Difference between revisions of "Software:R"
| Line 5: | Line 5: | ||
== Starting R console == | == Starting R console == | ||
| + | Similar to any software stack on the cluster, based on the requirement one needs to load a specific version of R using the 'module load' command. You can load default version using | ||
| + | <pre> | ||
| + | $ module load r | ||
| + | </pre> | ||
| + | |||
| + | Use module spider command to list all the different version and their dependencies. | ||
| + | <pre> | ||
| + | $ module spider r | ||
| + | </pre> | ||
| + | |||
| + | Several version of R are available as module(r/3.3.3 to 4.1.2). You need to load all the dependent modules before load a specif r version and can be determine using module spider command | ||
| + | $ module spider r/4.1.2 | ||
| + | |||
| + | You will need to load all module(s) on any one of the lines below before the "r/4.1.2" module is available to load. | ||
| + | StdEnv/2020 | ||
| + | |||
| + | Now you can load r/4.1.2 using the following module load commands | ||
| + | <pre> | ||
| + | $ module load StdEnv/2020 | ||
| + | $ module load r/4.1.2 | ||
| + | </pre> | ||
| + | |||
| + | Similarly, if you want to load r/3.6.1 | ||
| + | <pre> | ||
| + | $ module spider r/3.6.1 | ||
| + | $ module load nixpkgs/16.09 gcc/7.3.0 | ||
| + | $ module load r/3.6.1 | ||
| + | </pre> | ||
| + | Typically, one needs to load a corresponding gcc compiler before loading R. Note: StdEnv/2020 modules contains gcc/9.3.0 and is sufficient to load r/4.1.2 | ||
== Installing R packages == | == Installing R packages == | ||
Revision as of 20:53, 22 March 2022
Introduction
R is a language and environment for statistical computing and graphics. It provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. Although R is not well-suited for HPC cluster, functionality and flexibility for data handling and analysis make it a essential tool for researcher from wide range of scientific discipline. In addition, R provide a large repository of user built packages suits for different range of applications.
You can run your R script from our Rstudio or through a batch script on compute nodes. Rstudio provides our user with an IDE to develop and run your program on a web browser. But it is constrained in term of the available packages and the compute resource. Alternative, you can run the program through command line /batch script which provides the user the flexibility to choose the different version of R available on our central software stack and their respective packages. This pages focus on primer for running Rscript on compute nodes.
Starting R console
Similar to any software stack on the cluster, based on the requirement one needs to load a specific version of R using the 'module load' command. You can load default version using
$ module load r
Use module spider command to list all the different version and their dependencies.
$ module spider r
Several version of R are available as module(r/3.3.3 to 4.1.2). You need to load all the dependent modules before load a specif r version and can be determine using module spider command $ module spider r/4.1.2
You will need to load all module(s) on any one of the lines below before the "r/4.1.2" module is available to load.
StdEnv/2020
Now you can load r/4.1.2 using the following module load commands
$ module load StdEnv/2020 $ module load r/4.1.2
Similarly, if you want to load r/3.6.1
$ module spider r/3.6.1 $ module load nixpkgs/16.09 gcc/7.3.0 $ module load r/3.6.1
Typically, one needs to load a corresponding gcc compiler before loading R. Note: StdEnv/2020 modules contains gcc/9.3.0 and is sufficient to load r/4.1.2
