#### Script to facilitate processing of MOD06 data

### This script is meant to be run iteratively, rather than unsupervised. There are several steps that require manual checking (such as choosing the number of cores, etc.)

## working directory

setwd("/nobackupp1/awilso10/mod35")

## load libraries

library(rgdal)

library(raster)

library(RSQLite)

## flag to increase verbosity of output

verbose=T

## get MODLAND tile information

tb=read.table("http://landweb.nascom.nasa.gov/developers/sn_tiles/sn_bound_10deg.txt",skip=6,nrows=648,header=T)

tb$tile=paste("h",sprintf("%02d",tb$ih),"v",sprintf("%02d",tb$iv),sep="")

tb=tb[tb$lon_min!=-999,]

save(tb,file="modlandTiles.Rdata")

load("modlandTiles.Rdata")

## Choose some tiles to process

### list of tiles to process

tiles=c("h10v08","h11v08","h12v08","h10v07","h11v07","h12v07")  # South America

## or a northern block of tiles

tiles=apply(expand.grid(paste("h",11:17,sep=""),v=c("v00","v01","v02","v03","v04")),1,function(x) paste(x,collapse="",sep=""))

## subset to MODLAND tiles

alltiles=system("ls -r MODTILES/ | grep tif$ | cut -c1-6 | sort | uniq - ",intern=T)

## or run all tiles

tiles=alltiles

## subset to tiles in global region (not outside global boundary in sinusoidal projection)

tiles=tiles[tiles%in%alltiles]

## subset tile corner matrix to tiles selected above

tile_bb=tb[tb$tile%in%tiles,]

### get list of files to process

datadir="/nobackupp4/datapool/modis/MOD35_L2.006/"

outdir="daily/" #paste("daily/",tile,sep="")

##find swaths in region from sqlite database for the specified tile

## this takes a while, about 30 minutes, so only rebuild if you need to update what's available...

rebuildswathtable=F

if(rebuildswathtable){

  ## path to swath database

  db="/nobackupp4/pvotava/DB/export/swath_geo.sql.sqlite3.db"

  con=dbConnect("SQLite", dbname = db)

  fs=do.call(rbind.data.frame,lapply(1:nrow(tile_bb),function(i){

    d=dbGetQuery(con,paste("SELECT * from swath_geo6

            WHERE east>=",tile_bb$lon_min[i]," AND

                  west<=",tile_bb$lon_max[i]," AND

                  north>=",tile_bb$lat_min[i]," AND

                  south<=",tile_bb$lat_max[i])

      )

    d$tile=tile_bb$tile[i]

    print(paste("Finished tile",tile_bb$tile[i]))

    return(d)

  }))

  con=dbDisconnect(con)

  fs$id=substr(fs$id,7,19)

  ## Identify which swaths are available in the datapool

  swaths=data.frame(path=list.files(datadir,pattern=paste("hdf$"),recursive=T,full=T),stringsAsFactors=F)  #all swaths in data pool

  swaths$id=substr(basename(swaths$path),10,22)

  fs$exists=fs$id%in%swaths$id 

  fs$path=swaths$path[match(fs$id,swaths$id)]

  ## write tile-swath list to disk

  save(fs,swaths,file="swathtile.Rdata")

}

if(!exists("fs")) load("swathtile.Rdata")

if(verbose) print(paste("###############",nrow(fs)," swath IDs recieved from database"))

## get all unique dates

fs$dateid=format(as.Date(paste(fs$year,fs$day,sep=""),"%Y%j"),"%Y%m%d")

#alldates=unique(fs$dateid[fs$exists])

#### Generate submission file

startdate="2000-03-01"

stopdate="2011-12-31"

## just 2005-2010

startdate="2009-01-01"

stopdate="2009-12-31"

alldates=format(seq(as.Date(startdate),as.Date(stopdate),1),"%Y%m%d")

proclist=expand.grid(date=alldates,tile=tiles)

proclist$year=substr(proclist$date,1,4)

 ## identify tile-dates with no available swaths

avail=unique(cbind.data.frame(tile=fs$tile,date=fs$dateid)[fs$exists, ])

proclist$avail=paste(proclist$tile,proclist$date,sep="_")%in%paste(avail$tile,avail$date,sep="_")

## identify which have been completed

#fdone=data.frame(path=system("ssh lou 'find MOD35/daily -name \"*.nc\"' ",intern=T))

fdone=data.frame(path=list.files(outdir,pattern="nc$",recursive=T))

fdone$date=substr(basename(as.character(fdone$path)),14,21)

fdone$tile=substr(basename(as.character(fdone$path)),7,12)

proclist$done=paste(proclist$tile,proclist$date,sep="_")%in%substr(basename(as.character(fdone$path)),7,21)

### report on what has already been processed

print(paste(sum(!proclist$done)," out of ",nrow(proclist)," (",round(100*sum(!proclist$done)/nrow(proclist),2),"%) remain"))

stem(table(tile=proclist$tile[proclist$done],year=proclist$year[proclist$done]))

#table(tile=proclist$tile[proclist$done],year=proclist$year[proclist$done])

table(table(tile=proclist$tile[!proclist$done],year=proclist$year[!proclist$done]))

### explore tile counts

#x=table(tile=proclist$tile[proclist$done],year=proclist$year[proclist$done])

#x=x[order(rownames(x)),]

script="/u/awilso10/environmental-layers/climate/procedures/MOD35_L2_process.r"

## write the table processed by mpiexec

tp=T  # rerun everything

tp=((!proclist$done)&proclist$avail)  #date-tiles to process

table(Available=proclist$avail,Completed=proclist$done)

table(tp)

write.table(paste("--verbose ",script," --date ",proclist$date[tp]," --verbose T --profile F --tile ",proclist$tile[tp],sep=""),

file=paste("notdone.txt",sep=""),row.names=F,col.names=F,quote=F)

## try running it once for a single tile-date to get estimate of time/tile-day

test=F

if(test){

  i=2

  time1=system.time(system(paste("Rscript --verbose ",script," --date ",proclist$date[i]," --profile T --verbose T --tile ",proclist$tile[i],sep="")))

  hours=round(length(proclist$date[tp])*142/60/60); hours

  hours=round(length(proclist$date[tp])*time1[3]/60/60,1); hours

  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 ###################"))

  summaryRprof("/nobackupp1/awilso10/mod35/log/profile.out")

}

### Set up submission script

queue="devel"

queue="normal" #"devel"

queue="long" #"devel"

nodes=120

walltime=2

### write qsub script to disk

cat(paste("

#PBS -S /bin/bash

#PBS -l select=",nodes,":ncpus=8:mpiprocs=8

#PBS -l walltime=",walltime,":00:00

#PBS -j n

#PBS -m be

#PBS -N mod35

#PBS -q ",queue,"

#PBS -V

CORES=",nodes*8,"

HDIR=/u/armichae/pr/

  source $HDIR/etc/environ.sh

  source /u/awilso10/environ.sh

  source /u/awilso10/.bashrc

IDIR=/nobackupp1/awilso10/mod35/

WORKLIST=$IDIR/notdone.txt

EXE=Rscript

LOGSTDOUT=$IDIR/log/mod35_stdout

LOGSTDERR=$IDIR/log/mod35_stderr

### use mpiexec to parallelize across days

mpiexec -np $CORES pxargs -a $WORKLIST -p $EXE -v -v -v --work-analyze 1> $LOGSTDOUT 2> $LOGSTDERR

",sep=""),file=paste("mod35_qsub",sep=""))

### Check the files

system(paste("cat mod35_qsub",sep=""))

system(paste("cat notdone.txt | head -n 4",sep=""))

system(paste("cat notdone.txt | wc -l ",sep=""))

## start interactive job on compute node for debugging

# system("qsub -I -l walltime=2:00:00 -lselect=2:ncpus=16:model=san -q devel")

## Submit it

system(paste("qsub mod35_qsub",sep=""))

system("qstat -u awilso10")

#######################################################

### Now submit the script to generate the climatologies

## report 'mostly' finished tiles

## this relies on proclist above so be sure to update above before running

md=table(tile=proclist$tile[!proclist$done],year=proclist$year[!proclist$done])

mdt=names(md[md<10,])

tiles=mdt

tiles

ctiles=c("h10v08","h11v08","h12v08","h10v07","h11v07","h12v07")  # South America

ctiles=tiles#[c(1:3)]  #subset to only some tiles (for example if some aren't finished yet)?

climatescript="/pleiades/u/awilso10/environmental-layers/climate/procedures/MOD35_Climatology.r"

## 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("ssh lou 'find MOD35/summary -name \"MOD35_h[0-9][0-9]v[0-9][0-9].nc\"' ",intern=T)),split="_"),function(x) x[2]))

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)

print(paste(length(ctiles[!ctiles%in%cdone$tile]),"Tiles still need to be processed"))

## write the table processed by mpiexec

write.table(paste("--verbose ",climatescript," --verbose T --tile ",ctiles[!ctiles%in%cdone$tile],sep=""),

file=paste("notdone_climate.txt",sep=""),row.names=F,col.names=F,quote=F)

## delay start until previous jobs have finished?

delay=F

## check running jobs to get JobID of job you want to wait for

system("qstat -u awilso10",intern=T)

## enter JobID here:

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

queue="devel"

nodes=1

walltime=2

### qsub script

cat(paste("

#PBS -S /bin/bash

#PBS -l select=",nodes,":ncpus=8:mem=94

#PBS -l walltime=",walltime,":00:00

#PBS -j n

#PBS -m be

#PBS -N mod35_climate

#PBS -q ",queue,"

#PBS -V

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

CORES=",nodes*8,"

HDIR=/u/armichae/pr/

  source $HDIR/etc/environ.sh

  source /pleiades/u/awilso10/environ.sh

  source /pleiades/u/awilso10/.bashrc

IDIR=/nobackupp1/awilso10/mod35/

##WORKLIST=$HDIR/var/run/pxrRgrs/work.txt

WORKLIST=$IDIR/notdone_climate.txt

EXE=Rscript

LOGSTDOUT=$IDIR/log/climatology_stdout

LOGSTDERR=$IDIR/log/climatology_stderr

### use mpiexec to parallelize across tiles

mpiexec -np $CORES pxargs -a $WORKLIST -p $EXE -v -v -v --work-analyze 1> $LOGSTDOUT 2> $LOGSTDERR

",sep=""),file=paste("mod35_climatology_qsub",sep=""))

## check files

system(paste("cat mod35_climatology_qsub",sep=""))        #qsub submission script

system(paste("cat notdone_climate.txt | head",sep=""))    #top of job file

system(paste("cat notdone_climate.txt | wc -l ",sep=""))  #number of jobs to be run

## Submit it

system(paste("qsub mod35_climatology_qsub",sep=""))

## check progress

system("qstat -u awilso10")

#################################################################

### copy the files back to Yale

#system("ssh lou")

#scp `find MOD35/summary -name "MOD35_h[0-9][0-9]v[0-9][0-9].nc"` adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod35/summary/

system("rsync -cavv `find summary -name \"MOD35_h[0-9][0-9]v[0-9][0-9]_mean.nc\"` adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod35/summary/")

system("rsync -cavv `find summary -name \"MOD35_h[0-9][0-9]v[0-9][0-9].nc\"` adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod35/summary/")

system("gdalbuildvrt MOD35C6_2009.vrt summary/*2009mean.nc ") 

system("gdal_translate -stats -co \"COMPRESS=LZW\" -of GTiff MOD35C6_2009.vrt MOD35C6_2009.tif ")              

system("scp MOD35C6_2009.tif adamw@acrobates.eeb.24.177.10.190:/Users/adamw/Downloads/")

exit