r
Table of Content
Versions and Availability
About the Software
R is 'GNU S', a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.
Usage
On Super Mike 2, R 3.2.0 was compiled by gcc 4.7.2. So make sure gcc 4.7.2 has been added into the user environment by softenv. If not, as the default gcc loaded is 4.4.6, following error messages when trying to use R 3.2.0 will appear:
$ R
WARNING: ignoring environment value of R_HOME
/usr/local/packages/R/3.2.0/gcc-4.7.2/lib64/R/bin/exec/R: error while loading shared libraries: libquadmath.so.0: cannot open shared object file: No such file or directory
and R will not run. So again please make sure gcc 4.7.2 has been loaded.
R may be run either interactively via the R console, or as a batch process reading commands from a script file.
To launch the R console, simply execute the R command. After the console is launched, users can run R commands at the prompt:
$ R
R version 3.1.0 (2014-04-10) -- "Spring Dance"
Copyright (C) 2014 The R Foundation for Statistical Computing
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.
Natural language support but running in an English locale
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.
> x <- 5
> x
[1] 5
> m <- matrix(1:6,2,3)
> m
[,1] [,2] [,3]
[1,] 1 3 5
[2,] 2 4 6
Rscript, on the other hand, can be used to run a R scirpt in which a sequence of R commands has been saved. The syntax is:
$ Rscript <options> <name of the R script>
For example:
$ cat hello.R
print("Hello World!")
$ Rscript hello.R
[1] "Hello World!"
▶ QSub FAQ?
Portable Batch System: qsub
qsub
All HPC@LSU clusters use the Portable Batch System (PBS) for production processing. Jobs are submitted to PBS using the qsub command. A PBS job file is basically a shell script which also contains directives for PBS.
Usage
$ qsub job_script
Where job_script is the name of the file containing the script.
PBS Directives
PBS directives take the form:
#PBS -X value
Where X is one of many single letter options, and value is the desired setting. All PBS directives must appear before any active shell statement.
Example Job Script
#!/bin/bash
#
# Use "workq" as the job queue, and specify the allocation code.
#
#PBS -q workq
#PBS -A your_allocation_code
#
# Assuming you want to run 16 processes, and each node supports 4 processes,
# you need to ask for a total of 4 nodes. The number of processes per node
# will vary from machine to machine, so double-check that your have the right
# values before submitting the job.
#
#PBS -l nodes=4:ppn=4
#
# Set the maximum wall-clock time. In this case, 10 minutes.
#
#PBS -l walltime=00:10:00
#
# Specify the name of a file which will receive all standard output,
# and merge standard error with standard output.
#
#PBS -o /scratch/myName/parallel/output
#PBS -j oe
#
# Give the job a name so it can be easily tracked with qstat.
#
#PBS -N MyParJob
#
# That is it for PBS instructions. The rest of the file is a shell script.
#
# PLEASE ADOPT THE EXECUTION SCHEME USED HERE IN YOUR OWN PBS SCRIPTS:
#
# 1. Copy the necessary files from your home directory to your scratch directory.
# 2. Execute in your scratch directory.
# 3. Copy any necessary files back to your home directory.
# Let's mark the time things get started.
date
# Set some handy environment variables.
export HOME_DIR=/home/$USER/parallel
export WORK_DIR=/scratch/myName/parallel
# Set a variable that will be used to tell MPI how many processes will be run.
# This makes sure MPI gets the same information provided to PBS above.
export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
# Copy the files, jump to WORK_DIR, and execute! The program is named "hydro".
cp $HOME_DIR/hydro $WORK_DIR
cd $WORK_DIR
mpirun -machinefile $PBS_NODEFILE -np $NPROCS $WORK_DIR/hydro
# Mark the time processing ends.
date
# And we're out'a here!
exit 0
Resources
Last modified: April 16 2021 13:19:28.