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Revision 827b4b87

Added by Adam Wilson about 12 years ago

MOD06_L2 now running properly but Rmpi is not running due to (probably) incompatability between Rmpi and the version of sgi-mpi available on Pleiades

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=1:ncpus=16:model=san


  		




  
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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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##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=10:00:00


  		




  
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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 -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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#PBS -N MOD06


  		




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source /usr/share/modules/init/bash


  		




  
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#source /usr/share/modules/init/bash


  		




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## cd to working directory


  		




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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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  source /usr/local/lib/global.profile


  		




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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 NCORES=16  # use to limit mclapply() to set nubmer of cores, should be select*ncpus above


  		




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


  		




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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("/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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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=2:ncpus=16:model=san -q devel")


  		




  
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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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## check progress


  		




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system("qstat -u awilso10")


  		












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