# Echo out library paths

.libPaths()

# Load the R MPI package if it is not already loaded

if (!is.loaded("mpi_initialize")) {

  library("Rmpi")

}

# Echo out libraries loaded

library()

# Echo out what is loaded

search()

# Spawn as many slaves as possible

mpi.spawn.Rslaves()

# In case R exits unexpectedly, have it automatically clean up

# resources taken up by Rmpi (slaves, memory, etc...)

.Last <- function(){

  if (is.loaded("mpi_initialize")){

            if (mpi.comm.size(1) > 0){

                              print("Please use mpi.close.Rslaves() to close slaves.")

                                              mpi.close.Rslaves()

                            }

                    print("Please use mpi.quit() to quit R")

                    .Call("mpi_finalize")

          }

}

# Tell all slaves to return a message identifying themselves

mpi.remote.exec(paste("I am",mpi.comm.rank(),"of",mpi.comm.size()))

# Tell all slaves to close down, and exit the program

mpi.close.Rslaves()

mpi.quit()

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"

Copyright (C) 2012 The R Foundation for Statistical Computing

ISBN 3-900051-07-0

Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.

You are welcome to redistribute it under certain conditions.

Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.

Type 'contributors()' for more information and

'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or

'help.start()' for an HTML browser interface to help.

Type 'q()' to quit R.

> # Echo out library paths

> .libPaths()

[1] "/home1/awilso10/R/x86_64-unknown-linux-gnu-library/2.15"

[2] "/nasa/R/2.15.1/lib64/R/library"                         

> 

> # Load the R MPI package if it is not already loaded

> if (!is.loaded("mpi_initialize")) {

+   library("Rmpi")

+ }

#require(ncdf4)

## packages for parallelization

#library(foreach)

#library(doMPI)

## register cluster and number of cores to use

#cl=startMPIcluster(20,verbose=F)

#registerDoMPI(cl)

mclapply(notdone,mod06,tile,mc.cores=ncores) # use ncores/2 because system() commands can add second process for each spawned R

#foreach(i=notdone[1:3],.packages=(.packages())) %dopar% mod06(i,tile)

#foreach(i=1:20) %dopar% print(i)

#PBS -S /bin/bash

#PBS -l select=1:ncpus=16:model=san

###PBS -l select=4:ncpus=8:model=neh

##PBS -l select=1:ncpus=12:model=wes

####### old: select=48:ncpus=8:mpiprocs=8:model=neh

#PBS -l walltime=2:00:00

#PBS -j oe

#PBS -m e

#PBS -V

####PBS -W group_list=s1007

#PBS -q devel

#PBS -o log/log_^array_index^

#PBS -o log/log_DataCompile

#PBS -M adam.wilson@yale.edu

#PBS -N MOD06

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

## cd to working directory

cd /nobackupp1/awilso10/mod06

## set some memory limits

#  ulimit -d 1500000 -m 1500000 -v 1500000  #limit memory usage

  source /u/awilso10/.bashrc

  source /usr/local/lib/global.profile

## export a few important variables

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

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

## load modules

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

## Run the script!

## current version not parallelizing across nodes!

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

exit 0

exit 0

#PBS -l select=1:ncpus=16:model=san

##PBS -l select=1:ncpus=12:model=wes

#PBS -l walltime=2:00:00

#PBS -q devel

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

  source /u/awilso10/moduleload

  source /usr/local/lib/global.profile

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

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

system("qsub MOD06_process")

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

# mpirun -np 1 -r ssh R --no-save

module load R

module load mpi-sgi/mpt.2.06a67

export MPIHOME=/nasa/sgi/mpt/2.06a67/

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

  CC=mpicc R CMD INSTALL --no-test-load --configure-args="--with-Rmpi-type=OPENMPI   --with-Rmpi-libpath=$MPIHOME/lib --with-Rmpi-include=$MPIHOME/include"   ~/Rmpi_0.6-1.tar.gz

mpirun -np 1 R --no-save

/u/scicon/tools/bin/qps