scripts/restart_analysis_file.R

In femeunier/SoilSensitivity:

rm(list = ls())

library(dplyr)
library(tidyr)
library(purrr)
library(rrtm)
library(ED2scenarios)
library(PEcAn.ED2)
library(purrr)
library(ggplot2)
library(ggridges)
library(cowplot)
library(pracma)
library(BayesianTools)
library(raster)
library(rhdf5)
library(stringr)

ED_REG_LATMIN = -19.5
ED_REG_LATMAX =  13.5
ED_REG_LONMIN = -84.5
ED_REG_LONMAX = -30.5

GRID_RES = 1

fyear = 2010

X = seq(ED_REG_LONMIN,ED_REG_LONMAX,GRID_RES)
Y = seq(ED_REG_LATMIN,ED_REG_LATMAX,GRID_RES)

ref_dir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/SoilSensitivity/run"
rundir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/SoilSensitivity/run/grid"
ICdir <- "/data/gent/vo/000/gvo00074/pecan/output/other_runs/LSliana/IC/"
outdir <- "/kyukon/scratch/gent/vo/000/gvo00074/felicien/SoilSensitivity/out"

scenars <- c("SoilGrids_mean","SoilGrids_min","SoilGrids_max")

land <- readRDS(file.path("maps","landmask.RDS"))

df.restart <- data.frame()

Nsimuperjob = 60
isimu = 0

list_dir <- list()
ed_exec <- "/user/scratchkyukon/gent/gvo000/gvo00074/felicien/ED2/ED/build/ed_2.1-opt-master-2bb6872"

all_depths <- c(-8,-7,-6.2,-5.5,-4.9,-4.3,-3.8,-3.3,-2.8,-2.3,-1.8,-1.3,-1,-0.6,-0.3,-0.15)

df.temp <- data.frame()

for(ix in seq(1,length(X))){
  for(iy in seq(1,length(Y))){
    clat = Y[iy]; clon = X[ix]

    if (land[which(rownames(land)==clon),which(colnames(land)==clat)] != 0){
      for (iscenar in seq(1,length(scenars))){

        run_name <- paste0("SoilSens_Amazon_historical_",scenars[iscenar],"_X_",abs(X[ix]),ifelse(X[ix]<0,"W","E"),
                           "_Y_",abs(Y[iy]),ifelse(Y[iy]<0,"S","N"))

        # run_origin <- paste0("SoilSens_Amazon_IC_",scenars[iscenar],"_X_",abs(X[ix]),ifelse(X[ix]<0,"W","E"),
        #                      "_Y_",abs(Y[iy]),ifelse(Y[iy]<0,"S","N"))
        #
        # run_name <- paste0("SoilSens_Amazon_IC_",scenars[iscenar],"_X_",abs(X[ix]),ifelse(X[ix]<0,"W","E"),
        #                    "_Y_",abs(Y[iy]),ifelse(Y[iy]<0,"S","N"))

        run_ref <- file.path(rundir,run_name)
        out_ref <- file.path(outdir,run_name)

        ed2in <- read_ed2in(file.path(run_ref,"ED2IN"))

        isimu <- isimu + 1

        history.file <- file.path(out_ref,"histo","history-S-2010-01-01-000000-g01.h5")
        if (file.exists(history.file)){
          ed2in$RUNTYPE <- "HISTORY"
          ed2in$IED_INIT_MODE <- 6
          ed2in$SFILIN <- file.path(out_ref,"histo","history")
          ed2in$ITIMEH <- 0
          ed2in$IDATEH <- 1
          ed2in$IMONTHH <- 1
          ed2in$IYEARH <- fyear
          ed2in$IMETAVG <- 3

          # Output year/month
          ed2in$IMONTHZ = 1
          ed2in$IYEARA = fyear
          ed2in$IYEARZ = fyear + 1
          ed2in$IQOUTPUT = 3

          ed2in$FRQSTATE = 1

          write_ed2in(ed2in,filename = file.path(run_ref,"ED2IN"))

          if (isimu == 1){
            isfirstjob = TRUE
            dir_joblauncher = run_ref
            list_dir[[run_name]] = run_ref
          } else{
            isfirstjob = FALSE
          }

          # job.sh
          write_joblauncher_noR_status(file =  file.path(dir_joblauncher,"job_analysis.sh"),
                                       nodes = 1,ppn = 18,mem = 16,walltime = 24,
                                       prerun = "ml purge ; ml UDUNITS/2.2.26-intel-2018a R/3.4.4-intel-2018a-X11-20180131 HDF5/1.10.1-intel-2018a; ulimit -s unlimited",
                                       CD = run_ref,
                                       ed_exec = ed_exec,
                                       ED2IN = "ED2IN",
                                       firstjob = isfirstjob,
                                       CD.main = dir_joblauncher,
                                       remove = FALSE)


          if (isimu == Nsimuperjob){
            isimu = 0
          }
        } else {

          df.temp <- bind_rows(list(df.temp,
                                    data.frame(run = run_name)))
        }
      }
    }
  }
}

dumb <- write_bash_submission(file = file.path(rundir,"all_jobs_analysis.sh"),
                              list_files = list_dir,
                              job_name = "job_analysis.sh")

# scp /home/femeunier/Documents/projects/SoilSensitivity/scripts/restart_analysis_file.R hpc:/data/gent/vo/000/gvo00074/felicien/R