Revision 9c8b4de6
Added by Adam Wilson over 11 years ago
climate/procedures/Pleiades.R | ||
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#### Script to facilitate processing of MOD06 data |
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setwd("/nobackupp1/awilso10/mod06") |
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setwd("/nobackupp1/awilso10/mod06")
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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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txbb=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$iv),sep="") |
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save(tb,file="modlandTiles.Rdata") |
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load("modlandTiles.Rdata") |
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## delete temporary log file that can grow to GB |
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system("rm /nobackupp1/awilso10/software/heg/TOOLKIT_MTD/runtime/LogStatus") |
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tile="h11v08" # Venezuela |
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#tile="h11v07" # Venezuela coast |
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#tile="h09v04" # Oregon |
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tile="h21v09" #Kenya |
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### list of tiles to process |
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tiles=c("h11v08","h21v09","h08v04","h09v04","h08v05","h09v05","h20v11","h31v11") |
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tiles=tiles[c(5,7,8)] |
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tile_bb=tb[tb$tile%in%tiles,] |
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### get list of files to process |
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datadir="/nobackupp4/datapool/modis/MOD06_L2.005/" |
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#datadir="/nobackupp1/awilso10/mod06/data" #for data downloaded from |
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outdir=paste("daily/",tile,sep="") |
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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=dbGetQuery(con,paste("SELECT * from swath_geo |
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WHERE east>=",tile_bb$lon_min," AND |
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west<=",tile_bb$lon_max," AND |
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north>=",tile_bb$lat_min," AND |
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south<=",tile_bb$lat_max) |
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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_geo |
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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$id,7,19) |
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... | ... | |
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alldates=unique(fs$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$date,1,4) |
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## identify which have been completed |
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fdone=list.files(outdir,pattern="nc$") |
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done=alldates%in%substr(fdone,14,21) |
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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$path)),14,21) |
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## identify which date-tiles have already been run |
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proclist$done=paste(proclist$tile,proclist$date,sep="_")%in%substr(basename(as.character(fdone$path)),7,21) |
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### report on what has already been processed |
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print(paste(table(done)[2]," out of",length(alldates), |
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"(",round(100*table(done)[2]/length(alldates),1), |
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"%) dates for tile",tile, |
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"have been processed. Breakdown by year of completed days:")) |
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print(table(substr(alldates[done],1,4))) |
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print(paste("Overview of completed tile-days (",round(sum(proclist$done)/nrow(proclist),2),"%)")) |
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table(tile=proclist$tile[proclist$done],year=proclist$year[proclist$done]) |
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#updatedone=F #update the "done" list using the |
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#if(updatedone&exists("fdly")){ #update using table from below |
... | ... | |
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## Identify which dates still need to be processed |
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## This vector will be used to tell mpiexec which days to include |
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notdone=alldates[!done] |
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#notdone=alldates[!done]
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script="/u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r" |
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climatescript="/u/awilso10/environmental-layers/climate/procedures/MOD06_Climatology.r" |
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## write the table processed by mpiexec |
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write.table(paste("--verbose ",script," --date ",notdone," --verbose T --tile \"",tile,"\"",sep=""),file=paste(tile,"_notdone.txt",sep=""),row.names=F,col.names=F,quote=F) |
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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=50:ncpus=8:mpiprocs=8 |
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##PBS -l select=2:ncpus=4:mpiprocs=4 |
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#PBS -l walltime=2:00:00
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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 mod06 |
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#PBS -q devel
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#PBS -q normal
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#PBS -V |
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CORES=400 |
... | ... | |
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source /u/awilso10/.bashrc |
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IDIR=/nobackupp1/awilso10/mod06/ |
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##WORKLIST=$HDIR/var/run/pxrRgrs/work.txt |
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WORKLIST=$IDIR/",tile,"_notdone.txt
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WORKLIST=$IDIR/notdone.txt |
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EXE=Rscript |
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LOGSTDOUT=$IDIR/log/",tile,"_stdout
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LOGSTDERR=$IDIR/log/",tile,"_stderr
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LOGSTDOUT=$IDIR/log/swath_stdout
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LOGSTDERR=$IDIR/log/swath_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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### Now process the climatologies |
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Rscript --verbose ",climatescript," --verbose T --tile \"",tile,"\" |
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",sep=""),file=paste(tile,"_mod06_qsub",sep="")) |
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",sep=""),file=paste("mod06_qsub",sep="")) |
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### Check the file |
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system(paste("cat ",tile,"_mod06_qsub",sep="")) |
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### Check the files |
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system(paste("cat mod06_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 (and keep the pid)!
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system(paste("qsub ",tile,"_mod06_qsub",sep=""))
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## Submit it |
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system(paste("qsub mod06_qsub",sep="")) |
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## work in interactive mode |
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# system("qsub -I -l walltime=2:00:00 -lselect=2:ncpus=16:model=san -q devel") |
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# mpirun -np 1 -r ssh R --no-save |
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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(1,3)] #subset to only some tiles (for example if some aren't finished yet)? |
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climatescript="/u/awilso10/environmental-layers/climate/procedures/MOD06_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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### qsub script |
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cat(paste(" |
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#PBS -S /bin/bash |
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#PBS -l select=1: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 mod06_climate |
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#PBS -q normal |
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#PBS -V |
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CORES=8 |
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HDIR=/u/armichae/pr/ |
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source $HDIR/etc/environ.sh |
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source /u/awilso10/.bashrc |
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IDIR=/nobackupp1/awilso10/mod06/ |
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##WORKLIST=$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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### Now process the climatologies |
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",sep=""),file=paste("mod06_climatology_qsub",sep="")) |
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## check files |
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system(paste("cat mod06_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 mod06_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 ",summarydir,"/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 ",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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#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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Also available in: Unified diff
Updated submit script to process multiple tiles and days in the same batch. Also separated the daily processing from the climatologies