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annotate parallelSticsRRotation.R @ 0:e8b0d1d0797d draft default tip

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"planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
author siwaa
date Tue, 21 Feb 2023 19:03:38 +0000
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e8b0d1d0797d "planemo upload for repository https://forgemia.inra.fr/quaysofthestics/sticsquays/-/tree/master/tools commit 34d462246915d2d24868042deeda35a01985d2aa"
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1 library(SticsRFiles)
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2 library(SticsOnR)
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3 library(parallel)
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4 library(doParallel)
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5 library(readxl)
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7 workspace <- paste0(getwd(), "/WS")
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8 javastics_path <- paste0(getwd(), "/JavaSTICS-1.5.1-STICS-10.0.0")
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10 # copy of the var.mod and rap.mod into the config folder
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11 file.copy(from = file.path(workspace, "var.mod"), to = "config/var.mod", overwrite = TRUE)
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12 file.copy(from = file.path(workspace, "rap.mod"), to = "config/rap.mod", overwrite = TRUE)
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14 txt_path <- paste0(getwd(), "/WS/txt_files")
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15 dir.create(txt_path,recursive = T)
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17 print("==================================")
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19 print(paste0("Cores=", detectCores()))
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20 print(paste0("javastics=", javastics_path))
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21 print(paste0("ws=", workspace))
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22 print(paste0("out_dir=", txt_path))
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24 print("==================================")
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27 # List of successive USMs
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28 successive_usms_file <- ("rotationPlan.xlsx")
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29 successive_usms_tab <- read_excel(path = file.path(workspace, successive_usms_file), sheet = "usms")
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31 no_cores <- detectCores() - 1
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32 cl <- makeCluster(no_cores)
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33 registerDoParallel(cl)
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35 result <- foreach(i=1:nrow(successive_usms_tab),
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36 .packages = c("SticsRFiles", "SticsOnR") ) %dopar% {
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38 nusms <- as.numeric(successive_usms_tab[i,2])
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40 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))])
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42 list_successive_usms <- list(vec)
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44 sim_options <- stics_wrapper_options(javastics = javastics_path,
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45 stics_exe = paste0(javastics_path,"/bin/stics_modulo"),
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46 workspace = txt_path,
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47 verbose = TRUE,
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48 successive = list_successive_usms)
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49 list_usms <- vec
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51 stics_wrapper(model_options = sim_options, situation = list_usms)
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52 }
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54 stopCluster(cl)
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56 for (i in 1:nrow(successive_usms_tab)) { #i=1
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57 if (i == 1) {
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58 simPCP <- result[[i]]
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59 } else {
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60 simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list)
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61 }
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63 }
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65 save(simPCP, file = "results.RData")