fdly=data.frame(path=list.files(outdir,pattern="nc$",full=T),stringsAsFactors=F)

  fdly$file=basename(fdly$path)

  fdly$dateid=substr(fdly$file,14,21)

  fdly$month=format(fdly$date,"%m")

  fdly$year=format(fdly$date,"%Y")

nrow(fdly)

## merge all daily files to create a single file with all dates

system(paste(ncopath,"ncrcat -O ",outdir,"/*nc ",outdir2,"/MOD35_",tile,"_daily.nc",sep=""))

system(paste("ncdump -h ",outdir2,"/MOD35_",tile,"_daily.nc",sep=""))

## Update attributes

  nodes=100

  threads=nodes*8

  writeLines(paste(" ################### \n Hours per date-tile:",round(time1[3]/60/60,2),"\n Date-tiles to process:",sum(tp)," \n Estimated CPU time: ",hours,"hours \n  With ",threads,"threads:",round(hours/threads,2),"hours \n ###################"))

}

### Set up submission script

queue="devel"

queue="normal" #"devel"

### write qsub script to disk

cat(paste("

## check which tiles have been processed and are on lou with a filename "MOD35_[tile].nc"

cdone=data.frame(path="",tile="")  #use this if you want to re-run everything

cdone=data.frame(path=sapply(strsplit(basename(

                   system("find summary -name \"MOD35_h[0-9][0-9]v[0-9][0-9].nc\"",intern=T)),split="_"),function(x) x[2]))

cdone$tile=substr(basename(as.character(cdone$path)),1,6)

## enter JobID here:

job="2031668.pbspl1.nas.nasa.gov"

### qsub script

cat(paste("

#PBS -S /bin/bash

#PBS -j n

#PBS -m be

#PBS -N mod35_climate

#PBS -V

",if(delay) paste("#PBS -W depend=afterany:",job,sep="")," 

HDIR=/u/armichae/pr/

  source $HDIR/etc/environ.sh

  source /pleiades/u/awilso10/environ.sh