26.7 XML configuration

The relevant section of the PEcAn XML file is the <host> block. Here is a minimal example from one of my recent runs:

<host>
    <name>geo.bu.edu</name>
    <user>ashiklom</user>
    <tunnel>/home/carya/output//PEcAn_99000000008/tunnel/tunnel</tunnel>
</host>

Breaking this down:

  • name – The hostname of the machine where the runs will be performed. Set it to localhost to run on the local machine.
  • user – Your username on the remote machine (note that this may be different from the username on your local machine).
  • tunnel – This is the tunnel file for the connection used by all remote execution files. The tunnel is created automatically by the web interface, but must be created by the user for command line execution.

This configuration will run in serialized mode. To use qsub, the configuration is slightly more involved:

<host>
  <name>geo.bu.edu</name>
  <user>ashiklom</user>
  <qsub>qsub -V -N @NAME@ -o @STDOUT@ -e @STDERR@ -S /bin/bash</qsub>
  <qsub.jobid>Your job ([0-9]+) .*</qsub.jobid>
  <qstat>qstat -j @JOBID@ || echo DONE</qstat>
  <tunnel>/home/carya/output//PEcAn_99000000008/tunnel/tunnel</tunnel>
</host>

The additional fields are as follows:

  • qsub – The command used to submit jobs to the queue system. Despite the name, this can be any command used for any queue system. The following variables are available to be set here:
    • @NAME@ – Job name to display
    • @STDOUT@ – File to which stdout will be redirected
    • @STDERR@ – File to which stderr will be redirected
  • qsub.jobid – A regular expression, from which the job ID will be determined. This string will be parsed by R as jobid <- gsub(qsub.jobid, "\\1", output) – note that the first pattern match is taken as the job ID.
  • qstat – The command used to check the status of a job. Internally, PEcAn will look for the DONE string at the end, so a structure like <some command indicating if any jobs are still running> || echo DONE is required. The @JOBID@ here is the job ID determined from the qsub.jobid parsing.

Documentation for using the model launcher is currently unavailable.