Run simulations

library(tools)
library(gen3sis)


# if from comand line, read options
# optparse is not installed on hyperion
# try loading it, if it fails retry with a local library folder
if(!library(optparse, logical.return = T)){
  #library was not found, try local copy
  library(optparse, lib.loc = "~/lib/R")
}

option_list = list(
  make_option(c("-c", "--config_file"), action="store", default=NA, type='character',
              help="configuration file for experiment run"),
  make_option(c("-i", "--input_directory"), action="store",
              default=NA, type='character',
              help="input directory for simulation data
              \tnot set: derive input folder from config file path
              \t\"path\": use provided path (absolute or relative)"),
  make_option(c("-o", "--output_directory"), action="store",
              default=NA, type='character',
              help="output directory for simulation results
              \tnot set: derive output folder from config file path
              \t\"path\": use provided path (absolute or relative)"),
  make_option(c("-m", "--move_output_to_target"), action="store",
              default=NA, type='character',
              help="directory where final simulation data is moved to
              \tnot set: don't move
              \t\"path\": prepend provided path to [output_directory]"),
  make_option(c("-t", "--timestep_restart"), action="store", default=NA, type='character',
              help="Set the start time timestep:
              \tnot set: start at the beginning,
              \t\"ti\" \tto start from the last available timestep,
              \t\"x\" \tto start from timestep x "),
  make_option(c("-s", "--save_intermediate_results"), action="store", default=NA, type='character',
              help="save intermediate species and landscapes:
              \tnot set: save only initial (t_start) and final timesteps (t_end),
              \t\"x\" \t save x timesteps between t_start and t_end,
              \t\"all\" \t save all intermediate timesteps"),
  make_option(c("-f", "--save_state"), action="store", default=NA, type='character',
              help="save intermediate simulation state for restore points:
              \tnot set: do not save any state,
              \t\"last\" \t save only the last timestep,
              \t\"all\" \t save all intermediate timesteps"),
  make_option(c("-r", "--redirect_output"), action="store_true", default=FALSE,
              help="print the output to the file [gasm.out] in the output directory"),
  make_option(c("-p", "--enable_profiling"), action="store_true", default=FALSE,
              help="enable profiling [default %default]"),
  make_option(c("-g", "--enable_gc"), action="store_true", default=FALSE,
              help="enable extra garbage colletion steps on memory critical operations"),
  make_option(c("-v", "--verbose"), action="store_true", default=FALSE,
              help="Print extra stuff out [default %default]")
)

parser <- OptionParser(option_list=option_list, add_help_option = TRUE)
opt = parse_args(parser)

if(opt$verbose){
  print("parsed option arguments:")
  print(opt)
}

if(opt$enable_profiling){
  options("keep.source" = TRUE)
}

dir <- gen3sis::prepare_directories(opt$config_file,
                           opt$input_directory,
                           opt$output_directory)

if(opt$redirect_output){
  sink(file = file(file.path(dir$output, "gasm.out"), open = "w"))
}

if(opt$enable_profiling){
  Rprof(filename = file.path(dir$output, "profiling.out"),
        memory.profiling = TRUE,
        gc.profiling = TRUE,
        line.profiling = TRUE)
}

sim <- run_simulation(config = opt$config_file,
                      landscape = opt$input_directory,
                      output_directory = opt$output_directory,
                      save_state = NA,
                      call_observer = "all",
                      enable_gc = opt$enable_gc,
                      verbose = 1)

if(opt$enable_profiling){
  Rprof(NULL)
}

if(opt$redirect_output){
  sink() # close redirect
  closeAllConnections() # force close, bug fix for win/Rstudion
}

# move output folder
if(!is.na(opt$move_output_to_target)){
  target = file.path(opt$move_output_to_target, dir$output)
  dir.create(target, recursive=TRUE, showWarnings = FALSE)
  files <- list.files(dir$output, full.names = T)
  if(all(file.copy(files, target, recursive = T, copy.date = T))){
    unlink(dir$output, recursive = T)
  }
}