options(warn = 2)
all_prediction_targets <- c(#'Season_onset',
'Season_peak_week',
# 'Season_peak_percentage',
'1_wk_ahead'#,
# '2_wk_ahead',
# '3_wk_ahead',
# '4_wk_ahead'
)
#all_regions <- "National"
#all_prediction_targets <- "onset"
cores_req <- "4"
mem_req <- "15000"
time_req <- "360:00"
#queue_req <- "condo_uma_nicholas_reich"
queue_req <- "long"
for(prediction_target in all_prediction_targets) {
output_path <- "/home/er71a/2018-2019-cdc-flu-contest/inst/estimation/region-stacking/cluster-output"
lsfoutfilename <- "adaptively-weighted-ensemble-xgb-stack-est.out"
case_descriptor <- paste0(
"prediction_target_", prediction_target
)
filename <- paste0(output_path, "/submit-stacking-estimation-step-", case_descriptor, ".sh")
requestCmds <- "#!/bin/bash\n"
requestCmds <- paste0(requestCmds, "#BSUB -n ", cores_req, " # how many cores we want for our job\n",
"#BSUB -R span[hosts=1] # ask for all the cores on a single machine\n",
"#BSUB -R rusage[mem=", mem_req, "] # ask for memory\n",
"#BSUB -o ", lsfoutfilename, " # log LSF output to a file\n",
"#BSUB -W ", time_req, " # run time\n",
"#BSUB -q ", queue_req, " # which queue we want to run in\n")
cat(requestCmds, file = filename)
cat("module load openmpi/2.0.1\n", file = filename, append = TRUE)
cat("module load R/3.2.2\n", file = filename, append = TRUE)
cat(paste0("R CMD BATCH --vanilla \'--args ",
prediction_target, " ",
cores_req,
"\' /home/er71a/2018-2019-cdc-flu-contest/inst/estimation/region-stacking/stacking_estimation.R ",
output_path, "/output-stacking-estimation-", case_descriptor, ".Rout"),
file = filename, append = TRUE)
bsubCmd <- paste0("bsub < ", filename)
system(bsubCmd)
} # prediction_target
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