11 The PEcAn XML

The PEcAn system is configured using a XML file, often called pecan.xml. It contains the following major sections (“nodes”):

• Core configuration
  • Top level structure
  • info – Run metadata
  • outdir – Output directory
  • database – PEcAn database settings
  • pft – Plant functional type selection
  • meta.analysis – Trait meta analysis
  • model – Model configuration
  • run – Run setup
  • host – Host information for remote execution
• Advanced features
  • ensemble – Ensemble runs
  • sensitivity.analysis – Sensitivity analysis
  • parameter.data.assimilation – Parameter data assimilation
  • multi.settings – Multi Site Settings
  • (experimental) state.data.assimilation – State data assimilation
  • (experimental) browndog – Brown Dog configuration
  • (experimental) benchmarking – Benchmarking
  • remote_process – Remote data module

A basic example looks like this:

<?xml version="1.0" encoding="UTF-8"?>
<pecan>
  <info>
    <notes>Example run</notes>
    <userid>-1</userid>
    <username>guestuser</username>
    <date>2018/09/18 19:12:28 +0000</date>
  </info>
  <outdir>/data/workflows/PEcAn_99000000006</outdir>
  <database>
    <bety>
      <user>bety</user>
      <password>bety</password>
      <host>postgres</host>
      <dbname>bety</dbname>
      <driver>PostgreSQL</driver>
      <write>true</write>
    </bety>
    <dbfiles>/data/dbfiles</dbfiles>
  </database>
  <pfts>
    <pft>
      <name>tundra.grasses</name> 
      <constants>
        <num>1</num>
      </constants>
    </pft>
  </pfts>
  <meta.analysis>
    <iter>3000</iter>
    <random.effects>
     <on>FALSE</on>
     <use_ghs>TRUE</use_ghs>
    </random.effects>
  </meta.analysis>
  <ensemble>
   <size>1</size>
   <variable>NPP</variable>
   <samplingspace>
   <parameters>
    <method>uniform</method>
   </parameters>
   <met>
    <method>sampling</method>
    </met>
   </samplingspace>
  </ensemble>
  <model>
    <id>5000000002</id>
  </model>
  <workflow>
    <id>99000000006</id>
  </workflow>
  <run>
    <site>
      <id>1000000098</id>
      <met.start>2004/01/01</met.start>
      <met.end>2004/12/31</met.end>
    </site>
    <inputs>
      <met>
        <source>CRUNCEP</source>
        <output>SIPNET</output>
      </met>
    </inputs>
    <start.date>2004/01/01</start.date>
    <end.date>2004/12/31</end.date>
  </run>
  <host>
    <name>localhost</name>
    <rabbitmq>
      <uri>amqp://guest:guest@rabbitmq:5672/%2F</uri>
      <queue>SIPNET_136</queue>
    </rabbitmq>
  </host>
</pecan>

In the following sections, we step through each of these sections in detail.