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Revision 92fd8a10

Added by Adam Wilson about 12 years ago

Updated script to accurately set paths for HEG tool to facilitate parallel processing of gridding procedure using swtif. Multicore package is used to parallelize which limits processing to a single node. Next step is to explore use of foreach package to allow multiple nodes

View differences:

climate/procedures/Pleiades.R
11 11 

  		




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cat(paste("


  		




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#PBS -S /bin/bash


  		




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#PBS -l select=32:ncpus=4:mpiprocs=4:model=wes


  		




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####old PBS -l select=64:ncpus=4:mpiprocs=4:model=wes


  		




  
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##PBS -l select=1: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=1:00:00


  		




  
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#PBS -l walltime=10:00:00


  		




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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 -W group_list=s1007


  		




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#PBS -q devel


  		




  
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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


  		




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#PBS -M adam.wilson@yale.edu


  		




  ......




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  source /usr/local/lib/global.profile


  		




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  source /u/awilso10/.bashrc


  		




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## export a few important variables


  		




  
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  export NCORES=24  # use to limit mclapply() to set nubmer of cores, should be select*ncpus above


  		




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  export PATH=$PATH:/nobackupp1/awilso10/bin:/nobackupp1/awilso10/software/bin


  		




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  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/nobackupp1/awilso10/software/lib


  		




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  export MRTDATADIR=/nobackupp1/awilso10/software/heg/data


  		




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  export PGSHOME=/nobackupp1/awilso10/software/heg


  		




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  export MRTBINDIR=/nobackupp1/awilso10/software/TOOLKIT_MTD


  		




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


  		




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  export TMPDIR=/nobackupp1/awilso10/mod06/tmp


  		




  
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## HEG related variables


  		




  
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  export MRTDATADIR=/nobackupp1/awilso10/software/heg/data


  		




  
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  export PGSHOME=/nobackupp1/awilso10/software/heg/TOOLKIT_MTD


  		




  
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  export HEGUSER=ME


  		




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## load modules


  		




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  module load gcc 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 


  		




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exit 0


  		




  
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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 ~/environmental-layers/climate/procedures/MOD06_L2_process.r")


  		




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## check queue status


  		




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


  		




  
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## Submit it (and keep the pid)!


  		




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pid=system("qsub MOD06_process",intern=T); pid; pid=strsplit(pid,split="[.]")[[1]][1]


  		




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#system("qsub MOD06_process")


  		




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## work in interactive mode


  		




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#system("qsub -I -l walltime=1:00:00 -lselect=1:ncpus=2:model=wes -q devel")


  		




  
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# system("qsub -I -l walltime=1:00:00 -lselect=2:ncpus=16:model=san -q devel")


  		




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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("qstat -t -x",pid))


  		




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system("qstat devel ") 


  		












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