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Revision 0bddce86

Added by Adam Wilson about 12 years ago

Script now runs except ncap2 is missing from the nco module

View differences:

climate/procedures/Pleiades.R
1 1 
#### Script to facilitate processing of MOD06 data
2 2 

  		




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setwd("/nobackupp1/awilso10/mod06")


  		




  
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library(rgdal)


  		




  
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library(raster)


  		




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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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tile="h11v08"   #can move this to submit script if needed


  		




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script="/u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r"


  		




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#write.table(paste("--verbose ",script," date=",notdone," tile=\"",tile,"\"",sep=""),file="notdone.txt",row.names=F,col.names=F,quote=F)


  		




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write.table(paste("--verbose ",script," date=",notdone[1:30],sep=""),file="notdone.txt",row.names=F,col.names=F,quote=F)


  		




  
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#write.table(paste("--verbose ",script," date=",notdone[1:30],sep=""),file="notdone.txt",row.names=F,col.names=F,quote=F)


  		




  
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write.table(notdone[1:30],file="notdone.txt",row.names=F,col.names=F,quote=F)


  		




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save(fs,alldates,gridfile,td,file="allfiles.Rdata")


  		




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## run script


  		




  
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cat(paste("


  		




  
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#! /bin/bash


  		




  
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source ~/moduleload


  		




  
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source ~/.bashrc


  		




  
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Rscript --verbose --vanilla /u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r date=$1


  		




  
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#Rscript --verbose --vanilla rtest


  		




  
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",sep=""),file="MOD06_process2")


  		




  
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system("chmod +x MOD06_process2")


  		




  
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cat(paste("


  		




  
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library(rgdal)


  		




  
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GDALinfo


  		




  
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",sep=""),file="rtest")


  		




  
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## Submission script


  		




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cat(paste("


  		




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## export a few important variables


  		




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  export NNODES=32


  		




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  export R_LIBS=\"/u/awilso10/R/x86_64-unknown-linux-gnu-library/2.15/\"


  		




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## load modules


  		




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#  module load gcc comp-intel/2012.0.032 netcdf mpi-sgi/mpt.2.06r6 hdf4 udunits R nco


  		




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## Run the script!


  		




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## current version not parallelizing across nodes!


  		




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  TMPDIR=$TMPDIR Rscript --verbose --vanilla /u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r date=20000403


  		




  
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#  TMPDIR=$TMPDIR Rscript --verbose --vanilla /u/awilso10/environmental-layers/climate/procedures/MOD06_L2_process.r date=20000403


  		




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WORKLIST=notdone.txt


  		




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EXE="Rscript"


  		




  
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#EXE=\"Rscript\"


  		




  
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EXE="./MOD06_process2"


  		




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LOG=log/log_DataCompile.log


  		




  
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MQUEUE=/nobackupp4/pvotava/software/share/mqueue-eg/mqueue/mqueue


  		




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TMPDIR=$TMPDIR mpiexec -np $NNODES  /nobackupp4/pvotava/software/share/mqueue-eg/mqueue/mqueue -l $WORKLIST -p $EXE -v -v -v --random-starts 2-4 --work-analyze #> $LOG


  		




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#mpiexec -np 2  /nobackupp4/pvotava/software/share/mqueue-eg/mqueue/mqueue -l testrun.txt -p $EXE -v -v -v  #> $LOG


  		




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#TMPDIR=$TMPDIR mpiexec -np $NNODES  /nobackupp4/pvotava/software/share/mqueue-eg/mqueue/mqueue -l $WORKLIST -p $EXE -v -v -v #> $LOG


  		




  
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TMPDIR=$TMPDIR mpiexec -np $NNODES $MQUEUE -l $WORKLIST -p $EXE -v -v -v --random-starts 2-4 --work-analyze #> $LOG


  		




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exit 0


  		




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",sep=""),file="MOD06_process")


  		




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  ......




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## check queue status


  		




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system("/u/scicon/tools/bin/node_stats.sh")


  		




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system("/u/scicon/tools/bin/qtop.pl 479343")


  		




  
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system("/u/scicon/tools/bin/qtop.pl 492352")


  		




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## Submit it (and keep the pid)!


  		




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system("qsub MOD06_process")


  		




  
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system("/u/scicon/tools/bin/pdsh_gdb -j 493281 -d tmp -s -u awilso10")


  		




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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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