createSitegroupMultiSettings.RdHelps to create a MultiSettings object to run some or all sites in a Sitegroup.
createSitegroupMultiSettings(
templateSettings,
sitegroupId,
nSite,
con = NULL,
params = templateSettings$database$bety
)A Settings object that will be the
template for the resulting MultiSettings.
The Bety ID of the sitegroup to draw from
The number of sites to randomly select (without replacement) from the siteGroup. Omit to use all sites in the group.
Bety DB connection or parameters.
Passed directly to db.query
A MultiSettings object with the same settings as
templateSettings but site information for the selected sites
Starts with a template settings object, and fills in the run block
with site info sampled from the sitegroup.
The template could be fully set up except for the site info,
or more or less empty if you plan to fill in the other settings later.
A MultiSettings is created from templateSettings,
nSite sites (or all of them, if nSite is unset) are selected
from Bety, and their info is dropped into the MultiSettings.
dontrun <- function() { # Added by Alexey Shiklomanov
# so this doesn't run and break the build
# This isn't necessarily a fully working settings object.
# Enough to get the idea though.
# Note it has a $run block with settings that will be shared across all sites
template <- Settings(list(
info = structure(list(
notes = NULL, userid = "1000000005", username = "Ryan Kelly",
date = "2016/07/13 13:23:46 -0400"),
.Names = c("notes", "userid", "username", "date")),
database = structure(list(
bety = structure(
list(user = "bety", password = "bety", host = "psql-pecan.bu.edu",
dbname = "bety", driver = "PostgreSQL", write = "TRUE"),
.Names = c("user", "password", "host", "dbname", "driver", "write")),
fia = structure(
list(user = "bety", password = "bety", host = "psql-pecan.bu.edu",
dbname = "fia5", driver = "PostgreSQL", write = "true"),
.Names = c("user", "password", "host", "dbname", "driver", "write"))),
.Names = c("bety", "fia")),
pfts = structure(list(
pft = structure(
list(comment = NULL, name = "temperate.Evergreen_Hardwood",
constants = structure(list(num = "1"), .Names = "num")),
.Names = c("comment", "name", "constants")),
pft = structure(
list(name = "temperate.Hydric",
constants = structure(list(num = "2"), .Names = "num")),
.Names = c("name", "constants"))),
.Names = c("pft", "pft")),
meta.analysis = structure(list(
iter = "3000", random.effects = list(on = FALSE, use_ghs = TRUE),
update = "AUTO", threshold = "1.2"),
.Names = c("iter", "random.effects", "update", "threshold")),
ensemble = structure(list(size = "1", variable = "NPP"),
.Names = c("size", "variable")),
model = structure(list(id = "2000000005",
edin = "/home/rykelly/pecan/RK_files/ED2IN/ED2IN.rgit.mandifore_04",
config.header = structure(list(
radiation = structure(list(lai_min = "0.01"), .Names = "lai_min"),
ed_misc = structure(list(output_month = "12"),
.Names = "output_month")),
.Names = c("radiation", "ed_misc")),
phenol.scheme = "0", prerun = "module load hdf5/1.8.11",
binary = "/usr2/postdoc/rykelly/ED2/ED/build/ed_2.1-opt"),
.Names = c("id", "edin", "config.header", "phenol.scheme", "prerun",
"binary")),
host = structure(list(name = "geo.bu.edu", user = "rykelly",
folder = "/projectnb/dietzelab/pecan.data/output/rykelly",
qsub = "qsub -V -N @NAME@ -o @STDOUT@ -e @STDERR@ -S /bin/bash",
qsub.jobid = "Your job ([0-9]+) .*",
qstat = "qstat -j @JOBID@ || echo DONE",
prerun = "module load udunits R/R-3.0.0_gnu-4.4.6",
dbfiles = "/projectnb/dietzelab/pecan.data/input",
modellauncher = structure(list(
binary = "/usr2/postdoc/rykelly/pecan/utils/modellauncher/modellauncher",
qsub.extra = "-pe omp 20"),
.Names = c("binary", "qsub.extra"))),
.Names = c("name", "user", "folder", "qsub", "qsub.jobid", "qstat",
"prerun", "dbfiles", "modellauncher")),
run = structure(list(
inputs = structure(list(
met = structure(list(source = "NARR", output = "ED2"),
.Names = c("source", "output")),
lu = structure(list(id = "294",
path = "/projectnb/dietzelab/EDI/ed_inputs/glu/"),
.Names = c("id", "path")),
soil = structure(list(id = "297",
path = "/projectnb/dietzelab/EDI/faoOLD/FAO_"),
.Names = c("id", "path")),
thsum = structure(list(id = "295",
path = "/projectnb/dietzelab/EDI/ed_inputs/"),
.Names = c("id", "path")),
veg = structure(list(id = "296",
path = "/projectnb/dietzelab/EDI/oge2OLD/OGE2_"),
.Names = c("id", "path")),
pss = structure(list(source = "FIA"), .Names = "source")),
.Names = c("met", "lu", "soil", "thsum", "veg", "pss")),
start.date = "2004/01/01",
end.date = "2004/01/31"),
.Names = c("inputs", "start.date", "end.date"))
))
sitegroupId <- 1000000002
startDate <- "2000/01/01"
endDate <- "2015/12/31"
nSite <- 10
outDir <- "~/multisite_setup_test"
template <- setDates(template, startDate = startDate, endDate = endDate)
template <- setOutDir(template, outDir)
multiRunSettings <- createSitegroupMultiSettings(
template,
sitegroupId = sitegroupId,
nSite = nSite)
dir.create(outDir, showWarnings = FALSE)
write.settings(multiRunSettings, outputfile = "pecan.xml")
} # dontrun