Applications/Savu

Application Details

• Description: R is an open source programming language and software environment for statistical computing and graphics
• Version: 2.0
• Modules: savu/2.0/gcc-5.2.0/openmpi-2.0.2

Usage Examples

Interactive

Note: savu supports interactive mode (as below) and execution mode running as an interpreted script.

[username@login01 ~]$ interactive
salloc: Granted job allocation 402968
Job ID 402968 connecting to c059, please wait...
Last login: Wed Jul 12 16:23:48 2017 from 10.254.5.246
[username@c059 ~]$ module load savu/2.0/gcc-5.2.0/openmpi-2.0.2
[username@c059~]$ savu_config

or

[username@c059~]$  savu /Path/To_input/Data/file.nxs /List/Of_processes/To_be_performed/process.nxs /path /to/output/directory

Example: this will run basic_tomo_process.nxs on file 24737.nxs and place the output in your current directory under results

[username@c059~]$  savu /trinity/clustervision/CentOS/7/apps/savu/2.0/gcc-5.2.0/openmpi-2.0.2/Savu_2.0/miniconda/pkgs/savu-2.0-h4571989_0/lib/python2.7/site-packages/savu-2.0-py2.7.egg/test_data/data/24737.nxs /trinity/clustervision/CentOS/7/apps/savu/2.0/gcc-5.2.0/openmpi-2.0.2/Savu_2.0/miniconda/pkgs/savu-2.0-h4571989_0/lib/python2.7/site-packages/savu-2.0-py2.7.egg/test_data/test_process_lists/basic_tomo_process.nxs ./results

3.3.0

This version is to be deprecated, all new work should be done with version 3.4.1

3.4.1

This version has compiled support for these additional libraries:

• --enable-R-shlib
• --with-x --with-readline
• --with-cairo
• --with-tcltk
• --with-libpng
• --with-jpeglib

Install an R package

[username@login01 ~]$ module load R/3.4.1
[username@login01 ~]$ R

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> install.packages("ggplot2")

Batch Submission

#!/bin/bash
#SBATCH -J My_R_job              # Job name, you can change it to whatever you want
#SBATCH -N 1                # Number of nodes 
#SBATCH -o %N.%j.out        # Standard output will be written here
#SBATCH -e %N.%j.err        # Standard error will be written here
#SBATCH -p compute          # Slurm partition, where you want the job to be queued 
#SBATCH --exclusive            # run on one node without any other users
#SBATCH --mem=64G       # reserve 64Gbytes of RAM for my job (optional)
 
module purge
module add R/3.4.1
 
R CMD BATCH Random.R

[username@login01 ~]$ sbatch Rtest.job
Submitted batch job 289522