Revision 9d52d7e0
Added by Adam Wilson about 12 years ago
| climate/procedures/Pleiades.R | ||
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## get all unique dates |
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alldates=unique(fs$dateid) |
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## get MODLAND tile information |
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tb=read.table("http://landweb.nascom.nasa.gov/developers/sn_tiles/sn_bound_10deg.txt",skip=6,nrows=648,header=T)
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tb$tile=paste("h",sprintf("%02d",tb$ih),"v",sprintf("%02d",tb$iv),sep="")
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### use MODIS tile as ROI |
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#modt=readOGR("modgrid","modis_sinusoidal_grid_world",)
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#modt@data[,colnames(tb)[3:6]]=tb[match(paste(modt$h,modt$v),paste(tb$ih,tb$iv)),3:6] |
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#write.csv(modt@data,file="modistile.csv") |
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## write it out |
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save(fs,file="allfiles.Rdata") |
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save(alldates,file="alldates.Rdata") |
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save(fs,tb,file="allfiles.Rdata")
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#save(alldates,file="alldates.Rdata")
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notdonedates=alldates |
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save(notdonedates,file="notdonedates.Rdata") |
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## identify which have been completed |
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outdir="2_daily" |
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done=alldates%in%substr(list.files(outdir),5,12) |
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table(done) |
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notdone=alldates[!done] |
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#notdone=alldates[1:4] |
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save(notdone,file="notdone.Rdata") |
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## output ROI |
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#get bounding box of region in m |
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#ge=SpatialPoints(data.frame(lon=c(-125,-115),lat=c(40,47))) |
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#projection(ge)=CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
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#ge2=spTransform(ge, CRS(" +proj=sinu +lon_0=0 +x_0=0 +y_0=0"))
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## vars |
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vars=as.data.frame(matrix(c( |
| ... | ... | |
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### Submission script |
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cat("
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#PBS -S /bin/csh |
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#PBS -N cfd |
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# This example uses the Harpertown nodes |
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# User job can access ~7.6 GB of memory per Harpertown node. |
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# A memory intensive job that needs more than ~0.9 GB |
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# per process should use less than 8 cores per node |
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# to allow more memory per MPI process. This example |
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# asks for 64 nodes and 4 MPI processes per node. |
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# This request implies 64x4 = 256 MPI processes for the job. |
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#PBS -l select=64:ncpus=8:mpiprocs=4:model=har |
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#PBS -l walltime=4:00:00 |
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cat(paste("
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#PBS -S /bin/sh |
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#PBS -J 700-899 |
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###PBS -J 1-",length(notdone)," |
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#PBS -l walltime=0:10:00 |
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#PBS -l ncpus=100 |
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#PBS -j oe |
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#PBS -W group_list=a0801
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#PBS -o log/log_^array_index^
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#PBS -m e |
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# Load some modules |
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module load gcc |
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module load hdf5 |
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module load netcdf/4.1.3/gcc/mpt |
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module load mpi |
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module load tcl-tk/8.5.11 |
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module load udunits/2.1.19 |
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module load szip/2.1/gcc |
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module load R |
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module load git |
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# By default, PBS executes your job from your home directory. |
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# However, you can use the environment variable |
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# PBS_O_WORKDIR to change to the directory where |
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# you submitted your job. |
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cd $PBS_O_WORKDIR |
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# use of dplace to pin processes to processors may improve performance |
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# Here you request to pin processes to processors 2, 3, 6, 7 of each node. |
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# This helps for using the Harpertown nodes, but not for Nehalem-EP or |
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# Westmere-EP nodes |
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# The resource request of select=64 and mpiprocs=4 implies |
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# that you want to have 256 MPI processes in total. |
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# If this is correct, you can omit the -np 256 for mpiexec |
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# that you might have used before. |
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mpiexec dplace -s1 -c2,3,6,7 ./grinder < run_input > output |
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# It is a good practice to write stderr and stdout to a file (ex: output) |
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# Otherwise, they will be written to the PBS stderr and stdout in /PBS/spool, |
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# which has limited amount of space. When /PBS/spool is filled up, any job |
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# that tries to write to /PBS/spool will die. |
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# -end of script- |
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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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## 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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## export a few important variables |
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export PATH=$PATH:/nobackupp1/awilso10/bin:/nobackupp1/awilso10/software/bin |
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export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/nobackupp1/awilso10/software/lib |
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export MRTDATADIR=/nobackupp1/awilso10/software/heg/data |
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export PGSHOME=/nobackupp1/awilso10/software/heg |
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export MRTBINDIR=/nobackup1/awilso10/software/TOOLKIT_MTD |
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export R_LIBS=\"/u/awilso10/R/x86_64-unknown-linux-gnu-library/2.15/\" |
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## load modules |
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module load gcc mpi-sgi/mpt.2.06r6 hdf4 udunits R |
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## Run the script! |
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Rscript --verbose --vanilla /u/awilso10/environmental-layers/climate/procedures/MOD06_L2_data_compile_Pleiades.r i=${PBS_ARRAY_INDEX}
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rm -r $TMPDIR |
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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("chmod +x MOD06_process")
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## Submit it! |
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#system("qsub -q devel MOD06_process")
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system("qsub MOD06_process")
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## check progress |
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system("qstat -u awilso10")
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system("qstat -t 391843[]")
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system("qstat -f 391843[2]")
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#system("qstat devel ")
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#system("qstat | grep awilso10")
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#print(paste(max(0,length(system("qstat",intern=T))-2)," processes running"))
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# system("ssh c0-8.farm.caes.ucdavis.edu")
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# system("qalter -p +1024 25964") #decrease priority of job to run extraction below.
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system("cat log/InterpScript.o55934.2")
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## check log |
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system(paste("cat",list.files("log",pattern="InterpScript",full=T)[100]))
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#system(paste("cat",list.files("log",pattern="InterpScript",full=T)[13]," | grep \"Temporary Directory\""))
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Also available in: Unified diff
Successfully running MOD06 processing on Pleiades as an array job (though submissions are limited to < 365 jobs so will have to find another way to submit them)