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run_mse.R
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run_mse.R
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### ------------------------------------------------------------------------ ###
### R script to run MSE on HPC ####
### ------------------------------------------------------------------------ ###
### This is designed to be called by a job submission script
### ------------------------------------------------------------------------ ###
### load arguments from job script ####
### ------------------------------------------------------------------------ ###
args <- commandArgs(TRUE)
print("arguments passed on to this script:")
print(args)
### evaluate arguments, if they are passed to R:
if (length(args) > 0) {
### extract arguments
for (i in seq_along(args)) eval(parse(text = args[[i]]))
## alternative OMs with different natural mortality rates (M)
if( !exists("m_criteria") ) {
# Assuming base
m_criteria <- ""
} else {
# Remove zero
m_criteria <- gsub("[.]", "", m_criteria)
if(m_criteria %in% c("01", "02", "03")) {
if(m_criteria == "01") { m_criteria <- "M01_" }
else if(m_criteria == "02") { m_criteria <- "" }
else if(m_criteria == "03") { m_criteria <- "M03_" }
} else {
stop("m_criteria must be 0.1, 0.2 or 0.3")
}
}
} else {
stop("no argument passed to R")
}
### ------------------------------------------------------------------------ ###
### set up environment ####
### ------------------------------------------------------------------------ ###
### load packages
library(FLfse)
library(stockassessment)
library(ggplotFL)
library(FLAssess)
library(mse)
library(FLash)
library(tidyr)
library(dplyr)
### load additional functions
source("flr_mse_WKNSMSE_funs.R")
### ------------------------------------------------------------------------ ###
### setup parallel environment ####
### ------------------------------------------------------------------------ ###
if (exists("par_env") && exists("n_workers") && exists("nblocks") && nblocks > 1) {
### par_env=1 -> MPI (Rmpi, DoMPI)
### par_env=2 -> DoParallel
if (par_env == 1) {
library(doMPI)
cl <- startMPIcluster()
registerDoMPI(cl)
cl_length <- cl$workerCount
pmethod <- "MPI"
n_workers <- cl_length
} else if (par_env == 2) {
library(doParallel)
cl <- makeCluster(n_workers, outfile="")
registerDoParallel(cl)
cl_length <- length(cl)
pmethod <- "MultiCore"
}
print(paste0("Starting ", n_workers, " parallel workers with ", pmethod))
### load packages and functions into workers
. <- foreach(i = seq(cl_length)) %dopar% {
#devtools::load_all("../mse/")
library(mse)
library(FLash)
library(FLfse)
library(stockassessment)
library(foreach)
library(doRNG)
source("flr_mse_WKNSMSE_funs.R")
}
### set random seed for reproducibility
library(doRNG)
registerDoRNG(123)
} else {
nblocks <- 1
}
### ------------------------------------------------------------------------ ###
### load data for MSE ####
### ------------------------------------------------------------------------ ###
### data path
path_data <- paste0("input/pok/", iters, "_", years, "/", m_criteria)
### load input objects
input <- readRDS(paste0(path_data, "base_run.rds"))
### modify input for running in parallel
input$genArgs$nblocks <- nblocks
### ------------------------------------------------------------------------ ###
### set up HCR & options ####
### ------------------------------------------------------------------------ ###
### set HCR option: A, B, C
if (exists("HCRoption")) {
input$ctrl.mp$ctrl.hcr@args$option <- switch(HCRoption,
"1" = "A",
"2" = "B",
"3" = "C",
"4" = "A",
"5" = "B",
"6" = "C",
"7" = "A")
cat(paste0("\nSetting custom HCR option: HCRoption = ", HCRoption,
" => HCR ", input$ctrl.mp$ctrl.hcr@args$option, "\n\n"))
} else {
cat(paste0("\nUsing default HCR option: HCR ",
input$ctrl.mp$ctrl.hcr@args$option, "\n\n"))
HCRoption <- 0
}
### After combinations run -- this section is turned on without running the above grid
### Btrigger and Ftrgt numbers must be updated with any changes
if (HCRoption %in% 1:7) {
comb_max <- switch(HCRoption,
"1" = c(250000, 0.35),
"2" = c(200000, 0.39),
"3" = c(250000, 0.35),
"4" = c(210000, 0.41),
"5" = c(220000, 0.39),
"6" = c(230000, 0.36),
"7" = c(230000, 0.36))
hcr_vals <- expand.grid(Ftrgt = c(comb_max[2], 0.34, 0.33, 0.32, 0.31,
0.36, 0.37, 0.38, 0.39, 0.40),
Btrigger = comb_max[1])
}
### implement
if (exists("HCR_comb")) {
### set Btrigger
Btrigger <- hcr_vals[HCR_comb, "Btrigger"]
input$ctrl.mp$ctrl.phcr@args$Btrigger <- Btrigger
input$ctrl.mp$ctrl.is@args$hcrpars$Btrigger <- Btrigger
### set Ftrgt
Ftrgt <- hcr_vals[HCR_comb, "Ftrgt"]
input$ctrl.mp$ctrl.phcr@args$Ftrgt <- Ftrgt
input$ctrl.mp$ctrl.is@args$hcrpars$Ftrgt <- Ftrgt
cat(paste0("\nSetting custom Btrigger/Ftrgt values.\n",
"Using HCR_comb = ", HCR_comb, "\n",
"Ftrgt = ", Ftrgt, "\n",
"Btrigger = ", Btrigger, "\n\n"))
} else {
cat(paste0("\nUsing default Btrigger/Ftrgt values.\n",
"Ftrgt = ", input$ctrl.mp$ctrl.phcr@args$Ftrgt, "\n",
"Btrigger = ", input$ctrl.mp$ctrl.phcr@args$Btrigger, "\n\n"))
}
### ------------------------------------------------------------------------ ###
### TAC constraint
input$ctrl.mp$ctrl.is@args$TAC_constraint <- FALSE
### check conditions
### either manually requested or as part of HCR options 4-7
if (exists("TAC_constraint")) {
if (isTRUE(as.logical(TAC_constraint))) {
input$ctrl.mp$ctrl.is@args$TAC_constraint <- TRUE
}
}
if (HCRoption %in% 4:7) {
input$ctrl.mp$ctrl.is@args$TAC_constraint <- TRUE
}
### implement
if (isTRUE(input$ctrl.mp$ctrl.is@args$TAC_constraint)) {
if(HCRoption == 7){
input$ctrl.mp$ctrl.is@args$lower <- 85
input$ctrl.mp$ctrl.is@args$upper <- 115
input$ctrl.mp$ctrl.is@args$Btrigger_cond <- TRUE
} else {
input$ctrl.mp$ctrl.is@args$lower <- 80
input$ctrl.mp$ctrl.is@args$upper <- 125
input$ctrl.mp$ctrl.is@args$Btrigger_cond <- TRUE
}
cat(paste0("\nImplementing TAC constraint.\n\n"))
} else {
cat(paste0("\nTAC constraint NOT implemented.\n\n"))
}
### ------------------------------------------------------------------------ ###
### banking & borrowing
input$ctrl.mp$ctrl.is@args$BB <- FALSE
input$iem <- NULL
### check conditions
### either manually requested or as part of HCR options 4-7
if (exists("BB")) {
if (isTRUE(as.logical(BB))) {
input$iem <- FLiem(method = iem_WKNSMSE, args = list(BB = TRUE))
input$ctrl.mp$ctrl.is@args$BB <- TRUE
input$ctrl.mp$ctrl.is@args$BB_check_hcr <- TRUE
input$ctrl.mp$ctrl.is@args$BB_check_fc <- TRUE
input$ctrl.mp$ctrl.is@args$BB_rho <- c(-0.1, 0.1)
}
}
if (HCRoption %in% 4:7) {
input$iem <- FLiem(method = iem_WKNSMSE, args = list(BB = TRUE))
input$ctrl.mp$ctrl.is@args$BB <- TRUE
input$ctrl.mp$ctrl.is@args$BB_rho <- c(-0.1, 0.1)
input$ctrl.mp$ctrl.is@args$BB_check_hcr <- FALSE
input$ctrl.mp$ctrl.is@args$BB_check_fc <- FALSE
if (HCRoption %in% 4) {
input$ctrl.mp$ctrl.is@args$BB_check_hcr <- TRUE
} else if (HCRoption %in% 5:7) {
input$ctrl.mp$ctrl.is@args$BB_check_fc <- TRUE
}
}
if (!is.null(input$iem)) {
cat(paste0("\nImplementing banking and borrowing.\n\n"))
} else {
cat(paste0("\nBanking and borrowing NOT implemented.\n\n"))
}
### ------------------------------------------------------------------------ ###
### specify the levels of bias in assessment
input$ctrl.mp$ctrl.est@args$prop_biasN <- 1.0+prop_biasN ## bias in N-at-age from sam fit
input$ctrl.mp$ctrl.est@args$prop_biasF <- 1.0+prop_biasF ## bias in F-at-age from sam fit
### ------------------------------------------------------------------------ ###
### run MSE ####
### ------------------------------------------------------------------------ ###
### Use A1 for Option 7
if(HCRoption == 7) {
HCRopt <- "A1"
} else {
HCRopt <- input$ctrl.mp$ctrl.hcr@args$option
}
### Create output file name
path_out <- paste0("output/runs/pok/", iters, "_", years)
dir.create(path = path_out, recursive = TRUE)
file_out <- paste0("HCR-", HCRopt,
"_Ftrgt-", input$ctrl.mp$ctrl.phcr@args$Ftrgt,
"_Btrigger-", input$ctrl.mp$ctrl.phcr@args$Btrigger,
"_TACconstr-", input$ctrl.mp$ctrl.is@args$TAC_constraint,
"_BB-", input$ctrl.mp$ctrl.is@args$BB,
"_biasN-", input$ctrl.mp$ctrl.est@args$prop_biasN,
"_biasF-", input$ctrl.mp$ctrl.est@args$prop_biasF
)
outFile <- paste0(path_out, "/", m_criteria, file_out, ".rds")
### Checking if output exists. If yes, quit
print(paste("Saving to: ", outFile))
if( file.exists(outFile) && !(exists("forceOverwrite") && forceOverwrite) ) {
print("File exists. Not overwriting.")
quit(save = "no")
}
### run MSE
res1 <- mp(om = input$om,
oem = input$oem,
iem = input$iem,
ctrl.mp = input$ctrl.mp,
genArgs = input$genArgs,
tracking = input$tracking)
### save output
saveRDS(object = res1, file = outFile)
### ------------------------------------------------------------------------ ###
### terminate ####
### ------------------------------------------------------------------------ ###
### close R
### mpi.finalize() or mpi.quit() hang...
### -> kill R, the MPI processes stop afterwards
### clean up
if (exists("cl")) {
if (par_env == 1 && exists("kill")) {
system("bkill $LSB_JOBID")
} else if (par_env == 2) {
stopCluster(cl)
}
}
quit(save = "no")