*** parallel runs on greenfield, example.R and example.pbs

helen:ms02GINPPI hqin$ cat example.R 

#20150914 testing parallel jobs on greenfield

# R CMD BATCH ./example.R --args 2 35 red

rm(list=ls())

source("lifespan.r")

source("network.r")

#R -f file --args start end

options(echo=TRUE) # if you want see commands in output file

args <- commandArgs(trailingOnly = TRUE)

print(args)

# trailingOnly=TRUE means that only your arguments are returned, check:

# print(commandsArgs(trailingOnly=FALSE))

start = as.integer(args[1]); start; 

end = as.integer(args[2]); end; 

tag = args[3]

  

myhost = 'greenfield'  # 'byte' 'blacklight' 'mactower'

myhost = 'byte'  # 'byte' 'blacklight' 'mactower'

myhost = 'helen'  # 'byte' 'blacklight' 'helen'

mydir = "/crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI"

if (myhost == 'byte') {  mydir = "/Users/hqin/github/mactower-network-failure-simulation/ms02GINPPI"

} else if (myhost == 'helen') { mydir = "/Users/hqin/github/mactower-network-failure-simulation/ms02GINPPI";  

}

print(paste("current dir is:", mydir))

list.files()

getwd()

print(paste("Now setwd"))

setwd(mydir)

list.files()

debug = 0; 

x = start:end 

outfile = paste( tag, start, end, "tab", sep='.')

write.csv( x, outfile, row.names=F)

[hqin2@greenfield ms02GINPPI]$ cat example.pbs

#!/bin/bash

# Request 15 cores

#PBS -l nodes=1:ppn=15

#  Request 1hr of cpu time

#PBS -l walltime=0:00:01:00

module load R/3.2.1-mkl

echo hostname

pwd

cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI

pwd

numactl -C +0 R --vanilla --slave -f ./example.R --args 1 199999 '_zero' &

numactl -C +1 R --vanilla --slave -f ./example.R --args 2 299999 '_one' &

numactl -C +2 R --vanilla --slave -f ./example.R --args 3 399999 '_two' &

numactl -C +3 R --vanilla --slave -f ./example.R --args 4 499999 '_three' &

numactl -C +4 R --vanilla --slave -f ./example.R --args 4 499999 '_four' &

numactl -C +5 R --vanilla --slave -f ./example.R --args 4 499999 '_five' &

numactl -C +6 R --vanilla --slave -f ./example.R --args 4 499999 '_six' &

numactl -C +7 R --vanilla --slave -f ./example.R --args 4 499999 '_seven' &

numactl -C +8 R --vanilla --slave -f ./example.R --args 4 499999 '_eight' &

numactl -C +9 R --vanilla --slave -f ./example.R --args 4 499999 '_nine' &

wait