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Revision 848e34fd

Added by Adam Wilson about 11 years ago

Submitted global run for 2009

View differences:

climate/procedures/Pleiades_MOD35.R
27 27 
## subset to MODLAND tiles
28 28 
alltiles=system("ls -r MODTILES/ | grep tif$ | cut -c1-6 | sort | uniq - ",intern=T)
29 29 

  		




  
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## or run all tiles


  		




  
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#tiles=alltiles


  		




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


  		




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tiles=tiles[tiles%in%alltiles]


  		




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  ......




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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


  		




  
  44
  
    
##find swaths in region from sqlite database for the specified tile


  		




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


  		




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rebuildswathtable=F


  		




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if(rebuildswathtable){


  		




  ......




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


  		




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}


  		




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load("swathtile.Rdata")


  		




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


  		




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


  		




  75
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  ......




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


  		




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table(tp)


  		




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  121
  
  
    
write.table(paste("--verbose ",script," --date ",proclist$date[tp]," --verbose T --tile ",proclist$tile[tp],sep=""),


  		




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


  		




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


  		




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


  		




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test=F


  		




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if(test){


  		




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  i=2


  		




  128
  
  
    
  time1=system.time(system(paste("Rscript --verbose ",script," --date ",proclist$date[i]," --verbose T --tile ",proclist$tile[i],sep="")))


  		




  129
  
  
    
  hours=round(length(proclist$date[tp])*142/60/60)


  		




  
  131
  
    
  time1=system.time(system(paste("Rscript --verbose ",script," --date ",proclist$date[i]," --profile T --verbose T --tile ",proclist$tile[i],sep="")))


  		




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


  		




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


  		




  131
  
  
    
  hours/400


  		




  132
  
  
    
  print(paste("Based on runtime of previous command, it will take",hours," hours to process the full set"))


  		




  
  134
  
    
  nodes=100


  		




  
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  threads=nodes*8


  		




  
  136
  
    
  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 ###################"))


  		




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}


  		




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### Set up submission script


  		




  
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queue="devel"


  		




  
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queue="normal" #"devel"


  		




  
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nodes=50


  		




  
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walltime=2


  		




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  136
  
  
    
### qsub script


  		




  
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### write qsub script to disk


  		




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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


  		




  140
  
  
    
##PBS -l select=100:ncpus=8:mpiprocs=8


  		




  141
  
  
    
##PBS -l walltime=8:00:00


  		




  142
  
  
    
#PBS -l walltime=2:00:00


  		




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


  		




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


  		




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#PBS -j n


  		




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#PBS -m be


  		




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#PBS -N mod35


  		




  146
  
  
    
##PBS -q normal


  		




  147
  
  
    
#PBS -q devel


  		




  
  153
  
    
#PBS -q ",queue,"


  		




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#PBS -V


  		




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  150
  
  
    
#CORES=800


  		




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CORES=400


  		




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CORES=",nodes*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/environ.sh


  		




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  source /u/awilso10/.bashrc


  		




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IDIR=/nobackupp1/awilso10/mod35/


  		




  158
  
  
    
##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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### 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 | head -n 4",sep=""))


  		




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


  		




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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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## Submit it


  		




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system(paste("qsub mod35_qsub",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=T


  		




  
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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",intern=T)


  		




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## enter JobID here:


  		




  ......




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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


  		




  254
  
  
    
# 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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  261
  
  
    
system("ssh lou")


  		




  
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#system("ssh lou")


  		




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#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/


  		




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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/")


  		




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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/")


  		












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