Revision 07f76f37
Added by Adam Wilson almost 12 years ago
| climate/procedures/Pleiades.R | ||
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| 42 | 42 |
table(done) |
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notdone=alldates[!done] #these are the dates that still need to be processed |
| 44 | 44 |
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if(exists("fdly")){
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notdone=notdone[notdone%in%fdly$dateid[is.na(fdly$npar)]] |
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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," --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(notdone[1:30],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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#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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#",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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#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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#PBS -S /bin/bash |
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#PBS -l select=2:ncpus=16:model=san |
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###PBS -l select=4:ncpus=8:model=neh |
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##PBS -l select=1:ncpus=12:model=wes |
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####### old: select=48:ncpus=8:mpiprocs=8:model=neh |
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#PBS -l walltime=2:00:00 |
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#PBS -j oe |
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#PBS -m e |
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#PBS -V |
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#PBS -q devel |
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#PBS -o log/log_^array_index^ |
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#PBS -o log/log_DataCompile.log |
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#PBS -M adam.wilson@yale.edu |
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#PBS -N MOD06 |
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#cat(paste("
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##PBS -S /bin/bash
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##PBS -l select=2:ncpus=16:model=san
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####PBS -l select=4:ncpus=8:model=neh
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###PBS -l select=1:ncpus=12:model=wes
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######## old: select=48:ncpus=8:mpiprocs=8:model=neh
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##PBS -l walltime=2:00:00
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##PBS -j oe
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##PBS -m e
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##PBS -V
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##PBS -q devel
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##PBS -o log/log_^array_index^
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##PBS -o log/log_DataCompile.log
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##PBS -M adam.wilson@yale.edu
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##PBS -N MOD06
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## cd to working directory |
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cd /nobackupp1/awilso10/mod06 |
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#cd /nobackupp1/awilso10/mod06
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## set some memory limits |
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# ulimit -d 1500000 -m 1500000 -v 1500000 #limit memory usage |
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source /usr/local/lib/global.profile |
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source /u/awilso10/.bashrc |
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source /u/awilso10/moduleload |
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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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## Run the script! |
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# source /usr/local/lib/global.profile
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# source /u/awilso10/.bashrc
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# source /u/awilso10/moduleload
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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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### 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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WORKLIST=notdone.txt |
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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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#WORKLIST=notdone.txt |
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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 $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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### simplified qsub script |
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cat(paste("
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#PBS -S /bin/bash |
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#PBS -l select=48:ncpus=8:mpiprocs=8 |
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##PBS -l select=2:ncpus=4:mpiprocs=4 |
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#PBS -l walltime=02:00:00 |
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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 -V |
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CORES=384 |
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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=$IDIR/notdone.txt |
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EXE=Rscript |
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LOGSTDOUT=$IDIR/log/log.stdout |
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LOGSTDERR=$IDIR/log/log.stderr |
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mpiexec -np $CORES pxargs -a $WORKLIST -p $EXE -v -v -v --work-analyze 1> $LOGSTDOUT 2> $LOGSTDERR |
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"),file="mod06_qsub") |
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TMPDIR=$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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### Check the file |
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system("cat MOD06_process")
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system("cat mod06_qsub")
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#system("cat ~/environmental-layers/climate/procedures/MOD06_L2_process.r")
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## check queue status |
| ... | ... | |
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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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system("qsub mod06_qsub")
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system("/u/scicon/tools/bin/pdsh_gdb -j 568835 -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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| ... | ... | |
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## check progress |
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system("qstat -u awilso10")
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system(paste("/u/scicon/tools/bin/qps ",pid))
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system(paste("/u/scicon/tools/bin/qps ",568835))
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system(paste("qstat -t -x",pid))
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system("qstat devel ")
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| ... | ... | |
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fdly=data.frame( |
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path=list.files(outdir,pattern="nc$",full=T), |
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file=list.files(outdir,pattern="nc$")) |
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fdly$date=as.Date(substr(fdly$file,7,14),"%Y%m%d") |
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fdly$month=format(fdly$date,"%m") |
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fdly$year=format(fdly$date,"%Y") |
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fdly$dateid=substr(fdly$file,7,14) |
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fdly$date=as.Date(substr(fdly$file,7,14),"%Y%m%d") |
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fdly$month=format(fdly$date,"%m") |
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fdly$year=format(fdly$date,"%Y") |
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## check validity (via npar and ntime) of nc files |
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for(i in 1:nrow(fdly)){
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fdly$ntime[i]=as.numeric(system(paste("cdo sinfo ",fdly$path[i]),intern=T))
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fdly$npar[i]=as.numeric(system(paste("cdo -s npar ",fdly$path[i]),intern=T))
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# fdly$ntime[i]<-as.numeric(system(paste("cdo sinfo ",fdly$path[i]),intern=T))
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fdly$npar[i]<-as.numeric(system(paste("cdo -s npar ",fdly$path[i]),intern=T))
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print(i) |
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} |
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|
| ... | ... | |
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tsdir=paste(tempdir(),"/summary",sep="") |
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dir.create(tsdir) |
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lapply(unique(fdly$year),function(y){
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system(paste("cdo -O mergetime ",paste(fdly$path[fdly$year==y],collapse=" ")," ",tsdir,"/MOD09_",tile,"_",y,"_daily.nc",sep=""))
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system(paste("cdo -O mergetime ",paste(fdly$path[!is.na(fdly$npar)&fdly$year==y],collapse=" ")," ",tsdir,"/MOD09_",tile,"_",y,"_daily.nc",sep=""))
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print(paste("Finished merging daily files for year",y))
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}) |
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## Combine the year-by-year files into a single daily file |
| ... | ... | |
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print("Finished! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
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## quit R |
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q("no")
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#q("no")
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################################################################# |
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### copy the files back to Yale |
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list.files("2_daily")
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system("scp 2_daily/* adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela")
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system(paste("scp ",outdir2,"/*_ymonmean.nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela/summary",sep=""))
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system("scp /tmp/Rtmp6I6tFn/MOD06_L2.A2000061.1615.051.2010273184629.hdf adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela")
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| 181 | 213 |
system("scp 2_daily/MOD06_20000410.nc adamw@acrobates.eeb.yale.edu:/data/personal/adamw/projects/interp/data/modis/Venezuela")
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| 182 | 214 |
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list.files(" /tmp/Rtmp6I6tFn")
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Also available in: Unified diff
MOD06 processing running successfully using Pleiades environment set up by Andrew Michaelis at NASA.