debugging workflow.R

pecan64.ed.xml

<?xml version="1.0"?>
<pecan>
  <outdir>pecan</outdir>

  <database>
    <bety>
      <driver>PostgreSQL</driver>      
      <user>bety</user>
      <password>bety</password>
      <host>postgres</host>
      <dbname>bety</dbname>
      <write>FALSE</write>
    </bety>
  </database>

  <pfts>
    <pft>
      <name>ebifarm.c4grass.doe_vd</name> 
    </pft>
  </pfts>

  <meta.analysis>
    <iter>3000</iter>
    <random.effects>FALSE</random.effects>
    <threshold>1.2</threshold>
    <update>AUTO</update>
  </meta.analysis>

  <ensemble>
    <variable>NPP</variable>
  </ensemble>

<!--
  <sensitivity.analysis>
    <quantiles>
      <sigma>-1</sigma>
      <sigma>1</sigma>
    </quantiles>
    <variable>NPP</variable>
  </sensitivity.analysis>
-->

  <model>
    <binary>/usr/local/bin/ed2.git</binary>
    <type>ED2</type>
    <revision>git</revision>
    <config.header>
      <radiation>
        <lai_min>0.01</lai_min>
      </radiation>
      <ed_misc>
        <output_month>12</output_month>
      </ed_misc>
    </config.header>
    <phenol.scheme>0</phenol.scheme>
  </model>

  <run>
    <site>
      <id>76</id>
      <met.start>2004-01-01 00:00:00</met.start>
      <met.end>2009-12-31 23:59:59</met.end>
    </site>
    <inputs>
      <met>/home/carya/sites/ebifarm/ED_MET_DRIVER_HEADER</met>
      <veg>/home/carya/oge2OLD/OGE2_</veg>
      <soil>/home/carya/faoOLD/FAO_</soil>
      <pss>/home/carya/sites/ebifarm/ebifarm.lat40.0lon-88.0.pss</pss>
      <css>/home/carya/sites/ebifarm/ebifarm.lat40.0lon-88.0.css</css>
      <site>/home/carya/sites/ebifarm/ebifarm.lat40.0lon-88.0.site</site>
      <lu>/home/carya/ed_inputs/glu</lu>
      <thsum>/home/carya/ed_inputs</thsum>
    </inputs>
    <start.date>2006/01/01</start.date>
    <end.date>2006/12/31</end.date>
    <host>
      <name>docker</name>
    </host>
    <dbfiles>pecan/dbfiles</dbfiles>
  </run>
</pecan>

some_workflow.R

devtools::install_github("pecanproject/pecan/api@develop")
options(pecanapi.user_id = 99000000002)
con <- DBI::dbConnect(
RPostgres::Postgres(),
user = "bety",
password = "bety",
host = "localhost",
port = 5432
)
options(pecanapi.user_id = 99000000002)
con <- DBI::dbConnect(
RPostgres::Postgres(),
user = "bety",
password = "bety",
host = "localhost",
port = 5433
)
con <- DBI::dbConnect(
RPostgres::Postgres(),
user = "bety",
password = "bety",
host = "localhost",
port = 5433
)
# ----------------------------------------------------------------------
# PEcAn Workflow
# ----------------------------------------------------------------------
# Open and read in settings file for PEcAn run.
args <- commandArgs(trailingOnly = TRUE)
host = "localhost",
settings <- PEcAn.settings::read.settings("pecan/tests/pecan64.ed2.xml")
settings <- PEcAn.settings::read.settings("pecan/tests/pecan64.ed2.xml")
settings <- PEcAn.settings::read.settings("pecan/tests/pecan64.ed.xml")
# Check for additional modules that will require adding settings
if ("benchmarking" %in% names(settings)) {
library(PEcAn.benchmark)
settings <- papply(settings, read_settings_BRR)
}
if ("sitegroup" %in% names(settings)) {
if (is.null(settings$sitegroup$nSite)) {
settings <- PEcAn.settings::createSitegroupMultiSettings(
settings,
sitegroupId = settings$sitegroup$id)
} else {
settings <- PEcAn.settings::createSitegroupMultiSettings(
settings,
sitegroupId = settings$sitegroup$id,
nSite = settings$sitegroup$nSite)
}
# zero out so don't expand a second time if re-reading
settings$sitegroup <- NULL
}
# Update/fix/check settings.
# Will only run the first time it's called, unless force=TRUE
settings <- PEcAn.settings::prepare.settings(settings, force = FALSE)
settings$host
settings$host <- settings$run$host
# Check for additional modules that will require adding settings
if ("benchmarking" %in% names(settings)) {
library(PEcAn.benchmark)
settings <- papply(settings, read_settings_BRR)
}
if ("sitegroup" %in% names(settings)) {
if (is.null(settings$sitegroup$nSite)) {
settings <- PEcAn.settings::createSitegroupMultiSettings(
settings,
sitegroupId = settings$sitegroup$id)
} else {
settings <- PEcAn.settings::createSitegroupMultiSettings(
settings,
sitegroupId = settings$sitegroup$id,
nSite = settings$sitegroup$nSite)
}
# zero out so don't expand a second time if re-reading
settings$sitegroup <- NULL
}
# Update/fix/check settings.
# Will only run the first time it's called, unless force=TRUE
settings <- PEcAn.settings::prepare.settings(settings, force = FALSE)
settings$run$host <- NULL
# Check for additional modules that will require adding settings
if ("benchmarking" %in% names(settings)) {
library(PEcAn.benchmark)
settings <- papply(settings, read_settings_BRR)
}
if ("sitegroup" %in% names(settings)) {
if (is.null(settings$sitegroup$nSite)) {
settings <- PEcAn.settings::createSitegroupMultiSettings(
settings,
sitegroupId = settings$sitegroup$id)
} else {
settings <- PEcAn.settings::createSitegroupMultiSettings(
settings,
sitegroupId = settings$sitegroup$id,
nSite = settings$sitegroup$nSite)
}
# zero out so don't expand a second time if re-reading
settings$sitegroup <- NULL
}
# Update/fix/check settings.
# Will only run the first time it's called, unless force=TRUE
settings <- PEcAn.settings::prepare.settings(settings, force = FALSE)
# ----------------------------------------------------------------------
# Load required libraries
# ----------------------------------------------------------------------
library(PEcAn.all)
library(PEcAn.utils)
library(RCurl)
# Update/fix/check settings.
# Will only run the first time it's called, unless force=TRUE
settings <- PEcAn.settings::prepare.settings(settings, force = FALSE)