DALEC issue log

workflow.Rout

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> #!/usr/bin/env Rscript
> #-------------------------------------------------------------------------------
> # Copyright (c) 2012 University of Illinois, NCSA.
> # All rights reserved. This program and the accompanying materials
> # are made available under the terms of the 
> # University of Illinois/NCSA Open Source License
> # which accompanies this distribution, and is available at
> # http://opensource.ncsa.illinois.edu/license.html
> #-------------------------------------------------------------------------------
> 
> # ----------------------------------------------------------------------
> # Load required libraries
> # ----------------------------------------------------------------------
> library(PEcAn.all)
Loading required package: PEcAn.DB
Loading required package: DBI
Loading required package: PEcAn.utils
Loading required package: XML
Loading required package: ggplot2
Loading required package: randtoolbox
Loading required package: rngWELL
This is randtoolbox. For overview, type 'help("randtoolbox")'.
Loading required package: abind
Loading required package: RCurl
Loading required package: bitops
Loading required package: PEcAn.settings
Loading required package: PEcAn.MA
Loading required package: lattice
Loading required package: MASS
Loading required package: PEcAn.uncertainty
Loading required package: PEcAn.priors
Loading required package: gridExtra
Loading required package: PEcAn.data.atmosphere
Loading required package: PEcAn.data.land
Loading required package: PEcAn.data.remote
Loading required package: PEcAn.assim.batch
Loading required package: ellipse
Loading required package: dplyr

Attaching package: 'dplyr'

The following object is masked from 'package:gridExtra':

    combine

The following object is masked from 'package:MASS':

    select

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Loading required package: parallel
Loading required package: GPfit
Loading required package: IDPmisc
Loading required package: grid
Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.2.0
Loaded modules: basemod,bugs
Loading required package: BayesianTools

Attaching package: 'PEcAn.assim.batch'

The following object is masked from 'package:BayesianTools':

    correlationPlot

Loading required package: PEcAn.emulator
Loading required package: mvtnorm
Loading required package: MCMCpack
##
## Markov Chain Monte Carlo Package (MCMCpack)
## Copyright (C) 2003-2017 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
##
## Support provided by the U.S. National Science Foundation
## (Grants SES-0350646 and SES-0350613)
##
Loading required package: PEcAn.benchmark
> library(PEcAn.utils)
> library(RCurl)
> 
> # make sure always to call status.end
> options(warn=1)
> options(error=quote({
+   status.end("ERROR")
+   kill.tunnel(settings)
+   if (!interactive()) {
+     q()
+   }
+ }))
> 
> #options(warning.expression=status.end("ERROR"))
> 
> 
> # ----------------------------------------------------------------------
> # PEcAn Workflow
> # ----------------------------------------------------------------------
> # Open and read in settings file for PEcAn run.
> args <- commandArgs(trailingOnly = TRUE)
> if (is.na(args[1])){
+   settings <- PEcAn.settings::read.settings("pecan.xml")
+ } else {
+   settings.file = args[1]
+   settings <- PEcAn.settings::read.settings(settings.file)
+ }
2017-05-15 08:34:43 INFO   [PEcAn.settings::read.settings] : 
   Loading inpufile= pecan.xml 
> 
> # Check for additional modules that will require adding settings
> if("benchmarking" %in% names(settings)){
+   library(PEcAn.benchmark)
+   settings <- papply(settings, read_settings_RR)
+ }
> 
> # Update/fix/check settings. Will only run the first time it's called, unless force=TRUE
> settings <- PEcAn.settings::prepare.settings(settings, force=FALSE)
2017-05-15 08:34:43 INFO   [fix.deprecated.settings] : 
   Fixing deprecated settings... 
2017-05-15 08:34:43 INFO   [update.settings] : 
   Fixing deprecated settings... 
2017-05-15 08:34:43 INFO   [check.settings] : Checking settings... 
Loading required package: RPostgreSQL
2017-05-15 08:34:43 INFO   [check.database] : 
   Successfully connected to database : bety bety localhost bety PostgreSQL 
   true 
2017-05-15 08:34:43 DEBUG  [check.database.settings] : 
   Writing all runs/configurations to database. 
2017-05-15 08:34:43 WARN   [check.bety.version] : 
   Last migration 20170118205944 is more recent than expected 
   20141009160121. This could result in PEcAn not working as expected. 
2017-05-15 08:34:44 INFO   [fn] : 
   No start date passed to ensemble - using the run date ( 2002 ). 
2017-05-15 08:34:44 INFO   [fn] : 
   No end date passed to ensemble - using the run date ( 2002 ). 
2017-05-15 08:34:44 INFO   [fn] : 
   Setting site name to Metolius-first young aged pine (US-Me5) 
2017-05-15 08:34:44 INFO   [fn] : 
   Setting site lat to 44.4372 
2017-05-15 08:34:44 INFO   [fn] : 
   Setting site lon to -121.567 
2017-05-15 08:34:44 INFO   [check.settings] : 
   Setting meta.analysis threshold to 1.2 
2017-05-15 08:34:44 INFO   [check.settings] : 
   Setting meta.analysis update to only update if no previous meta analysis 
   was found 
2017-05-15 08:34:44 INFO   [check.model.settings] : 
   Setting model type to DALEC 
2017-05-15 08:34:44 INFO   [check.model.settings] : 
   Setting model revision to 
2017-05-15 08:34:44 INFO   [check.model.settings] : 
   Option to delete raw model output not set or not logical. Will keep all 
   model output. 
2017-05-15 08:34:44 INFO   [check.model.settings] : 
   Setting model binary to /usr/local/bin/dalec_seqMH 
2017-05-15 08:34:44 INFO   [check.workflow.settings] : 
   output folder = /home/carya/output//PEcAn_99000000003 
2017-05-15 08:34:44 INFO   [check.settings] : 
   Storing pft evergreen in 
   /home/carya/output//PEcAn_99000000003/pft/evergreen 
> 
> # Write pecan.CHECKED.xml
> PEcAn.settings::write.settings(settings, outputfile = "pecan.CHECKED.xml")
[1] "/home/carya/output//PEcAn_99000000003/pecan.CHECKED.xml"
> 
> # start from scratch if no continue is passed in
> statusFile <- file.path(settings$outdir, "STATUS")
> if (length(which(commandArgs() == "--continue")) == 0 && file.exists(statusFile)) {
+   file.remove(statusFile)
+ }
>   
> # Do conversions
> settings <- do.conversions(settings)
> 
> 
> # Query the trait database for data and priors
> if (status.check("TRAIT") == 0){
+   status.start("TRAIT")
+   settings <- runModule.get.trait.data(settings)
+   PEcAn.settings::write.settings(settings, outputfile='pecan.TRAIT.xml')
+   status.end()
+ } else if (file.exists(file.path(settings$outdir, 'pecan.TRAIT.xml'))) {
+   settings <- PEcAn.settings::read.settings(file.path(settings$outdir, 'pecan.TRAIT.xml'))
+ }
[1] "---------------------------------------------------------"
[1] "leaf_turnover_rate"
[1] "Median leaf_turnover_rate : 0.426"
[1] "---------------------------------------------------------"
2017-05-15 08:34:45 INFO   [FUN] : 
   Summary of Prior distributions for: evergreen 
2017-05-15 08:34:45 INFO   [FUN] : 
   distn parama paramb n 
2017-05-15 08:34:45 INFO   [FUN] : 
   root_turnover_rate unif 0.0000 10.0000 NA 
2017-05-15 08:34:45 INFO   [FUN] : 
   leaf_turnover_rate unif 0.0400 1.0000 NA 
2017-05-15 08:34:45 INFO   [FUN] : 
   SLA unif 3.0000 30.0000 NA 
2017-05-15 08:34:45 INFO   [FUN] : 
   autotrophic_respiration_fraction beta 8.4229 9.3356 0 
2017-05-15 08:34:45 INFO   [FUN] : 
   leaf_allocation_fraction beta 8.9103 18.9848 0 
2017-05-15 08:34:45 INFO   [FUN] : 
   litter_decomposition_to_SOM exp 157176.2000 0.0000 0 
2017-05-15 08:34:45 INFO   [FUN] : 
   litter_respiration_rate gamma 0.3265 3.9822 0 
2017-05-15 08:34:45 INFO   [FUN] : 
   wood_turnover_rate gamma 0.0782 0.1123 0 
2017-05-15 08:34:45 INFO   [FUN] : 
   som_respiration_rate exp 261565.0000 0.0000 0 
2017-05-15 08:34:45 INFO   [FUN] : 
   root_allocation_fraction beta 15.2563 19.7635 0 
2017-05-15 08:34:45 INFO   [FUN] : 
   number of observations per trait for evergreen 
2017-05-15 08:34:45 INFO   [FUN] : 
   4 observations of leaf_turnover_rate 
> 
>   
> # Run the PEcAn meta.analysis
> if(!is.null(settings$meta.analysis)) {
+   if (status.check("META") == 0){
+     status.start("META")
+     runModule.run.meta.analysis(settings)
+     status.end()
+   }
+ }
2017-05-15 08:34:46 INFO   [FUN] : 
   ------------------------------------------------------------------- 
2017-05-15 08:34:46 INFO   [FUN] : 
   Running meta.analysis for PFT: evergreen 
2017-05-15 08:34:46 INFO   [FUN] : 
   ------------------------------------------------------------------- 
2017-05-15 08:34:46 INFO   [check_consistent] : 
   OK!  leaf_turnover_rate data and prior are consistent: 
2017-05-15 08:34:46 INFO   [check_consistent] : 
   leaf_turnover_rate P[X<x] = 0.397135416666667 
Each meta-analysis will be run with: 
3000 total iterations,
4 chains, 
a burnin of 1500 samples,
, 
thus the total number of samples will be 6000
################################################
------------------------------------------------
starting meta-analysis for:

 leaf_turnover_rate 

------------------------------------------------
NO ERROR STATS PROVIDED, DROPPING RANDOM EFFECTS
prior for leaf_turnover_rate
                     (using R parameterization):
unif(0.04, 1)
data max: 0.42125 
data min: 0.42125 
mean: 0.421 
n: 1
stem plot of data points
no estimates of SD for leaf_turnover_rate
Read 28 items
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 1
   Unobserved stochastic nodes: 3
   Total graph size: 19

Initializing model


Iterations = 1002:4000
Thinning interval = 2 
Number of chains = 4 
Sample size per chain = 1500 

1. Empirical mean and standard deviation for each variable,
   plus standard error of the mean:

         Mean    SD Naive SE Time-series SE
beta.o 0.4381 0.157 0.002027       0.002674
sd.y   1.0648 8.442 0.108982       0.110690

2. Quantiles for each variable:

          2.5%     25%    50%    75%  97.5%
beta.o 0.11323 0.38318 0.4225 0.4712 0.8789
sd.y   0.01295 0.05325 0.1645 0.5531 5.5635

2017-05-15 08:34:47 INFO   [check_consistent] : 
   OK!  leaf_turnover_rate data and prior are consistent: 
2017-05-15 08:34:47 INFO   [check_consistent] : 
   leaf_turnover_rate P[X<x] = 0.398410400003477 
2017-05-15 08:34:48 INFO   [pecan.ma.summary] : 
   JAGS model converged for evergreen leaf_turnover_rate GD MPSRF = 1.001 
>   
> # Write model specific configs
> if (status.check("CONFIG") == 0){
+   status.start("CONFIG")
+   settings <- runModule.run.write.configs(settings)
+   PEcAn.settings::write.settings(settings, outputfile='pecan.CONFIGS.xml')
+   status.end()
+ } else if (file.exists(file.path(settings$outdir, 'pecan.CONFIGS.xml'))) {
+   settings <- PEcAn.settings::read.settings(file.path(settings$outdir, 'pecan.CONFIGS.xml'))
+ }
2017-05-15 08:34:49 WARN   [dbfile.check] : 
   Multiple Valid Files found on host machine. Returning last updated 
   record 
2017-05-15 08:34:49 INFO   [get.parameter.samples] : 
   Selected PFT(s): evergreen 
Warning in rm(prior.distns, post.distns, trait.mcmc) :
  object 'prior.distns' not found
Warning in rm(prior.distns, post.distns, trait.mcmc) :
  object 'post.distns' not found
Warning in rm(prior.distns, post.distns, trait.mcmc) :
  object 'trait.mcmc' not found
2017-05-15 08:34:49 INFO   [get.parameter.samples] : 
   PFT evergreen has MCMC samples for: leaf_turnover_rate 
2017-05-15 08:34:49 INFO   [get.parameter.samples] : 
   PFT evergreen will use prior distributions for: root_turnover_rate SLA 
   autotrophic_respiration_fraction leaf_allocation_fraction 
   litter_decomposition_to_SOM litter_respiration_rate wood_turnover_rate 
   som_respiration_rate root_allocation_fraction 
2017-05-15 08:34:49 INFO   [get.parameter.samples] : 
   using 5004 samples per trait 
Loading required package: PEcAn.DALEC
2017-05-15 08:34:49 INFO   [write.config.DALEC] : 
   t7 t5 SLA t2 t3 t1 t8 t6 t9 t4 
[1] 99000000003
2017-05-15 08:34:49 INFO   [run.write.configs] : 
   ###### Finished writing model run config files ##### 
2017-05-15 08:34:49 INFO   [run.write.configs] : 
   config files samples in /home/carya/output//PEcAn_99000000003/run 
2017-05-15 08:34:49 INFO   [run.write.configs] : 
   parameter values for runs in 
   /home/carya/output//PEcAn_99000000003/samples.RData 
>     
> if ((length(which(commandArgs() == "--advanced")) != 0) && (status.check("ADVANCED") == 0)) {
+   status.start("ADVANCED")
+   q();
+ }
> 
> # Start ecosystem model runs
> if (status.check("MODEL") == 0) {
+   status.start("MODEL")
+   runModule.start.model.runs(settings)
+   status.end()
+ }
2017-05-15 08:34:49 INFO   [start.model.runs] : 
   ------------------------------------------------------------------- 
2017-05-15 08:34:49 INFO   [start.model.runs] : 
   Starting model runs DALEC 
2017-05-15 08:34:49 INFO   [start.model.runs] : 
   ------------------------------------------------------------------- 

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
> 
> # Get results of model runs
> if (status.check("OUTPUT") == 0) {
+   status.start("OUTPUT")
+   runModule.get.results(settings)
+   status.end()
+ }
2017-05-15 08:34:53 INFO   [read.ensemble.output] : 
   reading ensemble output from run id: 99000000003 
2017-05-15 08:34:53 INFO   [read.output] : 
   Reading output for Years: 2002 - 2002 in directory: 
   /home/carya/output//PEcAn_99000000003/out/99000000003 including files 
   2002.nc 
2017-05-15 08:34:54 INFO   [read.output] : 
   NPP Mean: 1.93e-08 Median: 1.86e-08 
> 
> # Run ensemble analysis on model output. 
> if ('ensemble' %in% names(settings) & status.check("ENSEMBLE") == 0) {
+   status.start("ENSEMBLE")
+   runModule.run.ensemble.analysis(settings, TRUE)    
+   status.end()
+ }
[1] "----- Variable: NPP"
[1] "----- Running ensemble analysis for site:  Metolius-first young aged pine (US-Me5)"
[1] "----- Done!"
[1] " "
[1] "-----------------------------------------------"
[1] " "
[1] " "
[1] "------ Generating ensemble time-series plot ------"
[1] "----- Variable: NPP"
[1] "----- Reading ensemble output ------"
[1] 9.9e+10
2017-05-15 08:34:54 INFO   [read.output] : 
   Reading output for Years: 2002 - 2002 in directory: 
   /home/carya/output//PEcAn_99000000003/out/99000000003 including files 
   2002.nc 
2017-05-15 08:34:55 INFO   [read.output] : 
   NPP Mean: 1.93e-08 Median: 1.86e-08 
> 
> # Run sensitivity analysis and variance decomposition on model output
> if ('sensitivity.analysis' %in% names(settings) & status.check("SENSITIVITY") == 0) {
+   status.start("SENSITIVITY")
+   runModule.run.sensitivity.analysis(settings)
+   status.end()
+ }
> 
> # Run parameter data assimilation
> if ('assim.batch' %in% names(settings)) {
+   if (status.check("PDA") == 0) {
+     status.start("PDA")
+     settings <- PEcAn.assim.batch::runModule.assim.batch(settings)
+     status.end()
+   }
+ }
> 
> # Run state data assimilation
> if ('state.data.assimilation' %in% names(settings)) {
+   if (status.check("SDA") == 0) {
+     status.start("SDA")
+     settings <- sda.enfk(settings)
+     status.end()
+   }
+ }
> 
> # Run benchmarking
> if("benchmarking" %in% names(settings)){
+   status.start("BENCHMARKING")
+   results <- papply(settings, function(x) calc_benchmark(x, bety))
+   status.end()
+ }
>   
> # Pecan workflow complete
> if (status.check("FINISHED") == 0) {
+   status.start("FINISHED")
+   kill.tunnel(settings)
+   db.query(paste("UPDATE workflows SET finished_at=NOW() WHERE id=", settings$workflow$id, "AND finished_at IS NULL"), params=settings$database$bety)
+ 
+   # Send email if configured
+   if (!is.null(settings$email) && !is.null(settings$email$to) && (settings$email$to != "")) {
+     sendmail(settings$email$from, settings$email$to,
+              paste0("Workflow has finished executing at ", base::date()),
+              paste0("You can find the results on ", settings$email$url))
+   }
+   status.end()
+ }
> 
> db.print.connections()
2017-05-15 08:34:55 INFO   [db.print.connections] : 
   Created 11 connections and executed 87 queries 
2017-05-15 08:34:55 INFO   [db.print.connections] : 
   Created 11 connections and executed 87 queries 
2017-05-15 08:34:55 DEBUG  [db.print.connections] : 
   No open database connections. 
> print("---------- PEcAn Workflow Complete ----------")
[1] "---------- PEcAn Workflow Complete ----------"
> 
> proc.time()
   user  system elapsed 
 12.796   0.616  14.328