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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