Mercurial > repos > siwaa > redelac
comparison parallelSticsRRotation.R @ 0:e8b0d1d0797d draft default tip
"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 |
| parents | |
| children |
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| -1:000000000000 | 0:e8b0d1d0797d |
|---|---|
| 1 library(SticsRFiles) | |
| 2 library(SticsOnR) | |
| 3 library(parallel) | |
| 4 library(doParallel) | |
| 5 library(readxl) | |
| 6 | |
| 7 workspace <- paste0(getwd(), "/WS") | |
| 8 javastics_path <- paste0(getwd(), "/JavaSTICS-1.5.1-STICS-10.0.0") | |
| 9 | |
| 10 # copy of the var.mod and rap.mod into the config folder | |
| 11 file.copy(from = file.path(workspace, "var.mod"), to = "config/var.mod", overwrite = TRUE) | |
| 12 file.copy(from = file.path(workspace, "rap.mod"), to = "config/rap.mod", overwrite = TRUE) | |
| 13 | |
| 14 txt_path <- paste0(getwd(), "/WS/txt_files") | |
| 15 dir.create(txt_path,recursive = T) | |
| 16 | |
| 17 print("==================================") | |
| 18 | |
| 19 print(paste0("Cores=", detectCores())) | |
| 20 print(paste0("javastics=", javastics_path)) | |
| 21 print(paste0("ws=", workspace)) | |
| 22 print(paste0("out_dir=", txt_path)) | |
| 23 | |
| 24 print("==================================") | |
| 25 | |
| 26 | |
| 27 # List of successive USMs | |
| 28 successive_usms_file <- ("rotationPlan.xlsx") | |
| 29 successive_usms_tab <- read_excel(path = file.path(workspace, successive_usms_file), sheet = "usms") | |
| 30 | |
| 31 no_cores <- detectCores() - 1 | |
| 32 cl <- makeCluster(no_cores) | |
| 33 registerDoParallel(cl) | |
| 34 | |
| 35 result <- foreach(i=1:nrow(successive_usms_tab), | |
| 36 .packages = c("SticsRFiles", "SticsOnR") ) %dopar% { | |
| 37 | |
| 38 nusms <- as.numeric(successive_usms_tab[i,2]) | |
| 39 | |
| 40 vec <- as.character(successive_usms_tab[i,c(3:(2+nusms))]) | |
| 41 | |
| 42 list_successive_usms <- list(vec) | |
| 43 | |
| 44 sim_options <- stics_wrapper_options(javastics = javastics_path, | |
| 45 stics_exe = paste0(javastics_path,"/bin/stics_modulo"), | |
| 46 workspace = txt_path, | |
| 47 verbose = TRUE, | |
| 48 successive = list_successive_usms) | |
| 49 list_usms <- vec | |
| 50 | |
| 51 stics_wrapper(model_options = sim_options, situation = list_usms) | |
| 52 } | |
| 53 | |
| 54 stopCluster(cl) | |
| 55 | |
| 56 for (i in 1:nrow(successive_usms_tab)) { #i=1 | |
| 57 if (i == 1) { | |
| 58 simPCP <- result[[i]] | |
| 59 } else { | |
| 60 simPCP$sim_list <- c(simPCP$sim_list, result[[i]]$sim_list) | |
| 61 } | |
| 62 | |
| 63 } | |
| 64 | |
| 65 save(simPCP, file = "results.RData") |