06-applications.Rmd

---
title: "Using Applications"
output: html_document
---
# Wiki + Example
From [wiki](https://www.wiki.ed.ac.uk/display/ResearchServices/Applications), it provides a few guidance of using [R](https://www.wiki.ed.ac.uk/display/ResearchServices/R), [Tensorflow](https://www.wiki.ed.ac.uk/display/ResearchServices/Tensorflow), [Matlab](https://www.wiki.ed.ac.uk/display/ResearchServices/Matlab), [Java](https://www.wiki.ed.ac.uk/display/ResearchServices/Java), [Python](https://www.wiki.ed.ac.uk/display/ResearchServices/Python), [Singularity](https://www.wiki.ed.ac.uk/display/ResearchServices/Singularity).

## Example: Using R

R is available on both Knot and Pod, including different versions of R.

### Loading R

To load R on Knot for interactive use, enter the command

```
$ R
```

To load R on Pod for interactive use, enter the commands

```
$ load module R
$ R
```

To exit R, use the command `q()`.

Note that the RStudio IDE is not available for use on the clusters.

*Remember: Most analyses should be performed on compute nodes by submitting batch jobs. The login node should only be used for simple analyses, testing, or debugging.*

### Versions

On Knot, the available version of R is 3.2.2.

On Pod, the available versions of R include

```
R/3.2.2
R/3.4.4
R/3.5.1-multith
R/3.5.1
```

The default is the latest version. To load a specific version, for example, use the command `load module R/3.4.4`.

A different version of R can be installed inside your home directory. For more info see <http://csc.cnsi.ucsb.edu/docs/using-r-knot-braid-and-pod>.

### Packages

Packages can be installed using the R command `install.packages("<package>")` and should be stored inside your home folder. When using this command you may be prompted to select a CRAN mirror from which to download; select a USA (CA) mirror with an HTTPS connection for a fast and secure download. R should automatically add the home-based package library to `.libPaths()` (enter this command to confirm) and set it as default.

### Example job files

#### Knot

```
#!/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l walltime=2:00:00
#PBS -m abe
#PBS -M user@ucsb.edu

cd $PBS_O_WORKDIR

Rscript --vanilla script.R
```

#### Pod

```
#!/bin/bash -l
#SBATCH --nodes=1 --ntasks-per-node=1
#SBATCH --time=2:00:00
#SBATCH --mail-type=ALL
#SBATCH --mail-user=user@ucsb.edu

cd $SLURM_SUBMIT_DIR

module load R
Rscript --vanilla script.R
```