for(setting in c("freeliving")) {
for(location in c("ankle", "hip", "wrist")) {
# for(location in c("ankle")) {
for(class_var in c("y_intensity")) {
# for(fit_method in c("RFCRF", "parametricBoostCRF", "baggedFeatureSubsetGradientTreeBoostCRF")) {
for(fit_method in c("parametricBoostCRF")) {
# for(fit_method in c("RFCRF")) {
# set memory and processig time requirements for each method
if(identical(fit_method, "RFCRF")) {
cores_req <- "10"
mem_req <- "12000"
time_req <- "4:00"
queue_req <- "short"
} else if(identical(fit_method, "RFCRFseqbag")) {
cores_req <- "10"
mem_req <- "12000"
time_req <- "4:00"
queue_req <- "short"
} else if(identical(fit_method, "baggedFeatureSubsetGradientTreeBoostCRF")) {
cores_req <- "10"
mem_req <- "20000"
time_req <- "48:00"
queue_req <- "long"
} else if(identical(fit_method, "parametricBoostCRF")) {
cores_req <- "10"
mem_req <- "5000"
time_req <- "48:00"
queue_req <- "long"
} else if(identical(fit_method, "L2RegularizedCRF")) {
cores_req <- "10"
mem_req <- "5000"
time_req <- "48:00"
queue_req <- "long"
} else if(identical(fit_method, "gradientTreeBoostCRF")) {
cores_req <- "10"
mem_req <- "15000"
time_req <- "48:00"
queue_req <- "long"
} else if(identical(fit_method, "normalHMM")) {
cores_req <- "1"
mem_req <- "8000"
time_req <- "4:00"
queue_req <- "short"
}
for(reduced_trans_mat_parameterization in c(FALSE)) {
if(reduced_trans_mat_parameterization) {
update_trans_levels <- TRUE
} else {
update_trans_levels <- TRUE
}
for(update_trans in update_trans_levels) {
files_path <- file.path("/home", "er71a", "HMMapplication", "Sasaki", "intensity", setting, "2stage", "stage2", location, class_var, fit_method)
setwd(files_path)
basefilename <- "run_method_ShScript"
lsfoutfilename <- "lsfOutput_"
Routbasefilename <- "sasakiLOSOcrossval"
if(reduced_trans_mat_parameterization) {
basefilename <- paste0(basefilename, "ReducedTrans")
lsfoutfilename <- paste0(lsfoutfilename, "ReducedTrans")
Routbasefilename <- paste0(Routbasefilename, "ReducedTrans")
} else {
basefilename <- paste0(basefilename, "FullTrans")
lsfoutfilename <- paste0(lsfoutfilename, "FullTrans")
Routbasefilename <- paste0(Routbasefilename, "FullTrans")
}
if(!update_trans) {
basefilename <- paste0(basefilename, "NoUpdate")
lsfoutfilename <- paste0(lsfoutfilename, "NoUpdate")
Routbasefilename <- paste0(Routbasefilename, "NoUpdate")
}
basefilename <- paste0(basefilename, "_subject")
lsfoutfilename <- paste0(lsfoutfilename, ".out")
Routbasefilename <- paste0(Routbasefilename, "_subject")
requestCmds <- "#!/bin/bash\n"
requestCmds <- paste0(requestCmds, "#BSUB -n ", cores_req, " # how many cores we want for our job\n")
requestCmds <- paste0(requestCmds, "#BSUB -R span[hosts=1] # ask for all the cores on a single machine\n")
requestCmds <- paste0(requestCmds, "#BSUB -R rusage[mem=", mem_req, "] # ask for memory\n")
requestCmds <- paste0(requestCmds, "#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")
if(identical(setting, "freeliving")) {
N <- 15
}
for(subject in seq_len(N)) {
# for(subject in c(2)) {
filename <- paste0(files_path, "/", basefilename, subject, ".sh")
cat(requestCmds, file = filename)
cat("module load R/3.0.2\n", file = filename, append = TRUE)
cat(paste0("R CMD BATCH --vanilla \'--args ", subject, " ", setting, " ", location, " ", class_var, " ", fit_method, " ", reduced_trans_mat_parameterization, " ", update_trans,
"\' /home/er71a/HMMapplication/Sasaki/intensity/sasakiLOSOcrossval_2stage_stage2.R ", Routbasefilename, subject, ".Rout"),
file = filename, append = TRUE)
bsubCmd <- paste0("bsub < ", filename)
system(bsubCmd)
}
}
}
}
}
}
}
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