[R-sig-hpc] Loading rgdal as PBS script in R

[Hariom Singh]

Hey all,

I thought I'd share this since we spent quite some time with it and it
might be relevant to some of you. Or at least amusing, possibly.

It is stated that, I am getting difficulty in loading rgdal R library while
using  PBS script for parallel computing environment....

First of all I would like to share my relevant files....Please check the
error..

*#####   test.sh pbs script file for running R program*

#!/usr/bin/env bash

#PBS -N snow_1
#PBS -m abe
#PBS -q medium
#PBS -l nodes=2:ppn=12
#PBS -V

cd $PBS_O_WORKDIR


cp /UHOME/hariodce/R/x86_64-unknown-linux-gnu-library/3.2/Rmpi/Rprofile
./.Rprofile

cat $PBS_NODEFILE > pbsnodes

mpirun -machinefile $PBS_NODEFILE -np 24 R CMD BATCH *test.r *

*#### test.r ... test R file where rgdal is not loaded........*

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

if (is.loaded("mpi_initialize"))

{

library("Rmpi")
*library("rgdal")......*

}
 # 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(),system("hostname",intern=T)))

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

mpi.close.Rslaves()

*output file......*
..................
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.

master  (rank 0 , comm 1) of size 24 is running on: cn05
slave1  (rank 1 , comm 1) of size 24 is running on: cn05
slave2  (rank 2 , comm 1) of size 24 is running on: cn05
slave3  (rank 3 , comm 1) of size 24 is running on: cn05
... ... ...
slave22 (rank 22, comm 1) of size 24 is running on: cn07
slave23 (rank 23, comm 1) of size 24 is running on: cn07
[Previously saved workspace restored]

> # Load the R MPI package if it is not already loaded.
>
> if (is.loaded("mpi_initialize"))
+
+ {
+
+ library("Rmpi")
+ library("rgdal")
+
+ } ########error...*.it always loaded without pbs scipt like
library(rgdal) but here it is not loaded.....so what is the problem in
loading.......Plz help me out.*




*Loading required package: spError in dyn.load(file, DLLpath = DLLpath,
...) :   unable to load shared object
'/SOFT/R320/lib64/R/library/rgdal/libs/rgdal.so':  libgdal.so.20: cannot
open shared object file: No such file or directory*
Error: package or namespace load failed for ‘rgdal’
>
>
>
>      # 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(),system("hostname",intern=T)))
$slave1
[1] "I am 1 of 24 cn05"

$slave2
[1] "I am 2 of 24 cn05"

.......................
.............................


*# .bashrc *

# Source global definitions
if [ -f /etc/bashrc ]; then
    . /etc/bashrc
fi

export R_LIBS_USER=/SOFT/R320/lib64/R/library


*############## .bash_profile*

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
    . ~/.bashrc
fi

# User specific environment and startup programs

PATH=$PATH:$HOME/bin

export PATH
source /SOFT/ics_2013.1.046/icsxe/2013.1.046/ictvars.sh intel64
export JAVA_HOME=/usr/lib/jvm/java-1.7.0-openjdk-1.7.0.45.x86_64
export PATH=/SOFT/R320/bin/:/SOFT/mpich-3.1.1/bin:$PATH
export
LD_LIBRARY_PATH=/SOFT/R320/lib64/:/SOFT/mpich-3.1.1/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

Please help me. I would highly appreciate for your time and concern.

Thanks in anticipation.

Hariom Singh

Ph.D research scholar , IIT Roorkee.

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