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35d59dc1
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Adam M. Wilson @ pfe
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#### Script to facilitate processing of MOD06 data
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setwd("/nobackupp1/awilso10/mod35")
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library(rgdal)
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library(raster)
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library(RSQLite)
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verbose=T
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## get MODLAND tile information
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tb=read.table("http://landweb.nascom.nasa.gov/developers/sn_tiles/sn_bound_10deg.txt",skip=6,nrows=648,header=T)
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tb$tile=paste("h",sprintf("%02d",tb$ih),"v",sprintf("%02d",tb$iv),sep="")
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save(tb,file="modlandTiles.Rdata")
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load("modlandTiles.Rdata")
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## delete temporary log file that can grow to GB
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system("rm /nobackupp1/awilso10/software/heg/TOOLKIT_MTD/runtime/LogStatus")
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tile="h11v08" # Venezuela
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#tile="h11v07" # Venezuela coast
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#tile="h09v04" # Oregon
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tile="h21v09" #Kenya
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### list of tiles to process
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tiles=c("h11v08","h21v09","h08v04","h09v04","h08v05","h09v05","h20v11","h31v11")
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tiles=tiles[c(1,4)]
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tile_bb=tb[tb$tile%in%tiles,]
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### get list of files to process
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datadir="/nobackupp4/datapool/modis/MOD35_L2.006/"
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#datadir="/nobackupp1/awilso10/mod06/data" #for data downloaded from
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outdir="daily/" #paste("daily/",tile,sep="")
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##find swaths in region from sqlite database for the specified date/tile
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## path to swath database
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db="/nobackupp4/pvotava/DB/export/swath_geo.sql.sqlite3.db"
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con=dbConnect("SQLite", dbname = db)
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fs=do.call(rbind.data.frame,lapply(1:nrow(tile_bb),function(i){
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d=dbGetQuery(con,paste("SELECT * from swath_geo6
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WHERE east>=",tile_bb$lon_min[i]," AND
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west<=",tile_bb$lon_max[i]," AND
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north>=",tile_bb$lat_min[i]," AND
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south<=",tile_bb$lat_max[i])
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)
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d$tile=tile_bb$tile[i]
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print(paste("Finished tile",tile_bb$tile[i]))
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return(d)
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}))
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con=dbDisconnect(con)
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fs$id=substr(fs$id,7,19)
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### Identify which swaths are available in the datapool
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swaths=data.frame(path=list.files(datadir,pattern=paste("hdf$"),recursive=T,full=T),stringsAsFactors=F) #all swaths in data pool
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swaths$id=substr(basename(swaths$path),10,22)
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fs$exists=fs$id%in%swaths$id
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fs$path=swaths$path[match(fs$id,swaths$id)]
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if(verbose) print(paste("###############",nrow(fs)," swath IDs recieved from database"))
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## get all unique dates
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fs$dateid=format(as.Date(paste(fs$year,fs$day,sep=""),"%Y%j"),"%Y%m%d")
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alldates=unique(fs$dateid[fs$exists])
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#### Generate submission file
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alldates=format(seq(as.Date("2000-03-01"),as.Date("2011-12-31"),1),"%Y%m%d")
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proclist=expand.grid(date=alldates,tile=tiles)
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proclist$year=substr(proclist$date,1,4)
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## identify which have been completed
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fdone=data.frame(path=list.files(outdir,pattern="nc$",recursive=T))
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fdone$date=substr(basename(as.character(fdone$path)),14,21)
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fdone$tile=substr(basename(as.character(fdone$path)),7,12)
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## identify which date-tiles have already been run
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proclist$done=paste(proclist$tile,proclist$date,sep="_")%in%substr(basename(as.character(fdone$path)),7,21)
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### report on what has already been processed
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print(paste(sum(!proclist$done)," out of ",nrow(proclist)," (",round(100*sum(!proclist$done)/nrow(proclist),2),"%) remain"))
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table(tile=proclist$tile[proclist$done],year=proclist$year[proclist$done])
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script="/u/awilso10/environmental-layers/climate/procedures/MOD35_L2_process.r"
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## write the table processed by mpiexec
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write.table(paste("--verbose ",script," --date ",proclist$date[!proclist$done]," --verbose T --tile ",proclist$tile[!proclist$done],sep=""),
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file=paste("notdone.txt",sep=""),row.names=F,col.names=F,quote=F)
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### qsub script
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cat(paste("
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#PBS -S /bin/bash
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#PBS -l select=50:ncpus=8:mpiprocs=8
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##PBS -l select=2:ncpus=8:mpiprocs=8
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##PBS -l select=2:ncpus=4:mpiprocs=4
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#PBS -l walltime=5:00:00
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#PBS -j n
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#PBS -m be
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#PBS -N mod35
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#PBS -q normal
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#PBS -V
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CORES=400
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HDIR=/u/armichae/pr/
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# source $HDIR/etc/environ.sh
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source /u/awilso10/environ.sh
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source /u/awilso10/.bashrc
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IDIR=/nobackupp1/awilso10/mod35/
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##WORKLIST=$HDIR/var/run/pxrRgrs/work.txt
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WORKLIST=$IDIR/notdone.txt
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EXE=Rscript
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LOGSTDOUT=$IDIR/log/mod35_stdout
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LOGSTDERR=$IDIR/log/mod35_stderr
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### use mpiexec to parallelize across days
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mpiexec -np $CORES pxargs -a $WORKLIST -p $EXE -v -v -v --work-analyze 1> $LOGSTDOUT 2> $LOGSTDERR
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",sep=""),file=paste("mod35_qsub",sep=""))
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### Check the files
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system(paste("cat mod35_qsub",sep=""))
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system(paste("cat notdone.txt | head",sep=""))
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system(paste("cat notdone.txt | wc -l ",sep=""))
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## Submit it
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system(paste("qsub mod35_qsub",sep=""))
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#######################################################
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### Now submit the script to generate the climatologies
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tiles
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ctiles=tiles[c(2)] #subset to only some tiles (for example if some aren't finished yet)?
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climatescript="/u/awilso10/environmental-layers/climate/procedures/MOD35_Climatology.r"
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## write the table processed by mpiexec
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write.table(paste("--verbose ",climatescript," --verbose T --tile ",ctiles,sep=""),
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file=paste("notdone_climate.txt",sep=""),row.names=F,col.names=F,quote=F)
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## delay start until previous jobs have finished?
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delay=F
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## check running jobs to get JobID of job you want to wait for
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system("qstat -u awilso10")
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## enter JobID here:
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job="881394.pbspl1.nas.nasa.gov"
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### qsub script
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cat(paste("
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#PBS -S /bin/bash
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##PBS -l select=50:ncpus=8:mpiprocs=8
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#PBS -l select=4:ncpus=4:mpiprocs=4
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#PBS -l walltime=2:00:00
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#PBS -j n
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#PBS -m be
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#PBS -N mod35_climate
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#PBS -q devel
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#PBS -V
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",if(delay) paste("#PBS -W depend=afterany:",job,sep=""),"
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CORES=16
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HDIR=/u/armichae/pr/
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# source $HDIR/etc/environ.sh
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source /u/awilso10/environ.sh
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source /u/awilso10/.bashrc
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IDIR=/nobackupp1/awilso10/mod35/
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##WORKLIST=$HDIR/var/run/pxrRgrs/work.txt
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WORKLIST=$IDIR/notdone_climate.txt
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EXE=Rscript
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LOGSTDOUT=$IDIR/log/climatology_stdout
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LOGSTDERR=$IDIR/log/climatology_stderr
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### use mpiexec to parallelize across days
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mpiexec -np $CORES pxargs -a $WORKLIST -p $EXE -v -v -v --work-analyze 1> $LOGSTDOUT 2> $LOGSTDERR
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",sep=""),file=paste("mod35_climatology_qsub",sep=""))
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## check files
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system(paste("cat mod35_climatology_qsub",sep="")) #qsub submission script
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system(paste("cat notdone_climate.txt | head",sep="")) #top of job file
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system(paste("cat notdone_climate.txt | wc -l ",sep="")) #number of jobs to be run
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## Submit it
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system(paste("qsub mod35_climatology_qsub",sep=""))
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## check progress
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system("qstat -u awilso10")
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## start interactive job on compute node for debugging
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# system("qsub -I -l walltime=2:00:00 -lselect=2:ncpus=16:model=san -q devel")
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#################################################################
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### copy the files back to Yale
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summarydir="summary"
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sumfiles=list.files("summary",pattern="^MOD06_.*[0-9][.]nc",full=T)
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system(paste("scp ",paste(sumfiles,collapse=" ")," adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod06/summary",sep=""))
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#system(paste("scp ",tsdir,"/MOD06_",tile,"*.nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod06/summary",sep=""))
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#system(paste("scp ",paste(fs$path[40421:40422],collapse=" ")," adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/mod06/swaths",sep=""))
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