text:span text:style-name="T118">'</text:span><text:span text:style-name="T112">joe1234</text:span><text:span text:style-name="T118">'</text:span></text:p>
+ <text:p text:style-name="P140"><text:span text:style-name="T62"><text:s text:c="4"/>dt_stop = </text:span><text:span text:style-name="T109">2009, 1, 1, 0, 0, 0</text:span></text:p>
+ <text:p text:style-name="P125">/</text:p>
+ <text:h text:style-name="P223" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2580_1114405012"/><text:span text:style-name="T60">S</text:span><text:span text:style-name="T38">uppressing namelist groups or variables</text:span><text:bookmark-end text:name="__RefHeading__2580_1114405012"/></text:h>
<text:p text:style-name="P56">Both the namelist file sections and the namelist group section honor the special variable '.remove' which may be set to a list of names. Any namelist groups listed in the file's '.remove' variable, and any variables listed in the group's '.remove' variable will be deleted from the namelist definition.</text:p>
<text:p text:style-name="P56">The names may contain the usual file wildcards, '*' and '?' to remove a whole range of groups or variables.</text:p>
- <text:p text:style-name="P78"><text:span text:style-name="T38">While '.remove' is useful to </text:span><text:span text:style-name="T69">suppress</text:span><text:span text:style-name="T38"> 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="T70">Therefore, its use in model setups is strongly discouraged.</text:span></text:p>
- <text:h text:style-name="P218" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2714_1114405012"/>Using the namelist text<text:bookmark-end text:name="__RefHeading__2714_1114405012"/></text:h>
- <text:p text:style-name="P65"><text:span text:style-name="T60">T</text:span><text:span text:style-name="T62">he </text:span><text:span text:style-name="T51">formatted namelist text </text:span><text:span text:style-name="T38">is </text:span><text:span text:style-name="T62">stor</text:span><text:span text:style-name="T38">ed </text:span><text:span text:style-name="T62">in</text:span><text:span text:style-name="T38"> a global variable </text:span><text:span text:style-name="T62">that may be used by a template placeholder</text:span><text:span text:style-name="T38">. </text:span><text:span text:style-name="T60">This way, </text:span><text:span text:style-name="T38">all job information </text:span><text:span text:style-name="T62">available </text:span><text:span text:style-name="T60">is written to</text:span><text:span text:style-name="T38"> a single script or description file, </text:span><text:span text:style-name="T60">and </text:span><text:span text:style-name="T38">native script variables </text:span><text:span text:style-name="T60">may be used</text:span><text:span text:style-name="T38"> in the namelist definitions.</text:span></text:p>
- <text:p text:style-name="P67"><text:span text:style-name="T51">The name of </text:span><text:span text:style-name="T62">this </text:span><text:span text:style-name="T51">variable</text:span><text:span text:style-name="T52"> </text:span><text:span text:style-name="T62">is</text:span><text:span text:style-name="T51"> generated from </text:span><text:span text:style-name="T62">its</text:span><text:span text:style-name="T51"> </text:span><text:span text:style-name="T52">respective</text:span><text:span text:style-name="T51"> file name, </text:span><text:span text:style-name="T62">like</text:span><text:span text:style-name="T51"> 'namelist.echam', by </text:span><text:span text:style-name="T61">converting all letters to upper case </text:span><text:span text:style-name="T51">(</text:span><text:span text:style-name="T61">namelist.echam →</text:span><text:span text:style-name="T51"> </text:span><text:span text:style-name="T61">NAMELIST.ECHAM</text:span><text:span text:style-name="T51">) </text:span><text:span text:style-name="T52">and </text:span><text:span text:style-name="T51">replacing non-word characters by an underscore (NAMELIST.ECHAM → NAMELIST_ECHAM).</text:span></text:p>
+ <text:p text:style-name="P79"><text:span text:style-name="T38">While '.remove' is useful to </text:span><text:span text:style-name="T69">suppress</text:span><text:span text:style-name="T38"> 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="T70">Therefore, its use in model setups is strongly discouraged.</text:span></text:p>
+ <text:h text:style-name="P219" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2714_1114405012"/>Using the namelist text<text:bookmark-end text:name="__RefHeading__2714_1114405012"/></text:h>
+ <text:p text:style-name="P66"><text:span text:style-name="T60">T</text:span><text:span text:style-name="T62">he </text:span><text:span text:style-name="T51">formatted namelist text </text:span><text:span text:style-name="T38">is </text:span><text:span text:style-name="T62">stor</text:span><text:span text:style-name="T38">ed </text:span><text:span text:style-name="T62">in</text:span><text:span text:style-name="T38"> a global variable </text:span><text:span text:style-name="T62">that may be used by a template placeholder</text:span><text:span text:style-name="T38">. </text:span><text:span text:style-name="T60">This way, </text:span><text:span text:style-name="T38">all job information </text:span><text:span text:style-name="T62">available </text:span><text:span text:style-name="T60">is written to</text:span><text:span text:style-name="T38"> a single script or description file, </text:span><text:span text:style-name="T60">and </text:span><text:span text:style-name="T38">native script variables </text:span><text:span text:style-name="T60">may be used</text:span><text:span text:style-name="T38"> in the namelist definitions.</text:span></text:p>
+ <text:p text:style-name="P68"><text:span text:style-name="T51">The name of </text:span><text:span text:style-name="T62">this </text:span><text:span text:style-name="T51">variable</text:span><text:span text:style-name="T52"> </text:span><text:span text:style-name="T62">is</text:span><text:span text:style-name="T51"> generated from </text:span><text:span text:style-name="T62">its</text:span><text:span text:style-name="T51"> </text:span><text:span text:style-name="T52">respective</text:span><text:span text:style-name="T51"> file name, </text:span><text:span text:style-name="T62">like</text:span><text:span text:style-name="T51"> 'namelist.echam', by </text:span><text:span text:style-name="T61">converting all letters to upper case </text:span><text:span text:style-name="T51">(</text:span><text:span text:style-name="T61">namelist.echam →</text:span><text:span text:style-name="T51"> </text:span><text:span text:style-name="T61">NAMELIST.ECHAM</text:span><text:span text:style-name="T51">) </text:span><text:span text:style-name="T52">and </text:span><text:span text:style-name="T51">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="T112">[[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="P137">#! /bin/sh</text:p>
+ <text:p text:style-name="P138">#! /bin/sh</text:p>
<text:p text:style-name="Preformatted_20_Text">EXP_ID=%{EXP_ID}</text:p>
- <text:p text:style-name="P96">cat > namelist.echam << EOF</text:p>
- <text:p text:style-name="P103">%{NAMELIST_ECHAM}</text:p>
- <text:p text:style-name="P96">EOF</text:p>
- <text:p text:style-name="P66">which expand to</text:p>
- <text:p text:style-name="P137"><text:soft-page-break/>#! /bin/sh</text:p>
- <text:p text:style-name="Preformatted_20_Text">EXP_ID=joe1234</text:p>
- <text:p text:style-name="P96">cat > namelist.echam << EOF</text:p>
- <text:p text:style-name="P105">&runctl</text:p>
- <text:p text:style-name="P99"><text:s text:c="4"/>out_expname = '${EXP_ID}'</text:p>
- <text:p text:style-name="P105">/</text:p>
- <text:p text:style-name="P96">EOF</text:p>
- <text:p text:style-name="P68"><text:span text:style-name="T62">Note how this setup uses the native script variable 'EXP_ID' to set the </text:span><text:span text:style-name="T58">namelist contents.</text:span></text:p>
- <text:p text:style-name="P68"><text:span text:style-name="T63">As in the example above, the script template is responsible for writing the namelist text to an actual file. </text:span><text:span text:style-name="T62">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="T62"> </text:span><text:span text:style-name="T63">ha</text:span><text:span text:style-name="T62">s currently no way to enforce this. The template needs to be set up accordingly.</text:span></text:p>
- <text:h text:style-name="P223" text:outline-level="3">Using native script variables in namelists</text:h>
- <text:p text:style-name="P85">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="P149">[namelists]</text:p>
- <text:p text:style-name="P149"><text:s text:c="2"/><text:span text:style-name="T200">[[namelist.echam]]</text:span></text:p>
- <text:p text:style-name="P149"><text:s text:c="4"/><text:span text:style-name="T200">[[[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="T200">dt_stop = $$final_date</text:span></text:p>
- <text:p text:style-name="P125">final_date='2015, 12, 31, 23, 52, 30'</text:p>
<text:p text:style-name="P97">cat > namelist.echam << EOF</text:p>
<text:p text:style-name="P104">%{NAMELIST_ECHAM}</text:p>
- <text:p text:style-name="P126">EOF</text:p>
- <text:p text:style-name="P85">When the text for NAMELIST_ECHAM is generated, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> converts the value of 'dt_stop' to a string surrounded by single quotes (see 'EXP_ID' in the previous example), as '$$final_date' cannot be </text:span><text:span text:style-name="T85">recognized</text:span><text:span text:style-name="T38"> as a numer</text:span><text:span text:style-name="T85">ic</text:span><text:span text:style-name="T38"> or logical value. In the namelist context however it is </text:span><text:span text:style-name="T85">needed</text:span><text:span text:style-name="T38"> as a</text:span><text:span text:style-name="T85">n unquoted</text:span><text:span text:style-name="T38"> list of integers. </text:span><text:span text:style-name="T84">To fix this, simply use the special syntax 'raw(…)' </text:span><text:span text:style-name="T85">around the value:</text:span></text:p>
+ <text:p text:style-name="P97">EOF</text:p>
+ <text:p text:style-name="P67">which expand to</text:p>
+ <text:p text:style-name="P138"><text:soft-page-break/>#! /bin/sh</text:p>
+ <text:p text:style-name="Preformatted_20_Text">EXP_ID=joe1234</text:p>
+ <text:p text:style-name="P97">cat > namelist.echam << EOF</text:p>
+ <text:p text:style-name="P106">&runctl</text:p>
+ <text:p text:style-name="P100"><text:s text:c="4"/>out_expname = '${EXP_ID}'</text:p>
+ <text:p text:style-name="P106">/</text:p>
+ <text:p text:style-name="P97">EOF</text:p>
+ <text:p text:style-name="P69"><text:span text:style-name="T62">Note how this setup uses the native script variable 'EXP_ID' to set the </text:span><text:span text:style-name="T58">namelist contents.</text:span></text:p>
+ <text:p text:style-name="P69"><text:span text:style-name="T63">As in the example above, the script template is responsible for writing the namelist text to an actual file. </text:span><text:span text:style-name="T62">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="T62"> </text:span><text:span text:style-name="T63">ha</text:span><text:span text:style-name="T62">s currently no way to enforce this. The template needs to be set up accordingly.</text:span></text:p>
+ <text:h text:style-name="P224" text:outline-level="3">Using native script variables in namelists</text:h>
+ <text:p text:style-name="P86">When using native script variables in a namelist, it may be necessary to suppress the conversion of values to namelist conventions. Consider</text:p>
+ <text:p text:style-name="P150">[namelists]</text:p>
+ <text:p text:style-name="P150"><text:s text:c="2"/><text:span text:style-name="T200">[[namelist.echam]]</text:span></text:p>
+ <text:p text:style-name="P150"><text:s text:c="4"/><text:span text:style-name="T200">[[[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="T200">dt_stop = $$final_date</text:span></text:p>
+ <text:p text:style-name="P126">final_date='2015, 12, 31, 23, 52, 30'</text:p>
+ <text:p text:style-name="P98">cat > namelist.echam << EOF</text:p>
+ <text:p text:style-name="P105">%{NAMELIST_ECHAM}</text:p>
+ <text:p text:style-name="P127">EOF</text:p>
+ <text:p text:style-name="P86">When the text for NAMELIST_ECHAM is generated, <text:span text:style-name="T9">mkexp</text:span><text:span text:style-name="T38"> converts the value of 'dt_stop' to a string surrounded by single quotes (see 'EXP_ID' in the previous example), as '$$final_date' cannot be </text:span><text:span text:style-name="T85">recognized</text:span><text:span text:style-name="T38"> as a numer</text:span><text:span text:style-name="T85">ic</text:span><text:span text:style-name="T38"> or logical value. In the namelist context however it is </text:span><text:span text:style-name="T85">needed</text:span><text:span text:style-name="T38"> as a</text:span><text:span text:style-name="T85">n unquoted</text:span><text:span text:style-name="T38"> list of integers. </text:span><text:span text:style-name="T84">To fix this, simply use the special syntax 'raw(…)' </text:span><text:span text:style-name="T85">around the value:</text:span></text:p>
<text:p text:style-name="Preformatted_20_Text"><text:span text:style-name="T85"><text:s text:c="6"/></text:span><text:span text:style-name="T83">dt_stop = </text:span><text:span text:style-name="T85">raw(</text:span><text:span text:style-name="T83">$$final_date</text:span><text:span text:style-name="T85">)</text:span></text:p>
- <text:p text:style-name="P232">which disables the conversion to a valid namelist value, leaving the correct formatting of the native variable to the script.</text:p>
- <text:h text:style-name="P220" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2584_1114405012"/><text:soft-page-break/>Non-namelist configuration files<text:bookmark-end text:name="__RefHeading__2584_1114405012"/></text:h>
- <text:p text:style-name="P79"><text:span text:style-name="T73">A [namelists] subsection may not only define a Fortran namelist file but also a custom format configuration file. </text:span><text:span text:style-name="T71">F</text:span><text:span text:style-name="T38">or any </text:span><text:span text:style-name="T73">of these</text:span><text:span text:style-name="T72"> files, the special section variable '.use_template' must be set to 'true', </text:span><text:span text:style-name="T73">and the model setup must provide a template '</text:span><text:span text:style-name="T29">subsection</text:span><text:span text:style-name="T73">.tmpl'. This template is expanded using the subsection's variables to create a suitably formatted text. </text:span><text:span text:style-name="T74">As for genuine namelists, the result is stored in a global variable.</text:span></text:p>
+ <text:p text:style-name="P57">which disables the conversion to a valid namelist value, leaving the correct formatting of the native variable to the script.</text:p>
+ <text:h text:style-name="P221" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2584_1114405012"/><text:soft-page-break/>Non-namelist configuration files<text:bookmark-end text:name="__RefHeading__2584_1114405012"/></text:h>
+ <text:p text:style-name="P80"><text:span text:style-name="T73">A [namelists] subsection may not only define a Fortran namelist file but also a custom format configuration file. </text:span><text:span text:style-name="T71">F</text:span><text:span text:style-name="T38">or any </text:span><text:span text:style-name="T73">of these</text:span><text:span text:style-name="T72"> files, the special section variable '.use_template' must be set to 'true', </text:span><text:span text:style-name="T73">and the model setup must provide a template '</text:span><text:span text:style-name="T29">subsection</text:span><text:span text:style-name="T73">.tmpl'. This template is expanded using the subsection's variables to create a suitably formatted text. </text:span><text:span text:style-name="T74">As for genuine namelists, the result is stored in a global variable.</text:span></text:p>
<text:h text:style-name="Heading_20_2" text:outline-level="2"><text:bookmark-start text:name="__RefHeading__2831_1132221942"/><text:span text:style-name="T74">D</text:span><text:span text:style-name="T38">efining input files for an experiment</text:span><text:bookmark-end text:name="__RefHeading__2831_1132221942"/></text:h>
- <text:p text:style-name="P82"><text:span text:style-name="T38">While the namelist files determine the model properties, the model state </text:span><text:span text:style-name="T82">also </text:span><text:span text:style-name="T38">depends on input files for initial and boundary conditions or assimilation data. These files are defined in the [files] special section. </text:span><text:span text:style-name="T82">There are no restrictions on the content structure of this section, and the job script templates are responsible for converting this content into a suitable script text.</text:span></text:p>
- <text:h text:style-name="P216" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2833_1132221942"/>Overriding <text:span text:style-name="T198">input file</text:span>s <text:span text:style-name="T198">for certain</text:span> jobs<text:bookmark-end text:name="__RefHeading__2833_1132221942"/></text:h>
+ <text:p text:style-name="P83"><text:span text:style-name="T38">While the namelist files determine the model properties, the model state </text:span><text:span text:style-name="T82">also </text:span><text:span text:style-name="T38">depends on input files for initial and boundary conditions or assimilation data. These files are defined in the [files] special section. </text:span><text:span text:style-name="T82">There are no restrictions on the content structure of this section, and the job script templates are responsible for converting this content into a suitable script text.</text:span></text:p>
+ <text:h text:style-name="P217" text:outline-level="3"><text:bookmark-start text:name="__RefHeading__2833_1132221942"/>Overriding <text:span text:style-name="T198">input file</text:span>s <text:span text:style-name="T198">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="T199">As for namelists, t</text:span>here is special provision to change <text:span text:style-name="T198">the [</text:span>files<text:span text:style-name="T198">]</text:span> settings for a specific job. <text:span text:style-name="T198">Let us assume</text:span> <text:span text:style-name="T198">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="P131">[<text:span text:style-name="T198">files</text:span>]</text:p>
- <text:p text:style-name="P92"><text:s text:c="2"/>[[<text:span text:style-name="T198">echam</text:span>]]</text:p>
- <text:p text:style-name="P92"><text:s text:c="4"/>[[[<text:span text:style-name="T198">restart</text:span>]]]</text:p>
- <text:p text:style-name="P92"><text:s text:c="6"/><text:span text:style-name="T198">restart_myexp_echam.nc = restart_myexp_echam_18491231.nc</text:span></text:p>
- <text:p text:style-name="P83">The first run <text:span text:style-name="T199">will instead pick up its state from another experiment. This is done with </text:span><text:span text:style-name="T92"><text:s/>a job specific </text:span><text:span text:style-name="T101">'file</text:span><text:span text:style-name="T92">s</text:span><text:span text:style-name="T101">'</text:span><text:span text:style-name="T92"> subsection that – apart from the addition</text:span><text:span text:style-name="T94">al</text:span><text:span text:style-name="T92"> brackets – has the same structure as</text:span><text:span text:style-name="T91"> </text:span><text:span text:style-name="T92">the global </text:span><text:span text:style-name="T101">'files'</text:span><text:span text:style-name="T92"> section.</text:span></text:p>
- <text:p text:style-name="P131">[jobs]</text:p>
- <text:p text:style-name="P131"><text:s text:c="2"/>[[run_first]]</text:p>
- <text:p text:style-name="P131"><text:s text:c="4"/><text:span text:style-name="T112">[[[</text:span><text:span text:style-name="T121">file</text:span><text:span text:style-name="T112">s]</text:span><text:span text:style-name="T121">]</text:span><text:span text:style-name="T112">]</text:span></text:p>
- <text:p text:style-name="P92"><text:s text:c="6"/><text:span text:style-name="T150">[[</text:span>[[<text:span text:style-name="T199">echam</text:span>]]<text:span text:style-name="T150">]]</text:span></text:p>
- <text:p text:style-name="P92"><text:s text:c="8"/><text:span text:style-name="T150">[[</text:span>[[[<text:span text:style-name="T199">restart</text:span>]]]<text:span text:style-name="T150">]]</text:span></text:p>
- <text:p text:style-name="P93"><text:span text:style-name="T86"><text:s text:c="10"/></text:span><text:span text:style-name="T100">restart_myexp_echam.nc = restart_</text:span><text:span text:style-name="T104">another</text:span><text:span text:style-name="T105">exp</text:span><text:span text:style-name="T100">_echam_18491231.nc</text:span></text:p>
+ <text:p text:style-name="P132">[<text:span text:style-name="T198">files</text:span>]</text:p>
+ <text:p text:style-name="P93"><text:s text:c="2"/>[[<text:span text:style-name="T198">echam</text:span>]]</text:p>
+ <text:p text:style-name="P93"><text:s text:c="4"/>[[[<text:span text:style-name="T198">restart</text:span>]]]</text:p>
+ <text:p text:style-name="P93"><text:s text:c="6"/><text:span text:style-name="T198">restart_myexp_echam.nc = restart_myexp_echam_18491231.nc</text:span></text:p>
+ <text:p text:style-name="P84">The first run <text:span text:style-name="T199">will instead pick up its state from another experiment. This is done with </text:span><text:span text:style-name="T92"><text:s/>a job specific </text:span><text:span text:style-name="T101">'file</text:span><text:span text:style-name="T92">s</text:span><text:span text:style-name="T101">'</text:span><text:span text:style-name="T92"> subsection that – apart from the addition</text:span><text:span text:style-name="T94">al</text:span><text:span text:style-name="T92"> brackets – has the same structure as</text:span><text:span text:style-name="T91"> </text:span><text:span text:style-name="T92">the global </text:span><text:span text:style-name="T101">'files'</text:span><text:span text:style-name="T92"> section.</text:span></text:p>
+ <text:p text:style-name="P132">[jobs]</text:p>
+ <text:p text:style-name="P132"><text:s text:c="2"/>[[run_first]]</text:p>
+ <text:p text:style-name="P132"><text:s text:c="4"/><text:span text:style-name="T112">[[[</text:span><text:span text:style-name="T121">file</text:span><text:span text:style-name="T112">s]</text:span><text:span text:style-name="T121">]</text:span><text:span text:style-name="T112">]</text:span></text:p>
+ <text:p text:style-name="P93"><text:s text:c="6"/><text:span text:style-name="T150">[[</text:span>[[<text:span text:style-name="T199">echam</text:span>]]<text:span text:style-name="T150">]]</text:span></text:p>
+ <text:p text:style-name="P93"><text:s text:c="8"/><text:span text:style-name="T150">[[</text:span>[[[<text:span text:style-name="T199">restart</text:span>]]]<text:span text:style-name="T150">]]</text:span></text:p>
+ <text:p text:style-name="P94"><text:span text:style-name="T86"><text:s text:c="10"/></text:span><text:span text:style-name="T100">restart_myexp_echam.nc = restart_</text:span><text:span text:style-name="T104">another</text:span><text:span text:style-name="T105">exp</text:span><text:span text:style-name="T100">_echam_18491231.nc</text:span></text:p>
<text:p text:style-name="P47"><text:span text:style-name="T92">This</text:span><text:span text:style-name="T100"> will result in a '.run_first' </text:span><text:span text:style-name="T101">script</text:span><text:span text:style-name="T100"> tha</text:span><text:span text:style-name="T101">t gets the model state from 'anotherexp', while the '.run' script</text:span><text:span text:style-name="T100"> </text:span><text:span text:style-name="T101">uses 'myexp'.</text:span></text:p>
</office:text>
</office:body>
diff --git a/doc/mkexp.pdf b/doc/mkexp.pdf
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diff --git a/mkexp b/mkexp
index 2d512e1..aef02fa 100755
--- a/mkexp
+++ b/mkexp
@@ -259,9 +259,15 @@ command_line.add_argument('--path', '-p',
command_line.add_argument('--no-make-dirs', '-m',
action='store_false', dest='make_dirs',
help='do not create work and data directories')
+command_line.add_argument('--quiet', '-q',
+ action='store_true', dest='quiet',
+ help='suppress informative messages')
args = command_line.parse_args()
+if args.quiet:
+ feedback.setLevel(feedback.WARNING)
+
# Experiment configuration
if args.path:
config_roots = args.path.split(':')
diff --git a/setup.py b/setup.py
index f88fe0c..fe6fcb4 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,7 @@
from distutils.core import setup
name = 'mkexp'
-version = '0.3.4'
+version = '0.3.5dev'
setup(
name = name,
--
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