download bicoro regional and pecan@biocro-module2 to VM; update settings file

[dlebauer]

Download repositories

cd
git clone [email protected]:ebimodeling/biocro_regional
cd pecan
## this should work w/ git v >1.6.6 http://stackoverflow.com/a/1783426
git fetch --all
git checkout biocro-module2

update settings file

• browse to <vm_ipaddress>/rstudio
• open biocro_regional/vignettes/illinois_mxg_settings.xml
• change the <database> tag to

  <database>
    <bety>
      <user>bety</user>
      <password>bety</password>
      <dbname>bety</dbname>
      <host>localhost</host>
      <driver>PostgreSQL</driver>
    </bety>
  </database>

• make sure the run/host tag uses roger (and ppn is consistent with number of cores registered in regionalbiocro.Rscript located on roger (see below) in command registerDoMC(10)
  • on roger, regionalbiocro.Rscript is in /home/dlebauer/dev/pecan/models/biocro/inst/regionalbiocro.Rscript

      <name>roger-login.ncsa.illinois.edu</name>
      <qsub>qsub -l walltime=03:00:00,nodes=1:ppn=10 -N @NAME@ -o @STDOUT@ -e @STDERR@</qsub>

Run regional workflow

• at <vm_ipaddress>/rstudio, open biocro_regional/vignettes/regional_pecan_workflow.Rmd
• step through lines
• report any issues here