cores_req <- "3"
mem_req <- "1000"
time_req <- "4:00"
queue_req <- "short"
lsfoutfilename <- "lag1.out"
files_path <- file.path("/home", "ngr67a", "ssr-influenza-competition")
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")
phs <- 1:52
datasets <- c("ili_national",
paste0("ili_region", 1:10,))
for(data_set in datasets) {
for(prediction_horizon_limit in phs) {
filename <- paste0(files_path, "/submit-ph", prediction_horizon_limit, "-", data_set, ".sh")
cat(requestCmds, file = filename)
cat("module load R/3.2.1\n", file = filename, append = TRUE)
cat(paste0("R CMD BATCH --vanilla \'--args ", data_set, " ",
prediction_horizon_limit,
"\' ", files_path,
"/inst/estimation/fit-competition-ssr.R output-competition-ssr-ph",
prediction_horizon_limit, "-", data_set, ".Rout"),
file = filename, append = TRUE)
bsubCmd <- paste0("bsub < ", filename)
system(bsubCmd)
}
}
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