BwUniCluster2.0/Software/R: Difference between revisions

From bwHPC Wiki
Jump to navigation Jump to search
 
(64 intermediate revisions by 8 users not shown)
Line 1: Line 1:
{{Softwarepage|math/R}}

{| width=600px class="wikitable"
{| width=600px class="wikitable"
|-
|-
Line 23: Line 25:


= Description =
= Description =

'''R''' is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.
'''R''' is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.


Line 30: Line 33:


R is available as Free Software under the terms of the Free Software Foundation’s GNU General Public License in source code form. It compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), Windows and MacOS.
R is available as Free Software under the terms of the Free Software Foundation’s GNU General Public License in source code form. It compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), Windows and MacOS.


= Versions and Availability =
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
<br>
<big>

[https://cis-hpc.uni-konstanz.de/prod.cis/ Cluster Information System CIS]

</big>
{{#widget:Iframe
|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/math/R
|width=99%
|height=280
}}
<br>
On the command line interface of any bwHPC cluster, a list of the available R versions using
<pre>
$ module avail math/R
</pre>


= Usage =
= Usage =
The R installation also provides the standalone library libRmath. This library allows you to access R routines from your own C or C++ programs (see section 9 of the 'R Installation and Administration' manual.)
The R installation also provides the standalone library libRmath. This library allows you to access R routines from your own C or C++ programs (see section 9 of the 'R Installation and Administration' manual).


== Installing R-Packages into your home folder ==
== Loading the module ==
Since we cannot provide a software module for every R package, we recommend to install special R packages locally into your home folder. One possibility doing this is from within an interactive R session:
You can load the default version of R with the command
<pre>
$ module load math/R
</pre>


The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for R.

If you wish to load a specific (older) version, you can do so using e.g.
<pre>
<pre>
> library() # List preinstalled packages
$ module load math/R/3.1.2
> install.packages('package_name', repos="http://cran.r-project.org") # Installing your R package and the dependencies
> library(package_name) # Loading the package into you R instance
</pre>
</pre>
to load the version 3.1.2.


The package is now installed permanently in your home folder and is available every time you start R.
== Program Binaries ==
Standard usage:


'''Note:'''
<pre>
Usage: R [options] [< infile] [> outfile]
R CMD command [arguments]
Example: R CMD BATCH script.R
</pre>


By default R uses a version (and platform) specific path for personal libraries, such as
Executing R in batch mode:
"$HOME/R/x86_64-pc-linux-gnu-library/x.y" for R version x.y.z. This directory will be created automatically (after confirmation) when installing a personal package for the first time.


Users can customize a common location of their personal library packages, e.g. ~/R_libs, rather than the default location. A customized directory must exist before installing a personal package for the first time, i.e.
<pre>
R CMD BATCH --no-save --no-restore <INPUT_FILE>.R
</pre>


For help run
<pre>
<pre>
$ mkdir -p ~/R_libs
R --help
</pre>
</pre>


The location must also be defined in a configuration file ~/.Renviron within the home directory containing the following line:
For command help run
<pre>
R CMD command --help
</pre>


Further information and help
<pre>
<pre>
R_LIBS_USER="~/R_libs"
Man pages: man R man Rscript
Info pages. e.g.: info R-intro info R-FAQ
Manuals: $R_DOC_DIR/manual
</pre>
</pre>


By setting up a (fixed) custom location for personal library packages, any personal package installed into that directory will be visible across different R versions. This may be advantageous if the packages are to be used with different (future) R versions.
== Multithreading in R ==


A version specific path, such as the default path, allows users to maintain multiple personal library stacks for different (major and minor) R versions and does also prevent users from mixing their stack with libraries built with different R versions.
An easy way to use multiple cores on a single node in R is to use the [https://cran.r-project.org/web/packages/doParallel/vignettes/gettingstartedParallel.pdf| doParallel] package in combination with [https://cran.r-project.org/web/packages/foreach/vignettes/foreach.pdf| foreach].


The drawback is that, whenever switching to a new R release, the personal library stack '''must''' be rebuilt with that new R version into the corresponding (version specific) library path. This is considered good practice anyway in order to ensure a consistent personal library stack for any specific R version in use. Mixing libraries built with different major and minor R versions is discouraged, as this may (or may not) result in unpredictable and subtle errors. Packages that are built and installed with one version of R may be incompatible with a newer version of R, at least when the major or minor version changes. The same is true if several versions are used simultaneously, e.g. a newer R version for a more recently started project and and older version for another project (but eventually picking up libraries built with the newer R version).
= Examples =
As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.


Special care has also to be taken by users who always load the default version, i.e.
Example scripts are available in the directory $R_EXA_DIR:
<pre>
$ module show math/R # show environment variables, which will be available after 'module load'
$ module load math/R # load module
$ ls $R_EXA_DIR # show content of directory $R_EXA_DIR
$ cat $R_EXA_DIR/README # show examples README
</pre>


Run a first simple example job
<pre>
<pre>
$ module load math/R # load module
$ module load math/R
</pre>
$ mkdir Rtest # create test directory
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/ # copy example files to test directory
$ cd Rtest/ # change to directory
$ nano bwhpc-r.moab # change job options, quit with 'CTRL+X'
$ msub bwhpc-r.moab # submit job
$ checkjob -v <JOBID> # check state of job
$ ls # when job finishes the results will be visible in this directory
</pre>


as the default version number may change any time. It is therefore highly recommended to always load a specific version, e.g.
= Installing R-Packages into your home folder =
Since we cannot provide a software module for every R package, we recommend to install special R packages locally into your home folder. One possibility doing this is shown below:


<pre>
<pre>
$ module load math/R/3.6.3
cp $HOME/.bashrc $HOME/.bashrc.backup # Make a backup copy of your bashrc
</pre>
echo "export R_LIBS=\"${HOME}/R_libs\"" >> $HOME/.bashrc # Setting the environment variable R_LIBS permanently in your bashrc
source $HOME/.bashrc # Sourcing bashrc to make R_LIBS available
mkdir $R_LIBS # Create the R_libs folder in your HOME directory
module load math/R # Loading the matlab software module
R # Loading R
install.packages('package_name', repos="http://cran.r-project.org") # Installing your R package and the dependencies
library(package_name) # Loading the package into you R instance
</pre>


== Pre-installed R-packages ==
* Rmpi
* Rcpp (R 4.4.1 only)
* RcppEigen (R 4.4.1 only)
* iterators
* foreach
* doMPI
* doParallel
* <s>cummeRbund</s> (see [https://wiki.bwhpc.de/e/BwUniCluster2.0/Software/R/cummeRbund '''installation instructions'''] below)


== Optional packages for R ==
The package is now installed permanently in your home folder and is available every time you start R.


The following guides provide detailed instructions about how to build selected optional R packages on '''bwUniCluster''' for '''R version 4.1.2'''. Please write a [https://bw-support.scc.kit.edu/ ticket] if the instructions do not work for you or are outdated.
You can restore your old .bashrc if something goes wrong with:
<pre>
$ mv $HOME/.bashrc.backup $HOME/.bashrc # Restoring the original bashrc
</pre>


* [[BwUniCluster2.0/Software/R/Rgdal (R 4.2.1)]]
Installed packages can be deleted by deleting the folder ${HOME}/R_libs.
* [[BwUniCluster2.0/Software/R/Rgdal]]
* [[BwUniCluster2.0/Software/R/Rjags]]
* [[BwUniCluster2.0/Software/R/Rstan]]
* [[BwUniCluster2.0/Software/R/Glmnet]]
* [[BwUniCluster2.0/Software/R/stringi]]
* [[BwUniCluster2.0/Software/R/terra (R 4.2.1)]]
* [[BwUniCluster2.0/Software/R/terra]]
* [[BwUniCluster2.0/Software/R/cummeRbund]]


= Version-Specific Information =

For information specific to a single version, see the information available via the module system with the command
<pre>
$ module help math/R
</pre>

= Installed R plugins =
* [[CummeRbund_(R-package)|Bioinformatics: cummeRbund]]
<br>
<br>
<br>
----
[[Category:Mathematics software]][[Category:bwUniCluster]][[Category:BwForCluster_BinAC]][[Category:bwForCluster_MLS&WISO_Production]]

Latest revision as of 15:18, 30 October 2024

The main documentation is available via module help math/R on the cluster. Most software modules for applications provide working example batch scripts.


Description Content
module load math/R
License GPL
Citing n/a
Links Homepage | Documentation
Graphical Interface No
Plugins User dependent

Description

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R 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. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

One of R’s strengths is the ease with which well-designed publication-quality plots can be produced, including mathematical symbols and formulae where needed. Great care has been taken over the defaults for the minor design choices in graphics, but the user retains full control.

R is available as Free Software under the terms of the Free Software Foundation’s GNU General Public License in source code form. It compiles and runs on a wide variety of UNIX platforms and similar systems (including FreeBSD and Linux), Windows and MacOS.

Usage

The R installation also provides the standalone library libRmath. This library allows you to access R routines from your own C or C++ programs (see section 9 of the 'R Installation and Administration' manual).

Installing R-Packages into your home folder

Since we cannot provide a software module for every R package, we recommend to install special R packages locally into your home folder. One possibility doing this is from within an interactive R session: 

> library()                                                                # List preinstalled packages
> install.packages('package_name', repos="http://cran.r-project.org")      # Installing your R package and the dependencies 
> library(package_name)                                                    # Loading the package into you R instance

The package is now installed permanently in your home folder and is available every time you start R.

Note:

By default R uses a version (and platform) specific path for personal libraries, such as "$HOME/R/x86_64-pc-linux-gnu-library/x.y" for R version x.y.z. This directory will be created automatically (after confirmation) when installing a personal package for the first time.

Users can customize a common location of their personal library packages, e.g. ~/R_libs, rather than the default location. A customized directory must exist before installing a personal package for the first time, i.e. 

$ mkdir -p ~/R_libs

The location must also be defined in a configuration file ~/.Renviron within the home directory containing the following line: 

R_LIBS_USER="~/R_libs"

By setting up a (fixed) custom location for personal library packages, any personal package installed into that directory will be visible across different R versions. This may be advantageous if the packages are to be used with different (future) R versions.

A version specific path, such as the default path, allows users to maintain multiple personal library stacks for different (major and minor) R versions and does also prevent users from mixing their stack with libraries built with different R versions.

The drawback is that, whenever switching to a new R release, the personal library stack must be rebuilt with that new R version into the corresponding (version specific) library path. This is considered good practice anyway in order to ensure a consistent personal library stack for any specific R version in use. Mixing libraries built with different major and minor R versions is discouraged, as this may (or may not) result in unpredictable and subtle errors. Packages that are built and installed with one version of R may be incompatible with a newer version of R, at least when the major or minor version changes. The same is true if several versions are used simultaneously, e.g. a newer R version for a more recently started project and and older version for another project (but eventually picking up libraries built with the newer R version).

Special care has also to be taken by users who always load the default version, i.e. 

$ module load math/R

as the default version number may change any time. It is therefore highly recommended to always load a specific version, e.g. 

$ module load math/R/3.6.3

Pre-installed R-packages

  • Rmpi
  • Rcpp (R 4.4.1 only)
  • RcppEigen (R 4.4.1 only)
  • iterators
  • foreach
  • doMPI
  • doParallel
  • cummeRbund (see installation instructions below)

Optional packages for R

The following guides provide detailed instructions about how to build selected optional R packages on bwUniCluster for R version 4.1.2. Please write a ticket if the instructions do not work for you or are outdated.


Retrieved from "https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&oldid=13115"