Simulation/Cluster_mayo.R

In jchen1981/OrderShapeEM: Optimal false discovery rate control using auxiliary (order) information based on a shape-constrained EM algorithm

clsapply <- function(dat, func, df=NULL, tempdir="~/project/tempZ",
		queque="1-day", timespan="540", mem="8G", req.pack='stats',
		tidy=F) {
	# Apply to the row of dat by default (dim=2 for column)
	# Create temp dir
	if (!file.exists(tempdir)) {
		dir.create(tempdir)
	}
	setwd(tempdir)
	
	save(dat, func, df, file=("dat.RData"))
	
	nJob <- length(dat)
	# Create R script
	txt <- paste('
					args=(commandArgs(TRUE))
					if(length(args)==0){
						print("No arguments supplied.")
						##supply default values
					} else{
						for(i in 1:length(args)){
						eval(parse(text=args[[i]]))
					}
				}',
			paste(paste0('\nrequire(',req.pack, ')'), collapse="\n"),    
			'\n date()
					load("dat.RData")	
					if (is.list(dat)) {
						item <- dat[[part]]
					} 
					if (is.vector(dat)) {
						item <- dat[part]
					}           
					res0 <- func(item, df)
					save(res0, file=paste(part, ".res", sep=""))
					date()
			')
	writeLines(txt, "script.R")
	
	# Submit job
	cat("Submit jobs ...")
	prefix <- paste(c("J", sample(LETTERS, 4, repl=TRUE)), collapse="")
	for (part in 1:nJob) {
		rfile <- "script.R"
		rout <- paste(part, ".Rout", sep="")
			
		sh <- paste(
				"qsub",
				paste0("-N ", prefix, part),
				"-j y",
				"-cwd",
	#			"-t", timespan,
				"-q", queque,
				"-m abe",
				paste0("-l h_vmem=", mem),
				"-V",
				paste("-o ",  part, ".out", sep=""),
				paste("-e ",  part, ".err", sep=""),
				"-b y",
				paste("\'R CMD BATCH --no-save --no-restore \"--args  part=", part, "\" ", 
						rfile, " ", rout, "\'", sep="")
		)
		print(sh)
		system(sh)
	}
##	sbatch -J RP -t 240 -p general --mem 64000 -o RP.out -e RP.err --wrap='R CMD BATCH --no-save --no-restore ROC_SVA_PCA_ResultProcess_alpha.R RP.Rout'
#	cat("Please wait ...\n")
#	# To see if all the jobs have been finished
#	while (TRUE) {
#		Sys.sleep(20)
#		output1 <- system("qstat ", intern=TRUE)
#		output2 <- system("qstat ", intern=TRUE)
#		missingfile <- NULL
#		if (length(grep(prefix, output1)) == 0 & length(grep(prefix, output2)) == 0) {	
#			cat("All jobs finished and begin to combine\n")
#			res <- NULL
#			for (part in 1:nJob) {
#				resfile <- paste(part, ".res", sep="")
#				if (file.exists(resfile)) {
#					load(resfile)
#					res[[paste(part)]] <-  res0
#					rm(res0)
#					cat(".")
#				} else {
#					# cat("\n", resfile, " not found!\n")
#					missingfile <- c(missingfile, resfile)
#				}
#			}
#			cat("\n")
#			break
#		}
#		gc()
#	}
#	
#	cat("Missing files:\n")
#	if (length(missingfile) == 0) {
#		cat("No jobs dropped!\n")
#	} else{
#		cat(paste(missingfile, collapse="\n"))
#	} 
#	# Clean
#	if (tidy == TRUE) {
#		cat("\nBegin to tidy up ...")
#		system("rm *")
#	}
#	cat("\nDone!\n")
#	return(res)
}

#resdir <- "~/project/orderfdr/Sim9.4"
#setwd(resdir)
#missingfile <- NULL
#res <- NULL
#nJob <- 100
#for (part in 1:nJob) {
#	resfile <- paste('./tmpC/', part, ".res", sep="")
#	if (file.exists(resfile)) {
#		load(resfile)
#		res[[paste(part)]] <-  res0
#		rm(res0)
#		cat(".")
#	} else {
#		# cat("\n", resfile, " not found!\n")
#		missingfile <- c(missingfile, resfile)
#	}
#}
#
#cat("Missing files:\n")
#if (length(missingfile) == 0) {
#	cat("No jobs dropped!\n")
#} else{
#	cat(paste(missingfile, collapse="\n"))
#} 
#
#save(res, file=file.path(resdir, paste('Sim9.4', "_res.Rdata", sep="")))