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	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Schrodinger&amp;diff=3772</id>
		<title>JUSTUS2/Software/Schrodinger</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=JUSTUS2/Software/Schrodinger&amp;diff=3772"/>
		<updated>2016-01-28T14:56:08Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=600px}}   --&amp;gt;&lt;br /&gt;
&amp;lt;!--{|{{Softwarebox}}--&amp;gt;&lt;br /&gt;
{| width=600px class=&amp;quot;wikitable&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | Schrödinger&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| chem/schrodinger&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &amp;amp;#124; [[BwForCluster_Chemistry]] &amp;amp;#124; [http://www.zdv.uni-tuebingen.de/dienstleistungen/computing/bwhpc-c5-projekte.html#c278827 bwGRiD Tuebingen]&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| commercial&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
| 5. See Schrodinger manual&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [https://www.schrodinger.com Homepage] &amp;amp;#124; [http://www.schrodinger.com/supportdocs/18/  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| Yes, Maestro, Desmond&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&#039;&#039;&#039;Schrödinger&#039;&#039;&#039; is a collection of software chemical or biochemical use. It offers various tools, like Maestro, that acts like an interface to all other schrödinger software and it is supposed to be used for material science, to investigate the structure, the reactivity and properties of chemical systems. Maestro is part of the Materials science suite.&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
Schrödinger, especially Maestro, is available after registering for academical use for no charge. Downloadable here: [https://www.schroedinger.com/downloadcenter/ Download Center]&amp;lt;br&amp;gt;&lt;br /&gt;
Your request will be verified and after that you can download Maestro for academical use. That will take about 48 hours.&lt;br /&gt;
&lt;br /&gt;
== Prerequirements ==&lt;br /&gt;
&lt;br /&gt;
=== Requesting the License Key ===&lt;br /&gt;
After installing Maestro you need a license key which you can request from the „Competence Center for Bioinformatics“. Please contact &lt;br /&gt;
&lt;br /&gt;
==== Set environment variable for the license server ====&lt;br /&gt;
When you got the licence server information, set it as an environment variable, editing $LICENSE_SERVER$ in the following command.&lt;br /&gt;
&amp;lt;pre&amp;gt;export LM_LICENSE_FILE=$LICENSE_SERVER$&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
On a Mac system you should additionally execute following tasks&lt;br /&gt;
&amp;lt;pre&amp;gt;sudo vi /etc/launchd.conf&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Insert: &amp;lt;pre&amp;gt;setenv LM_LICENSE_FILE $LICENSE_SERVER$&amp;lt;/pre&amp;gt; and save the file.&lt;br /&gt;
&lt;br /&gt;
Execute following command and start Maestro from Sportlight:&lt;br /&gt;
&amp;lt;pre&amp;gt;launchctl setenv LM_LICENSE_FILE $LICENSE_FILE$&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
=== bwGRiD/bwUni/JUSTUS specific installation ===&lt;br /&gt;
&lt;br /&gt;
Follow the instruction for your operating system.&lt;br /&gt;
&lt;br /&gt;
==== Linux/Mac ====&lt;br /&gt;
&lt;br /&gt;
Download [https://raw.githubusercontent.com/marekdynowski/bwSchrodingerHosts/master/post-install.sh this file] and open a terminal in the download folder. Make the bash-script executable&lt;br /&gt;
&amp;lt;pre&amp;gt;chmod u+x post-install.sh&amp;lt;/pre&amp;gt;&lt;br /&gt;
and execute it.&lt;br /&gt;
&amp;lt;pre&amp;gt;./post-install.sh&amp;lt;/pre&amp;gt;&lt;br /&gt;
You will be asked for the License Server, your usernames on the cluster and the schrodinger path/version.&lt;br /&gt;
&lt;br /&gt;
==== Windows ====&lt;br /&gt;
&lt;br /&gt;
$SCHRODINGER ist the path to your schrodinger installation.&lt;br /&gt;
Download [https://codeload.github.com/marekdynowski/MOAB-Schroedinger-Submitter/zip/master this zipfile], extract it and copy the MOAB folder to $SCHRODINGER/queues/.&lt;br /&gt;
&lt;br /&gt;
Download the [https://raw.githubusercontent.com/marekdynowski/bwSchrodingerHosts/master/schrodinger.hosts sample schrodinger.hosts]&lt;br /&gt;
and change the entries&lt;br /&gt;
* %LICENSE_SERVER% the address of the license server&lt;br /&gt;
* %USER_BWHPC% your username on the bwhpc cluster&lt;br /&gt;
* %USER_BWUNI% your username on the bwUni cluster&lt;br /&gt;
* %USER_BWJUSTUS% your username on the Justus cluster&lt;br /&gt;
You can delete sections of the schrodinger.hosts if you don&#039;t have an account on these clusters.&lt;br /&gt;
&lt;br /&gt;
Please execute these commands in your windows shell.&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$SCHRODINGER/utilities/feature_flags.exe -d JOBCON_JSERVER_GO&lt;br /&gt;
$SCHRODINGER/utilities/jserver.exe -cleanall&lt;br /&gt;
$SCHRODINGER/utilities/jserver.exe -shutdown&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
=== Copy your public key ===&lt;br /&gt;
Maestro needs a passwordless login for submitting jobs on the cluster. &lt;br /&gt;
Login to the cluster and copy your public key of your host system from &amp;lt;tt&amp;gt;.ssh/id_rsa.pub&amp;lt;/tt&amp;gt; into &amp;lt;tt&amp;gt;.ssh/authorized_keys&amp;lt;/tt&amp;gt; file on the cluster.&lt;br /&gt;
&lt;br /&gt;
=== Using Maestro with the offered example ===&lt;br /&gt;
First start Maestro and choose the following menu items:&amp;lt;br&amp;gt;&lt;br /&gt;
[[File:Schrodinger-Usage01.jpg|200px]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Then load the molecularDynamicsExample.cms from your filesystem:&amp;lt;br&amp;gt;&lt;br /&gt;
[[File:Schrodinger-Usage02.jpg|200px]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Choose your desired host and click &amp;quot;Run&amp;quot;.&amp;lt;br&amp;gt;&lt;br /&gt;
[[File:Schrodinger-Usage03.jpg|200px]]&lt;br /&gt;
&lt;br /&gt;
=== Monitoring you job ===&lt;br /&gt;
Maestro offers an job monitoring interface, which you can start in the left corner of the molecule window.&lt;br /&gt;
[[File:Schrodinger-Monitor01.jpg]]&lt;br /&gt;
Furthermore you are able to manipulate you job on the cluster.&lt;br /&gt;
&lt;br /&gt;
[[Category:Chemistry software]][[Category:bwUniCluster]][[Category:bwForCluster_Chemistry]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Acknowledgement&amp;diff=2593</id>
		<title>BwUniCluster2.0/Acknowledgement</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Acknowledgement&amp;diff=2593"/>
		<updated>2015-10-15T07:13:35Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;The HPC resource bwUniCluster is funded by the Ministry of Science, Research and the Arts Baden-Württemberg and the Universities of the State of Baden-Württemberg:&lt;br /&gt;
* Albert Ludwig University of Freiburg&lt;br /&gt;
* Eberhard Karls University, Tübingen&lt;br /&gt;
* Karlsruhe Institute of Technology (KIT)&lt;br /&gt;
* Ruprecht-Karls-Universität Heidelberg&lt;br /&gt;
* Ulm University&lt;br /&gt;
* University of Hohenheim&lt;br /&gt;
* University of Konstanz&lt;br /&gt;
* University of Mannheim&lt;br /&gt;
* University of Stuttgart.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Therefore, any work performed on bwUniCluster should be appropriately cited:&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;quot;This work was performed on the computational resource bwUniCluster funded by the Ministry of Science, Research and the Arts Baden-Württemberg and the Universities of the State of Baden-Württemberg, Germany, within the framework program bwHPC.&amp;quot;&#039;&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Furthermore, please report any publication that cites bwUniCluster to [mailto:publications@bwhpc-c5.de publications@bwhpc-c5.de] stating:&lt;br /&gt;
* author(s)&lt;br /&gt;
* title &#039;&#039;or&#039;&#039; booktitle&lt;br /&gt;
* journal, volume, pages &#039;&#039;or&#039;&#039; editors, address, publisher &lt;br /&gt;
* year. &lt;br /&gt;
This information will be used for the evaluation of bwUniCluster.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
----&lt;br /&gt;
[[Category:bwUniCluster|Acknowledgement]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2449</id>
		<title>BwUniCluster2.0/Software/R</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2449"/>
		<updated>2015-07-27T15:38:48Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Installing R-Packages into your home folder */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=40%}}   --&amp;gt;&lt;br /&gt;
{|{{Softwarebox}}&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | R&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| math/R&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| GPL&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [http://www.r-project.org/ Homepage]; [http://cran.r-project.org/manuals.html  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| No &amp;lt;!-- Yes could link to some x11-forwarding/vnc instructions --&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Included in module&lt;br /&gt;
| &amp;lt;!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger --&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;R&#039;&#039;&#039; 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&amp;amp;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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
&lt;br /&gt;
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/math/R CIS Information on R]&lt;br /&gt;
&lt;br /&gt;
On the command line interface of any bwHPC cluster, a list of the available R versions using&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module avail math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
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 &#039;R Installation and Administration&#039; manual.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Loading the module ===&lt;br /&gt;
You can load the default version of R with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
If you wish to load a specific (older) version, you can do so using e.g. &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R/3.1.2&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
to load the version 3.1.2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Program Binaries ===&lt;br /&gt;
&lt;br /&gt;
Standard usage:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Usage: R [options] [&amp;lt; infile] [&amp;gt; outfile]&lt;br /&gt;
    R CMD command [arguments]&lt;br /&gt;
  &lt;br /&gt;
Example: R CMD BATCH script.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Executing R in batch mode:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD BATCH --no-save --no-restore &amp;lt;INPUT_FILE&amp;gt;.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For command help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD command --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Further informations and herlp_&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Man pages:          &#039;man R&#039; and &#039;man Rscript&#039;&lt;br /&gt;
Info pages. e.g.:   &#039;info R-intro&#039; or &#039;info R-FAQ&#039;&lt;br /&gt;
Manuals:               $R_DOC_DIR/manual&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
Example scripts are available in the directory $R_EXA_DIR:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module show math/R                                                                  # show environment variables, which will be available after &#039;module load&#039;&lt;br /&gt;
$ module load math/R                                                                    # load module&lt;br /&gt;
$ ls $R_EXA_DIR                                                                           # show content of directory $R_EXA_DIR&lt;br /&gt;
$ cat $R_EXA_DIR/README                                                          # show examples README&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Run a first simple example job&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R                                                                     # load module&lt;br /&gt;
$ mkdir Rtest                                                                                  # create test directory&lt;br /&gt;
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/          # copy example files to test directory&lt;br /&gt;
$ cd Rtest/                                                                                     # change to directory&lt;br /&gt;
$ nano bwhpc-r.moab                                                                    # change job options, quit with &#039;CTRL+X&#039;&lt;br /&gt;
$ msub bwhpc-r.moab                                                                   # submit job&lt;br /&gt;
$ checkjob -v &amp;lt;JOBID&amp;gt;                                                                   # check state of job&lt;br /&gt;
$ ls                                                                                                  # when job finishes the results will be visible in this directory&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Installing R-Packages into your home folder ==&lt;br /&gt;
&lt;br /&gt;
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: &lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
cp $HOME/.bashrc $HOME/.bashrc.backup                                    # Make a backup copy of your bashrc&lt;br /&gt;
echo &amp;quot;export R_LIBS=\&amp;quot;${HOME}/R_libs\&amp;quot;&amp;quot; &amp;gt;&amp;gt; $HOME/.bashrc                 # Setting the environment variable R_LIBS permanently in your bashrc&lt;br /&gt;
source $HOME/.bashrc                                                     # Sourcing bashrc to make R_LIBS available &lt;br /&gt;
mkdir $R_LIBS                                                            # Create the R_libs folder in your HOME directory  &lt;br /&gt;
module load math/R                                                       # Loading the matlab software module&lt;br /&gt;
R                                                                        # Loading R&lt;br /&gt;
install.packages(&#039;package_name&#039;, repos=&amp;quot;http://cran.r-project.org&amp;quot;)      # Installing your R package and the dependencies &lt;br /&gt;
library(package_name)                                                    # Loading the package into you R instance&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The package is now installed permanently in your home folder and is available every time you start R. &lt;br /&gt;
&lt;br /&gt;
You can restore your old .bashrc if something goes wrong with: &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ mv $HOME/.bashrc.backup $HOME/.bashrc      # Restoring the original bashrc&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Installed packages can be deleted by deleting the folder ${HOME}/R_libs.&lt;br /&gt;
&lt;br /&gt;
== Version-Specific Information ==&lt;br /&gt;
&lt;br /&gt;
For information specific to a single version, see the information available via the module system with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module help math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Category:Mathematics software]][[Category:bwUniCluster]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2448</id>
		<title>BwUniCluster2.0/Software/R</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2448"/>
		<updated>2015-07-27T15:37:57Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Installing R-Packages into your home folder */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=40%}}   --&amp;gt;&lt;br /&gt;
{|{{Softwarebox}}&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | R&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| math/R&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| GPL&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [http://www.r-project.org/ Homepage]; [http://cran.r-project.org/manuals.html  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| No &amp;lt;!-- Yes could link to some x11-forwarding/vnc instructions --&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Included in module&lt;br /&gt;
| &amp;lt;!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger --&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;R&#039;&#039;&#039; 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&amp;amp;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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
&lt;br /&gt;
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/math/R CIS Information on R]&lt;br /&gt;
&lt;br /&gt;
On the command line interface of any bwHPC cluster, a list of the available R versions using&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module avail math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
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 &#039;R Installation and Administration&#039; manual.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Loading the module ===&lt;br /&gt;
You can load the default version of R with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
If you wish to load a specific (older) version, you can do so using e.g. &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R/3.1.2&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
to load the version 3.1.2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Program Binaries ===&lt;br /&gt;
&lt;br /&gt;
Standard usage:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Usage: R [options] [&amp;lt; infile] [&amp;gt; outfile]&lt;br /&gt;
    R CMD command [arguments]&lt;br /&gt;
  &lt;br /&gt;
Example: R CMD BATCH script.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Executing R in batch mode:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD BATCH --no-save --no-restore &amp;lt;INPUT_FILE&amp;gt;.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For command help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD command --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Further informations and herlp_&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Man pages:          &#039;man R&#039; and &#039;man Rscript&#039;&lt;br /&gt;
Info pages. e.g.:   &#039;info R-intro&#039; or &#039;info R-FAQ&#039;&lt;br /&gt;
Manuals:               $R_DOC_DIR/manual&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
Example scripts are available in the directory $R_EXA_DIR:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module show math/R                                                                  # show environment variables, which will be available after &#039;module load&#039;&lt;br /&gt;
$ module load math/R                                                                    # load module&lt;br /&gt;
$ ls $R_EXA_DIR                                                                           # show content of directory $R_EXA_DIR&lt;br /&gt;
$ cat $R_EXA_DIR/README                                                          # show examples README&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Run a first simple example job&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R                                                                     # load module&lt;br /&gt;
$ mkdir Rtest                                                                                  # create test directory&lt;br /&gt;
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/          # copy example files to test directory&lt;br /&gt;
$ cd Rtest/                                                                                     # change to directory&lt;br /&gt;
$ nano bwhpc-r.moab                                                                    # change job options, quit with &#039;CTRL+X&#039;&lt;br /&gt;
$ msub bwhpc-r.moab                                                                   # submit job&lt;br /&gt;
$ checkjob -v &amp;lt;JOBID&amp;gt;                                                                   # check state of job&lt;br /&gt;
$ ls                                                                                                  # when job finishes the results will be visible in this directory&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Installing R-Packages into your home folder ==&lt;br /&gt;
&lt;br /&gt;
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: &lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ cp $HOME/.bashrc $HOME/.bashrc.backup                                    # Make a backup copy of your bashrc&lt;br /&gt;
$ echo &amp;quot;export R_LIBS=\&amp;quot;${HOME}/R_libs\&amp;quot;&amp;quot; &amp;gt;&amp;gt; $HOME/.bashrc                 # Setting the environment variable R_LIBS permanently in your bashrc&lt;br /&gt;
$ source $HOME/.bashrc                                                     # Sourcing bashrc to make R_LIBS available &lt;br /&gt;
$ mkdir $R_LIBS                                                            # Create the R_libs folder in your HOME directory  &lt;br /&gt;
$ module load math/R                                                       # Loading the matlab software module&lt;br /&gt;
$ R                                                                        # Loading R&lt;br /&gt;
$ install.packages(&#039;package_name&#039;, repos=&amp;quot;http://cran.r-project.org&amp;quot;)      # Installing your R package and the dependencies &lt;br /&gt;
$ library(package_name)                                                    # Loading the package into you R instance&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The package is now installed permanently in your home folder and is available every time you start R. &lt;br /&gt;
&lt;br /&gt;
You can restore your old .bashrc if something goes wrong with: &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ mv $HOME/.bashrc.backup $HOME/.bashrc      # Restoring the original bashrc&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Installed packages can be deleted by deleting the folder ${HOME}/R_libs.&lt;br /&gt;
&lt;br /&gt;
== Version-Specific Information ==&lt;br /&gt;
&lt;br /&gt;
For information specific to a single version, see the information available via the module system with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module help math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Category:Mathematics software]][[Category:bwUniCluster]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2447</id>
		<title>BwUniCluster2.0/Software/R</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2447"/>
		<updated>2015-07-27T15:35:12Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Installing R-Packages into your home folder */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=40%}}   --&amp;gt;&lt;br /&gt;
{|{{Softwarebox}}&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | R&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| math/R&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| GPL&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [http://www.r-project.org/ Homepage]; [http://cran.r-project.org/manuals.html  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| No &amp;lt;!-- Yes could link to some x11-forwarding/vnc instructions --&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Included in module&lt;br /&gt;
| &amp;lt;!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger --&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;R&#039;&#039;&#039; 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&amp;amp;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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
&lt;br /&gt;
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/math/R CIS Information on R]&lt;br /&gt;
&lt;br /&gt;
On the command line interface of any bwHPC cluster, a list of the available R versions using&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module avail math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
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 &#039;R Installation and Administration&#039; manual.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Loading the module ===&lt;br /&gt;
You can load the default version of R with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
If you wish to load a specific (older) version, you can do so using e.g. &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R/3.1.2&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
to load the version 3.1.2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Program Binaries ===&lt;br /&gt;
&lt;br /&gt;
Standard usage:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Usage: R [options] [&amp;lt; infile] [&amp;gt; outfile]&lt;br /&gt;
    R CMD command [arguments]&lt;br /&gt;
  &lt;br /&gt;
Example: R CMD BATCH script.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Executing R in batch mode:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD BATCH --no-save --no-restore &amp;lt;INPUT_FILE&amp;gt;.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For command help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD command --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Further informations and herlp_&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Man pages:          &#039;man R&#039; and &#039;man Rscript&#039;&lt;br /&gt;
Info pages. e.g.:   &#039;info R-intro&#039; or &#039;info R-FAQ&#039;&lt;br /&gt;
Manuals:               $R_DOC_DIR/manual&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
Example scripts are available in the directory $R_EXA_DIR:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module show math/R                                                                  # show environment variables, which will be available after &#039;module load&#039;&lt;br /&gt;
$ module load math/R                                                                    # load module&lt;br /&gt;
$ ls $R_EXA_DIR                                                                           # show content of directory $R_EXA_DIR&lt;br /&gt;
$ cat $R_EXA_DIR/README                                                          # show examples README&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Run a first simple example job&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R                                                                     # load module&lt;br /&gt;
$ mkdir Rtest                                                                                  # create test directory&lt;br /&gt;
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/          # copy example files to test directory&lt;br /&gt;
$ cd Rtest/                                                                                     # change to directory&lt;br /&gt;
$ nano bwhpc-r.moab                                                                    # change job options, quit with &#039;CTRL+X&#039;&lt;br /&gt;
$ msub bwhpc-r.moab                                                                   # submit job&lt;br /&gt;
$ checkjob -v &amp;lt;JOBID&amp;gt;                                                                   # check state of job&lt;br /&gt;
$ ls                                                                                                  # when job finishes the results will be visible in this directory&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Installing R-Packages into your home folder ==&lt;br /&gt;
&lt;br /&gt;
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: &lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ cp $HOME/.bashrc $HOME/.bashrc.backup      # Make a backup copy of your bashrc&lt;br /&gt;
$ echo &amp;quot;export R_LIBS=\&amp;quot;${HOME}/R_libs\&amp;quot;&amp;quot; &amp;gt;&amp;gt; $HOME/.bashrc      # Setting the environment variable R_LIBS permanently in your bashrc&lt;br /&gt;
$ source $HOME/.bashrc      # Sourcing bashrc to make R_LIBS available &lt;br /&gt;
$ mkdir $R_LIBS      # Create the R_libs folder in your HOME directory  &lt;br /&gt;
$ module load math/R      # Loading the matlab software module&lt;br /&gt;
$ R      # Loading R&lt;br /&gt;
$ install.packages(&#039;package_name&#039;, repos=&amp;quot;http://cran.r-project.org&amp;quot;)      # Installing your R package and the dependencies &lt;br /&gt;
$ library(package_name)      # Loading the package into you R instance&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The package is now installed permanently in your home folder and is available every time you start R. &lt;br /&gt;
&lt;br /&gt;
You can restore your old .bashrc if something goes wrong with: &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ mv $HOME/.bashrc.backup $HOME/.bashrc      # Restoring the original bashrc&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Installed packages can be deleted by deleting the folder ${HOME}/R_libs.&lt;br /&gt;
&lt;br /&gt;
== Version-Specific Information ==&lt;br /&gt;
&lt;br /&gt;
For information specific to a single version, see the information available via the module system with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module help math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Category:Mathematics software]][[Category:bwUniCluster]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2446</id>
		<title>BwUniCluster2.0/Software/R</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2446"/>
		<updated>2015-07-27T15:33:39Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Installing R-Packages into your home folder */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=40%}}   --&amp;gt;&lt;br /&gt;
{|{{Softwarebox}}&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | R&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| math/R&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| GPL&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [http://www.r-project.org/ Homepage]; [http://cran.r-project.org/manuals.html  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| No &amp;lt;!-- Yes could link to some x11-forwarding/vnc instructions --&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Included in module&lt;br /&gt;
| &amp;lt;!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger --&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;R&#039;&#039;&#039; 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&amp;amp;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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
&lt;br /&gt;
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/math/R CIS Information on R]&lt;br /&gt;
&lt;br /&gt;
On the command line interface of any bwHPC cluster, a list of the available R versions using&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module avail math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
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 &#039;R Installation and Administration&#039; manual.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Loading the module ===&lt;br /&gt;
You can load the default version of R with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
If you wish to load a specific (older) version, you can do so using e.g. &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R/3.1.2&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
to load the version 3.1.2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Program Binaries ===&lt;br /&gt;
&lt;br /&gt;
Standard usage:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Usage: R [options] [&amp;lt; infile] [&amp;gt; outfile]&lt;br /&gt;
    R CMD command [arguments]&lt;br /&gt;
  &lt;br /&gt;
Example: R CMD BATCH script.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Executing R in batch mode:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD BATCH --no-save --no-restore &amp;lt;INPUT_FILE&amp;gt;.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For command help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD command --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Further informations and herlp_&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Man pages:          &#039;man R&#039; and &#039;man Rscript&#039;&lt;br /&gt;
Info pages. e.g.:   &#039;info R-intro&#039; or &#039;info R-FAQ&#039;&lt;br /&gt;
Manuals:               $R_DOC_DIR/manual&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
Example scripts are available in the directory $R_EXA_DIR:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module show math/R                                                                  # show environment variables, which will be available after &#039;module load&#039;&lt;br /&gt;
$ module load math/R                                                                    # load module&lt;br /&gt;
$ ls $R_EXA_DIR                                                                           # show content of directory $R_EXA_DIR&lt;br /&gt;
$ cat $R_EXA_DIR/README                                                          # show examples README&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Run a first simple example job&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R                                                                     # load module&lt;br /&gt;
$ mkdir Rtest                                                                                  # create test directory&lt;br /&gt;
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/          # copy example files to test directory&lt;br /&gt;
$ cd Rtest/                                                                                     # change to directory&lt;br /&gt;
$ nano bwhpc-r.moab                                                                    # change job options, quit with &#039;CTRL+X&#039;&lt;br /&gt;
$ msub bwhpc-r.moab                                                                   # submit job&lt;br /&gt;
$ checkjob -v &amp;lt;JOBID&amp;gt;                                                                   # check state of job&lt;br /&gt;
$ ls                                                                                                  # when job finishes the results will be visible in this directory&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Installing R-Packages into your home folder ==&lt;br /&gt;
&lt;br /&gt;
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: &lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ cp $HOME/.bashrc $HOME/.bashrc.backup      # Make a backup copy of your bashrc&lt;br /&gt;
$ echo &amp;quot;export R_LIBS=\&amp;quot;${HOME}/R_libs\&amp;quot;&amp;quot; &amp;gt;&amp;gt; $HOME/.bashrc      # Setting the environment variable R_LIBS permanently in your bashrc&lt;br /&gt;
$ source $HOME/.bashrc      # Sourcing bashrc to make R_LIBS available &lt;br /&gt;
$ mkdir $R_LIBS      # Create the R_libs folder in your HOME directory  &lt;br /&gt;
$ module load math/R      # Loading the matlab software module&lt;br /&gt;
$ R      # Loading R&lt;br /&gt;
$ install.packages(&#039;package_name&#039;, repos=&amp;quot;http://cran.r-project.org&amp;quot;)      # Installing your R package and the dependencies &lt;br /&gt;
$ library(package_name)      # Loading the package into you R instance&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The package is now installed permanently in your home folder and is available every time you start R. &lt;br /&gt;
&lt;br /&gt;
You can restore your old .bashrc if something goes wrong with: &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
mv $HOME/.bashrc.backup $HOME/.bashrc&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Installed packages can be deleted by deleting the folder ${HOME}/R_libs.&lt;br /&gt;
&lt;br /&gt;
== Version-Specific Information ==&lt;br /&gt;
&lt;br /&gt;
For information specific to a single version, see the information available via the module system with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module help math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Category:Mathematics software]][[Category:bwUniCluster]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2445</id>
		<title>BwUniCluster2.0/Software/R</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2445"/>
		<updated>2015-07-27T15:26:18Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Installing R-Packages into your home folder */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=40%}}   --&amp;gt;&lt;br /&gt;
{|{{Softwarebox}}&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | R&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| math/R&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| GPL&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [http://www.r-project.org/ Homepage]; [http://cran.r-project.org/manuals.html  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| No &amp;lt;!-- Yes could link to some x11-forwarding/vnc instructions --&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Included in module&lt;br /&gt;
| &amp;lt;!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger --&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;R&#039;&#039;&#039; 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&amp;amp;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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
&lt;br /&gt;
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/math/R CIS Information on R]&lt;br /&gt;
&lt;br /&gt;
On the command line interface of any bwHPC cluster, a list of the available R versions using&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module avail math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
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 &#039;R Installation and Administration&#039; manual.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Loading the module ===&lt;br /&gt;
You can load the default version of R with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
If you wish to load a specific (older) version, you can do so using e.g. &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R/3.1.2&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
to load the version 3.1.2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Program Binaries ===&lt;br /&gt;
&lt;br /&gt;
Standard usage:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Usage: R [options] [&amp;lt; infile] [&amp;gt; outfile]&lt;br /&gt;
    R CMD command [arguments]&lt;br /&gt;
  &lt;br /&gt;
Example: R CMD BATCH script.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Executing R in batch mode:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD BATCH --no-save --no-restore &amp;lt;INPUT_FILE&amp;gt;.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For command help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD command --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Further informations and herlp_&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Man pages:          &#039;man R&#039; and &#039;man Rscript&#039;&lt;br /&gt;
Info pages. e.g.:   &#039;info R-intro&#039; or &#039;info R-FAQ&#039;&lt;br /&gt;
Manuals:               $R_DOC_DIR/manual&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
Example scripts are available in the directory $R_EXA_DIR:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module show math/R                                                                  # show environment variables, which will be available after &#039;module load&#039;&lt;br /&gt;
$ module load math/R                                                                    # load module&lt;br /&gt;
$ ls $R_EXA_DIR                                                                           # show content of directory $R_EXA_DIR&lt;br /&gt;
$ cat $R_EXA_DIR/README                                                          # show examples README&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Run a first simple example job&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R                                                                     # load module&lt;br /&gt;
$ mkdir Rtest                                                                                  # create test directory&lt;br /&gt;
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/          # copy example files to test directory&lt;br /&gt;
$ cd Rtest/                                                                                     # change to directory&lt;br /&gt;
$ nano bwhpc-r.moab                                                                    # change job options, quit with &#039;CTRL+X&#039;&lt;br /&gt;
$ msub bwhpc-r.moab                                                                   # submit job&lt;br /&gt;
$ checkjob -v &amp;lt;JOBID&amp;gt;                                                                   # check state of job&lt;br /&gt;
$ ls                                                                                                  # when job finishes the results will be visible in this directory&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Installing R-Packages into your home folder ==&lt;br /&gt;
&lt;br /&gt;
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: &lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ cp $HOME/.bashrc $HOME/.bashrc.backup&lt;br /&gt;
$ echo &amp;quot;export R_LIBS=\&amp;quot;${HOME}/R_libs\&amp;quot;&amp;quot; &amp;gt;&amp;gt; $HOME/.bashrc&lt;br /&gt;
$ source $HOME/.bashrc&lt;br /&gt;
$ mkdir $R_LIBS&lt;br /&gt;
$ module load math/R&lt;br /&gt;
$ R&lt;br /&gt;
$ install.packages(&#039;package_name&#039;, repos=&amp;quot;http://cran.r-project.org&amp;quot;)&lt;br /&gt;
$ library(package_name)&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The package is now installed permanently in your home folder and is available every time you start R. &lt;br /&gt;
&lt;br /&gt;
You can restore your old .bashrc if something goes wrong with: &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
mv $HOME/.bashrc.backup $HOME/.bashrc&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Installed packages can be deleted by deleting the folder ${HOME}/R_libs.&lt;br /&gt;
&lt;br /&gt;
== Version-Specific Information ==&lt;br /&gt;
&lt;br /&gt;
For information specific to a single version, see the information available via the module system with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module help math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Category:Mathematics software]][[Category:bwUniCluster]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2444</id>
		<title>BwUniCluster2.0/Software/R</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2444"/>
		<updated>2015-07-27T15:22:58Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Installing R-Packages into your home folder */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=40%}}   --&amp;gt;&lt;br /&gt;
{|{{Softwarebox}}&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | R&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| math/R&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| GPL&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [http://www.r-project.org/ Homepage]; [http://cran.r-project.org/manuals.html  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| No &amp;lt;!-- Yes could link to some x11-forwarding/vnc instructions --&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Included in module&lt;br /&gt;
| &amp;lt;!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger --&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;R&#039;&#039;&#039; 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&amp;amp;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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
&lt;br /&gt;
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/math/R CIS Information on R]&lt;br /&gt;
&lt;br /&gt;
On the command line interface of any bwHPC cluster, a list of the available R versions using&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module avail math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
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 &#039;R Installation and Administration&#039; manual.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Loading the module ===&lt;br /&gt;
You can load the default version of R with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
If you wish to load a specific (older) version, you can do so using e.g. &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R/3.1.2&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
to load the version 3.1.2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Program Binaries ===&lt;br /&gt;
&lt;br /&gt;
Standard usage:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Usage: R [options] [&amp;lt; infile] [&amp;gt; outfile]&lt;br /&gt;
    R CMD command [arguments]&lt;br /&gt;
  &lt;br /&gt;
Example: R CMD BATCH script.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Executing R in batch mode:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD BATCH --no-save --no-restore &amp;lt;INPUT_FILE&amp;gt;.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For command help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD command --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Further informations and herlp_&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Man pages:          &#039;man R&#039; and &#039;man Rscript&#039;&lt;br /&gt;
Info pages. e.g.:   &#039;info R-intro&#039; or &#039;info R-FAQ&#039;&lt;br /&gt;
Manuals:               $R_DOC_DIR/manual&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
Example scripts are available in the directory $R_EXA_DIR:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module show math/R                                                                  # show environment variables, which will be available after &#039;module load&#039;&lt;br /&gt;
$ module load math/R                                                                    # load module&lt;br /&gt;
$ ls $R_EXA_DIR                                                                           # show content of directory $R_EXA_DIR&lt;br /&gt;
$ cat $R_EXA_DIR/README                                                          # show examples README&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Run a first simple example job&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R                                                                     # load module&lt;br /&gt;
$ mkdir Rtest                                                                                  # create test directory&lt;br /&gt;
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/          # copy example files to test directory&lt;br /&gt;
$ cd Rtest/                                                                                     # change to directory&lt;br /&gt;
$ nano bwhpc-r.moab                                                                    # change job options, quit with &#039;CTRL+X&#039;&lt;br /&gt;
$ msub bwhpc-r.moab                                                                   # submit job&lt;br /&gt;
$ checkjob -v &amp;lt;JOBID&amp;gt;                                                                   # check state of job&lt;br /&gt;
$ ls                                                                                                  # when job finishes the results will be visible in this directory&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Installing R-Packages into your home folder ==&lt;br /&gt;
&lt;br /&gt;
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: &lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ cp $HOME/.bashrc $HOME/.bashrc.backup&lt;br /&gt;
$ echo &amp;quot;export R_LIBS=\&amp;quot;${HOME}/R_libs\&amp;quot;&amp;quot; &amp;gt;&amp;gt; $HOME/.bashrc&lt;br /&gt;
$ source $HOME/.bashrc&lt;br /&gt;
$ mkdir $R_LIBS&lt;br /&gt;
$ module load math/R&lt;br /&gt;
$ R&lt;br /&gt;
$ install.packages(&#039;package_name&#039;, repos=&amp;quot;http://cran.r-project.org&amp;quot;)&lt;br /&gt;
$ library(package_name)&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The package is now installed permanently in your home folder and is available every time you start R. &lt;br /&gt;
&lt;br /&gt;
You can restore your old .bashrc if something goes wrong with: &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
mv $HOME/.bashrc.backup $HOME/.bashrc&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Installed packages can be deleted by deleting the folder ${HOME}/R_libs.&lt;br /&gt;
&lt;br /&gt;
== Version-Specific Information ==&lt;br /&gt;
&lt;br /&gt;
For information specific to a single version, see the information available via the module system with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module help math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Category:Mathematics software]][[Category:bwUniCluster]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2443</id>
		<title>BwUniCluster2.0/Software/R</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2443"/>
		<updated>2015-07-27T15:22:19Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Installing R-Modules into your home folder */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=40%}}   --&amp;gt;&lt;br /&gt;
{|{{Softwarebox}}&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | R&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| math/R&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| GPL&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [http://www.r-project.org/ Homepage]; [http://cran.r-project.org/manuals.html  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| No &amp;lt;!-- Yes could link to some x11-forwarding/vnc instructions --&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Included in module&lt;br /&gt;
| &amp;lt;!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger --&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;R&#039;&#039;&#039; 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&amp;amp;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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
&lt;br /&gt;
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/math/R CIS Information on R]&lt;br /&gt;
&lt;br /&gt;
On the command line interface of any bwHPC cluster, a list of the available R versions using&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module avail math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
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 &#039;R Installation and Administration&#039; manual.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Loading the module ===&lt;br /&gt;
You can load the default version of R with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
If you wish to load a specific (older) version, you can do so using e.g. &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R/3.1.2&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
to load the version 3.1.2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Program Binaries ===&lt;br /&gt;
&lt;br /&gt;
Standard usage:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Usage: R [options] [&amp;lt; infile] [&amp;gt; outfile]&lt;br /&gt;
    R CMD command [arguments]&lt;br /&gt;
  &lt;br /&gt;
Example: R CMD BATCH script.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Executing R in batch mode:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD BATCH --no-save --no-restore &amp;lt;INPUT_FILE&amp;gt;.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For command help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD command --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Further informations and herlp_&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Man pages:          &#039;man R&#039; and &#039;man Rscript&#039;&lt;br /&gt;
Info pages. e.g.:   &#039;info R-intro&#039; or &#039;info R-FAQ&#039;&lt;br /&gt;
Manuals:               $R_DOC_DIR/manual&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
Example scripts are available in the directory $R_EXA_DIR:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module show math/R                                                                  # show environment variables, which will be available after &#039;module load&#039;&lt;br /&gt;
$ module load math/R                                                                    # load module&lt;br /&gt;
$ ls $R_EXA_DIR                                                                           # show content of directory $R_EXA_DIR&lt;br /&gt;
$ cat $R_EXA_DIR/README                                                          # show examples README&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Run a first simple example job&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R                                                                     # load module&lt;br /&gt;
$ mkdir Rtest                                                                                  # create test directory&lt;br /&gt;
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/          # copy example files to test directory&lt;br /&gt;
$ cd Rtest/                                                                                     # change to directory&lt;br /&gt;
$ nano bwhpc-r.moab                                                                    # change job options, quit with &#039;CTRL+X&#039;&lt;br /&gt;
$ msub bwhpc-r.moab                                                                   # submit job&lt;br /&gt;
$ checkjob -v &amp;lt;JOBID&amp;gt;                                                                   # check state of job&lt;br /&gt;
$ ls                                                                                                  # when job finishes the results will be visible in this directory&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Installing R-Packages into your home folder ==&lt;br /&gt;
&lt;br /&gt;
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: &lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ cp $HOME/.bashrc $HOME/.bashrc.backup&lt;br /&gt;
$ echo &amp;quot;export R_LIBS=\&amp;quot;${HOME}/R_libs\&amp;quot;&amp;quot; &amp;gt;&amp;gt; $HOME/.bashrc&lt;br /&gt;
$ source $HOME/.bashrc&lt;br /&gt;
$ mkdir $R_LIBS&lt;br /&gt;
$ module load math/R&lt;br /&gt;
$ R&lt;br /&gt;
$ install.packages(&#039;package_name&#039;, repos=&amp;quot;http://cran.r-project.org&amp;quot;)&lt;br /&gt;
library(package_name)&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The package is now installed permanently in your home folder and is available every time you start R. &lt;br /&gt;
&lt;br /&gt;
You can restore your old .bashrc if something goes wrong with: &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
mv $HOME/.bashrc.backup $HOME/.bashrc&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Installed packages can be deleted by deleting the folder ${HOME}/R_libs.&lt;br /&gt;
&lt;br /&gt;
== Version-Specific Information ==&lt;br /&gt;
&lt;br /&gt;
For information specific to a single version, see the information available via the module system with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module help math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Category:Mathematics software]][[Category:bwUniCluster]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2442</id>
		<title>BwUniCluster2.0/Software/R</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster2.0/Software/R&amp;diff=2442"/>
		<updated>2015-07-27T15:14:12Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!--{|  align=&amp;quot;right&amp;quot; {{Table|width=40%}}   --&amp;gt;&lt;br /&gt;
{|{{Softwarebox}}&lt;br /&gt;
|-&lt;br /&gt;
! colspan=&amp;quot;2&amp;quot;  style=&amp;quot;text-align:center&amp;quot; | R&lt;br /&gt;
|-&lt;br /&gt;
| module load&lt;br /&gt;
| math/R&lt;br /&gt;
&amp;lt;!-- Neben CIS auch bereits über Kategorien  abgedeckt--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Availability&lt;br /&gt;
| [[bwUniCluster]] &lt;br /&gt;
&amp;lt;!-- &lt;br /&gt;
[[bwForCluster ENM]],  [[bwForCluster MLS/WISO]],  [[bwForCluster Theochem]],  [[bwForCluster BinAC]]&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| License&lt;br /&gt;
| GPL&lt;br /&gt;
|-&lt;br /&gt;
|Citing&lt;br /&gt;
|-&lt;br /&gt;
| Links&lt;br /&gt;
| [http://www.r-project.org/ Homepage]; [http://cran.r-project.org/manuals.html  Documentation]&lt;br /&gt;
| &lt;br /&gt;
|-&lt;br /&gt;
| Graphical Interface&lt;br /&gt;
| No &amp;lt;!-- Yes could link to some x11-forwarding/vnc instructions --&amp;gt;&lt;br /&gt;
|-&lt;br /&gt;
| Included in module&lt;br /&gt;
| &amp;lt;!-- mention if there is more than one software in the module, i.e. icc, ifort and debugger --&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Description == &lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;R&#039;&#039;&#039; 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&amp;amp;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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Versions and Availability ==&lt;br /&gt;
&lt;br /&gt;
A current list of the versions available on the bwUniCluster and bwForClusters can be obtained from the Cluster Information System: [http://cis-hpc.uni-konstanz.de/prod.cis/math/R CIS Information on R]&lt;br /&gt;
&lt;br /&gt;
On the command line interface of any bwHPC cluster, a list of the available R versions using&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module avail math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Usage ==&lt;br /&gt;
&lt;br /&gt;
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 &#039;R Installation and Administration&#039; manual.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Loading the module ===&lt;br /&gt;
You can load the default version of R with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
If you wish to load a specific (older) version, you can do so using e.g. &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R/3.1.2&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
to load the version 3.1.2.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=== Program Binaries ===&lt;br /&gt;
&lt;br /&gt;
Standard usage:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Usage: R [options] [&amp;lt; infile] [&amp;gt; outfile]&lt;br /&gt;
    R CMD command [arguments]&lt;br /&gt;
  &lt;br /&gt;
Example: R CMD BATCH script.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Executing R in batch mode:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD BATCH --no-save --no-restore &amp;lt;INPUT_FILE&amp;gt;.R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
For command help run&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
R CMD command --help&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Further informations and herlp_&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
Man pages:          &#039;man R&#039; and &#039;man Rscript&#039;&lt;br /&gt;
Info pages. e.g.:   &#039;info R-intro&#039; or &#039;info R-FAQ&#039;&lt;br /&gt;
Manuals:               $R_DOC_DIR/manual&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Examples ==&lt;br /&gt;
&lt;br /&gt;
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.&lt;br /&gt;
&lt;br /&gt;
Example scripts are available in the directory $R_EXA_DIR:&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module show math/R                                                                  # show environment variables, which will be available after &#039;module load&#039;&lt;br /&gt;
$ module load math/R                                                                    # load module&lt;br /&gt;
$ ls $R_EXA_DIR                                                                           # show content of directory $R_EXA_DIR&lt;br /&gt;
$ cat $R_EXA_DIR/README                                                          # show examples README&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Run a first simple example job&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module load math/R                                                                     # load module&lt;br /&gt;
$ mkdir Rtest                                                                                  # create test directory&lt;br /&gt;
$ cp $R_EXA_DIR/bwhpc-r.moab $R_EXA_DIR/fit.R Rtest/          # copy example files to test directory&lt;br /&gt;
$ cd Rtest/                                                                                     # change to directory&lt;br /&gt;
$ nano bwhpc-r.moab                                                                    # change job options, quit with &#039;CTRL+X&#039;&lt;br /&gt;
$ msub bwhpc-r.moab                                                                   # submit job&lt;br /&gt;
$ checkjob -v &amp;lt;JOBID&amp;gt;                                                                   # check state of job&lt;br /&gt;
$ ls                                                                                                  # when job finishes the results will be visible in this directory&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Installing R-Modules into your home folder ==&lt;br /&gt;
&lt;br /&gt;
Since we cannot provide an software module for every R package we recommend to install special R packages locally into you home folder. One possibility how to do this is shown below. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ cp $HOME/.bashrc $HOME/.bashrc.backup&lt;br /&gt;
$ echo &amp;quot;export R_LIBS=\&amp;quot;${HOME}/R_libs\&amp;quot;&amp;quot; &amp;gt;&amp;gt; $HOME/.bashrc&lt;br /&gt;
$ source $HOME/.bashrc&lt;br /&gt;
$ mkdir $R_LIBS&lt;br /&gt;
$ module load math/R&lt;br /&gt;
$ R&lt;br /&gt;
$ install.packages(&#039;package_name&#039;, repos=&amp;quot;http://cran.r-project.org&amp;quot;)&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
You can restore your old .bashrc if something goes wrong with: &lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
mv $HOME/.bashrc.backup $HOME/.bashrc&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Version-Specific Information ==&lt;br /&gt;
&lt;br /&gt;
For information specific to a single version, see the information available via the module system with the command&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ module help math/R&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Category:Mathematics software]][[Category:bwUniCluster]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=2171</id>
		<title>BwForCluster User Access Members Uni Tübingen</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=2171"/>
		<updated>2015-03-16T10:05:06Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Login prerequisites */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= Access to bwForCluster for members of Tübingen University =&lt;br /&gt;
&lt;br /&gt;
== Login prerequisites == &lt;br /&gt;
&lt;br /&gt;
* A valid ZDV account is required for access to the bwForCluster. &lt;br /&gt;
&amp;lt;!-- * As part of the login procedure, you will get a page that shows the data on your account that will be transferred from Tübingen University to the cluster. This page shows your entitlements. It should list the entitlement: &amp;lt;pre&amp;gt;http://bwidm.de/entitlement/bwForCluster &amp;lt;/pre&amp;gt;  If it does not, please contact the ZDV support to receive the entitlement.--&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== ZDV Account ==&lt;br /&gt;
&lt;br /&gt;
Enrolled students of Tübingen University usually have a ZDV account &lt;br /&gt;
granting access to ZDV compute resources such as the bwUniCluster.&lt;br /&gt;
&lt;br /&gt;
Faculty and staff members of Tübingen University should have an ZDV account as well, visit the following home if you don&#039;t have it yet: http://www.zdv.uni-tuebingen.de/kontakt-antraege-beratung/antraege.html&lt;br /&gt;
&lt;br /&gt;
== Terms of Use ==&lt;br /&gt;
&lt;br /&gt;
As with any other ZDV service, users of bwForCluster must strictly adhere to the [http://www.zdv.uni-tuebingen.de/wir-ueber-uns/benutzungsordnung.html ZDV terms of use].&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=2170</id>
		<title>BwForCluster User Access Members Uni Tübingen</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=2170"/>
		<updated>2015-03-16T10:04:42Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Login prerequisites */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= Access to bwForCluster for members of Tübingen University =&lt;br /&gt;
&lt;br /&gt;
== Login prerequisites == &lt;br /&gt;
&lt;br /&gt;
* A valid ZDV account is required for access to the bwForCluster. &lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- * As part of the login procedure, you will get a page that shows the data on your account that will be transferred from Tübingen University to the cluster. This page shows your entitlements. It should list the entitlement: &amp;lt;pre&amp;gt;http://bwidm.de/entitlement/bwForCluster &amp;lt;/pre&amp;gt;  If it does not, please contact the ZDV support to receive the entitlement.--&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== ZDV Account ==&lt;br /&gt;
&lt;br /&gt;
Enrolled students of Tübingen University usually have a ZDV account &lt;br /&gt;
granting access to ZDV compute resources such as the bwUniCluster.&lt;br /&gt;
&lt;br /&gt;
Faculty and staff members of Tübingen University should have an ZDV account as well, visit the following home if you don&#039;t have it yet: http://www.zdv.uni-tuebingen.de/kontakt-antraege-beratung/antraege.html&lt;br /&gt;
&lt;br /&gt;
== Terms of Use ==&lt;br /&gt;
&lt;br /&gt;
As with any other ZDV service, users of bwForCluster must strictly adhere to the [http://www.zdv.uni-tuebingen.de/wir-ueber-uns/benutzungsordnung.html ZDV terms of use].&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=1969</id>
		<title>BwForCluster User Access Members Uni Tübingen</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=1969"/>
		<updated>2014-12-17T11:31:17Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* ZDV Account */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= Access to bwForCluster for members of Tübingen University =&lt;br /&gt;
&lt;br /&gt;
== Login prerequisites == &lt;br /&gt;
&lt;br /&gt;
* A valid ZDV account is required for access to the bwForCluster. &lt;br /&gt;
&lt;br /&gt;
* As part of the login procedure, you will get a page that shows the data on your account that will be transferred from Tübingen University to the cluster. This page shows your entitlements. It should list the entitlement: &amp;lt;pre&amp;gt;http://bwidm.de/entitlement/bwForCluster &amp;lt;/pre&amp;gt;  If it does not, please contact the ZDV support to receive the entitlement.&lt;br /&gt;
&lt;br /&gt;
== ZDV Account ==&lt;br /&gt;
&lt;br /&gt;
Enrolled students of Tübingen University usually have a ZDV account &lt;br /&gt;
granting access to ZDV compute resources such as the bwUniCluster.&lt;br /&gt;
&lt;br /&gt;
Faculty and staff members of Tübingen University should have an ZDV account as well, visit the following home if you don&#039;t have it yet: http://www.zdv.uni-tuebingen.de/kontakt-antraege-beratung/antraege.html&lt;br /&gt;
&lt;br /&gt;
== Terms of Use ==&lt;br /&gt;
&lt;br /&gt;
As with any other ZDV service, users of bwForCluster must strictly adhere to the [http://www.zdv.uni-tuebingen.de/wir-ueber-uns/benutzungsordnung.html ZDV terms of use].&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=1968</id>
		<title>BwForCluster User Access Members Uni Tübingen</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=1968"/>
		<updated>2014-12-17T11:30:28Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= Access to bwForCluster for members of Tübingen University =&lt;br /&gt;
&lt;br /&gt;
== Login prerequisites == &lt;br /&gt;
&lt;br /&gt;
* A valid ZDV account is required for access to the bwForCluster. &lt;br /&gt;
&lt;br /&gt;
* As part of the login procedure, you will get a page that shows the data on your account that will be transferred from Tübingen University to the cluster. This page shows your entitlements. It should list the entitlement: &amp;lt;pre&amp;gt;http://bwidm.de/entitlement/bwForCluster &amp;lt;/pre&amp;gt;  If it does not, please contact the ZDV support to receive the entitlement.&lt;br /&gt;
&lt;br /&gt;
== ZDV Account ==&lt;br /&gt;
&lt;br /&gt;
Enrolled students of Tübingen University usually have a ZDV account &lt;br /&gt;
granting access to ZDV compute resources such as the bwUniCluster.&lt;br /&gt;
&lt;br /&gt;
Faculty and staff members of Tübingen University should have an ZDV account by default, visit the following home if you don&#039;t have it yet: http://www.zdv.uni-tuebingen.de/kontakt-antraege-beratung/antraege.html&lt;br /&gt;
&lt;br /&gt;
== Terms of Use ==&lt;br /&gt;
&lt;br /&gt;
As with any other ZDV service, users of bwForCluster must strictly adhere to the [http://www.zdv.uni-tuebingen.de/wir-ueber-uns/benutzungsordnung.html ZDV terms of use].&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=1965</id>
		<title>BwForCluster User Access Members Uni Tübingen</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access_Members_Uni_T%C3%BCbingen&amp;diff=1965"/>
		<updated>2014-12-17T11:03:02Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: Created page with &amp;quot;= Access to bwForCluster for members of Tübingen University =  == Login prerequisites ==   * A valid ZDV account is required for access to the bwForCluster.   * As part of th...&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;= Access to bwForCluster for members of Tübingen University =&lt;br /&gt;
&lt;br /&gt;
== Login prerequisites == &lt;br /&gt;
&lt;br /&gt;
* A valid ZDV account is required for access to the bwForCluster. &lt;br /&gt;
&lt;br /&gt;
* As part of the login procedure, you will get a page that shows the data on your account that will be transferred from Tübingen University to the cluster. This page shows your entitlements. It should list the entitlement: &amp;lt;pre&amp;gt;http://bwidm.de/entitlement/bwForCluster &amp;lt;/pre&amp;gt;  If it does not, please write an email to hpcmaster(AT)uni-tuebingen.de to receive the entitlement.&lt;br /&gt;
&lt;br /&gt;
== ZDV Account ==&lt;br /&gt;
&lt;br /&gt;
Enrolled students of Tübingen University usually have a ZDV account &lt;br /&gt;
granting access to ZDV compute resources such as the bwUniCluster.&lt;br /&gt;
&lt;br /&gt;
Faculty and staff members of Tübingen University can receive this account upon&lt;br /&gt;
request of their department head (if they don&#039;t already have it). &lt;br /&gt;
&lt;br /&gt;
For more information please visit the related ZDV web pages: http://www.zdv.uni-tuebingen.de/kontakt-antraege-beratung/antraege.html&lt;br /&gt;
&lt;br /&gt;
== Terms of Use ==&lt;br /&gt;
&lt;br /&gt;
As with any other ZDV service, users of bwForCluster must strictly adhere to the [http://www.zdv.uni-tuebingen.de/wir-ueber-uns/benutzungsordnung.html ZDV terms of use].&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access&amp;diff=1964</id>
		<title>BwForCluster User Access</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwForCluster_User_Access&amp;diff=1964"/>
		<updated>2014-12-17T10:54:21Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Issueing bwForCluster entitlement */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;The usage of bwForCluster is free of charge. bwForClusters are customized to the requirements of particular research areas. &lt;br /&gt;
Each bwForCluster is/will be financed by the DFG (German Research Foundation) and by the Ministry of Science, Research and Arts of Baden-Württemberg based on scientifc grant proposal (compare proposals guidelines as per Art. 91b GG).&lt;br /&gt;
&lt;br /&gt;
{| style=&amp;quot;width: 100%; border-spacing: 5px;&amp;quot;&lt;br /&gt;
| style=&amp;quot;text-align:center; color:#000;vertical-align:middle;font-size:75%;&amp;quot; |[[File:Bwforreg.svg|center|border|500px|]] &lt;br /&gt;
|-&lt;br /&gt;
| style=&amp;quot;text-align:center; color:#000;vertical-align:middle;&amp;quot; |&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Granting user access to a &#039;&#039;&#039;&#039;&#039;bwForCluster&#039;&#039;&#039;&#039;&#039; requires 3 steps:&lt;br /&gt;
&lt;br /&gt;
# Registration of your &#039;&#039;&#039;&#039;&#039;Rechenvorhaben&#039;&#039;&#039;&#039;&#039; at [https://www.bwhpc-c5.de/ZAS/zas_uebersicht.php &amp;quot;Zentrale Antragsseite (ZAS)&amp;quot;]. A &#039;&#039;rechenvorhaben&#039;&#039; (RV) defines the planned compute activities of a group of researchers. As coworker of this group you only need to register your membership in the corresponding &#039;&#039;&#039;&#039;&#039;RV&#039;&#039;&#039;&#039;&#039;.&lt;br /&gt;
# Application for [[#Issueing bwForCluster entitlement | bwForCluster entitlement]] issued by your university,&lt;br /&gt;
# Personal registration at assigned cluster site based on approved &#039;&#039;&#039;&#039;&#039;RV&#039;&#039;&#039;&#039;&#039; [[File:Zas assignment icon.svg|25px|]] and issued bwForCluster entitlement [[File:bwfor entitlement icon.svg|25px|]].&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
Step 1 and 2 are pre-steps and requirements of step 3. Moreover, steps 1 and 2 can be done in parallel. The question, at which bwForCluster site to do step 3, will be answered by the cluster assignment team (CAT) based on the data of step 1, i.e. at ZAS. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
=  RV registration at ZAS =&lt;br /&gt;
&lt;br /&gt;
The &#039;&#039;rechenvorhaben&#039;&#039; (RV) registration at ZAS does &#039;&#039;&#039;NOT&#039;&#039;&#039; correspond to typical compute project proposals as for other HPC clusters, since:&lt;br /&gt;
* there is no scientific reviewing process&lt;br /&gt;
* the registration inquires only brief details and&lt;br /&gt;
* it covers a group of coworkers, and&lt;br /&gt;
* only the &#039;&#039;&#039;&#039;&#039;RV&#039;&#039;&#039;&#039;&#039; responsible must submit the &#039;&#039;rechenvorhaben&#039;&#039;.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== How to register? ==&lt;br /&gt;
=== RV ===&lt;br /&gt;
Typically only the leader of a scientific work group or the senior scientist of a research group/collaboration needs to login at&lt;br /&gt;
* https://www.bwhpc-c5.de/en/ZAS/bwforcluster_rv_registration.php&lt;br /&gt;
and to fill in all mandatory fields of the given web form. Please note that for your convenience you can also switch to the [https://www.bwhpc-c5.de/ZAS/bwforcluster_rechenvorhaben.php german version] of the web form. The submitter of the &#039;&#039;&#039;&#039;&#039;RV&#039;&#039;&#039;&#039;&#039; will be assigned the role &#039;&#039;&#039;RV responsible&#039;&#039;&#039;.&lt;br /&gt;
&lt;br /&gt;
The web form consists of the following &#039;&#039;&#039;fields&#039;&#039;&#039; to be filled:&lt;br /&gt;
{| style=&amp;quot;width:100%;border:3px solid darkgray; margin: 1em auto 1em auto;&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
! style=&amp;quot;width:25%;padding:2px;margin:3px; background:#AAA; font-size:100%; font-weight:bold; border:1px solid #BBBBBB; text-align:left; color:#000; padding:0.2em 0.4em;&amp;quot;| Field&lt;br /&gt;
! style=&amp;quot;padding:2px;margin:3px; background:#AAA; font-size:100%; font-weight:bold; border:1px solid #BBBBBB; text-align:left; color:#000; padding:0.2em 0.4em;&amp;quot; | Explanation&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| RV Title&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Define a short title of your planned compute activities, maximum of 255 characters including spaces.&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| RV Description&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Write a short abstract about your planned compute activities (maximum of 2048 characters including spaces). Research groups that contributed to the DFG grant proposal (Art. 91b GG) of the corresponding bwForCluster only need to give reference to that particular proposal.&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Scientific field&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Tick one or several scientific fields. Once all bwForClusters are up and running the full list of given scientific fields are supported and hence for &#039;&#039;rechenvorhaben&#039;&#039; applicable. If your &#039;&#039;rechenvorhaben&#039;&#039; does not match any given scientific field, please state your scientific field in the given text box. Grayed out scientific fields indicate that the corresponding bwForCluster(s) is/are not operational yet.&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Field of activity&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Define if your &#039;&#039;&#039;RV&#039;&#039;&#039; is primarily for research and/or teaching. If not applicable, use text box.&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Parallel paradigm&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | State what parallel paradigm your code or application uses. Multiple ticks are allowed. Further information can be provided via text box. If you are not sure about it, please state the software you are using.&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Programming language&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | State the programming language(s) of your code or application.&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Numerical methods&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | State the numerical or &amp;quot;calculation&amp;quot; methods your code or application utilises. If you do not know, write &amp;quot;unknown&amp;quot;. &lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Software packages&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | State all software package you will or want to use for your &#039;&#039;&#039;RV&#039;&#039;&#039;. Also include compiler, MPI and numerical packages (e.g. MKL, FFTW).&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Estimated requested computing resources&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Roughly estimate how many CPU hours are required to finish your &#039;&#039;&#039;RV&#039;&#039;&#039;. To calculate &amp;quot;CPU hours&amp;quot; multiply &amp;quot;elapsed parallel computing time&amp;quot; with &amp;quot;number of CPU core&amp;quot; per job. &lt;br /&gt;
&#039;&#039;Example: Your code uses 4 CPU cores and has a wall time of 1h. This makes 4 CPU hours.&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Planned maximum number of parallel used CPU cores per job&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Give an upper limit of how many CPU cores per job are required. Please cross-check with your statement about parallel paradigm. &lt;br /&gt;
&#039;&#039;Obviously, a sequential code can only use 1 CPU core per job.&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Estimated maximal memory requirements per CPU core&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Give an upper limit of how much RAM per CPU core your jobs require. Please give a value in GigaBytes.&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Estimated requested persistent disk space for the &#039;&#039;rechenvorhaben&#039;&#039;&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | State how much disk space in total you need for your &#039;&#039;&#039;RV&#039;&#039;&#039;. Please give a value in GigaBytes. &lt;br /&gt;
&#039;&#039;Example: If your &#039;&#039;&#039;RV&#039;&#039;&#039; has 4 more coworker and each of you produces until the end of your &#039;&#039;&#039;RV&#039;&#039;&#039; 20 GigaByte of output, your maximum disk space is 100 GigaByte.&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Estimated maximal temporary disk space per job&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | State how much space your intermediate files require during a job run. Please give a value in GigaBytes. &lt;br /&gt;
&#039;&#039;Example: Your final output of your job is 0.1 GigaByte, but during your job 10 temporary files, each with a size of 1 GigaByte, are written to disk, hence your correct answer is 10 GigaByte.&#039;&#039;&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| Institute&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | State the full name of your Institute.&lt;br /&gt;
|-&lt;br /&gt;
|}&lt;br /&gt;
Note that the fields - name, firstname, organization, mail, und EPPN - are auto-filled and can not be changed. These are your credentials as given by your home organization.&lt;br /&gt;
&amp;lt;br&amp;gt;&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;span style=&amp;quot;font-weight:bold;font-size:110%;&amp;quot;&amp;gt;Response&amp;lt;/span&amp;gt;&lt;br /&gt;
# After submitting you will get an email from ZAS confirming your submission. With this email you are given an unique&amp;lt;br&amp;gt;* acronym&amp;lt;br&amp;gt;* password&amp;lt;br&amp;gt;Please keep the password enclosed. Only with both, acronym and password, [[BwForCluster_User_Access#Coworkers|coworkers]] can be added to your &#039;&#039;rechenvorhaben&#039;&#039;.&lt;br /&gt;
# The cluster assignment team will be notified immediately about your submission.&lt;br /&gt;
# The cluster assignment team decides within 2 working days and based on your submitted data which bwForCluster most fits, and submits its decision to ZAS.&lt;br /&gt;
# ZAS notifies you in an email about your assigned bwForCluster and provides website details for [[BwForCluster_User_Access#Personal registration at bwForCluster|step 3]].&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
=== Coworkers ===&lt;br /&gt;
Important, each coworker must add herself/himself to a &#039;&#039;rechenvorhaben&#039;&#039;, since only via personal authentication the correctness of personal credentials (provided by your home organization) can be guaranteed. To become coworker of a &#039;&#039;rechenvorhaben&#039;&#039;, please login at&lt;br /&gt;
* https://www.bwhpc-c5.de/en/ZAS/bwforcluster_collaboration.php&lt;br /&gt;
and provide correct&lt;br /&gt;
* password&lt;br /&gt;
* acronym &lt;br /&gt;
of the &#039;&#039;rechenvorhaben&#039;&#039;. Your RV responsible will provide you with that information. The submitter will be assigned the role &#039;&#039;&#039;RV member&#039;&#039;&#039;.&lt;br /&gt;
&amp;lt;br&amp;gt;&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;span style=&amp;quot;font-weight:bold;font-size:110%;&amp;quot;&amp;gt;Response&amp;lt;/span&amp;gt;&lt;br /&gt;
# After submitting the request for participating a &#039;&#039;&#039;RV&#039;&#039;&#039;, the coworker will receive an email from ZAS about the process. The membership status in the &#039;&#039;&#039;RV&#039;&#039;&#039; is set active by default.&lt;br /&gt;
# Each person with the role of &#039;&#039;&#039;RV responsible&#039;&#039;&#039; or &#039;&#039;&#039;RV manager&#039;&#039;&#039; will be notified. Any of these persons can crosscheck via https://www.bwhpc-c5.de/en/ZAS/info_compute_project.php and clicking on the correct RV acronym the correctness of the process.&lt;br /&gt;
# The RV responsible can set any &#039;&#039;&#039;RV coworker&#039;&#039;&#039; to &#039;&#039;&#039;RV manager&#039;&#039;&#039; and vice versa as well as deactivate/reactivate any &#039;&#039;&#039;RV coworker&#039;&#039;&#039; or &#039;&#039;&#039;RV manager&#039;&#039;&#039;.&lt;br /&gt;
# Any RV manager can deactivate/reactivate any &#039;&#039;&#039;RV coworker&#039;&#039;&#039;.  &lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--=== RV extension === &lt;br /&gt;
Any RV is restricted to 1 year duration and the given compute resources during registration. Only the RV responsible can apply for an extension of the RV. The extension can be the duration by another year or the increase of computational resources. In any case, the RV responsible must login at:&lt;br /&gt;
&amp;lt;br&amp;gt;&amp;lt;br&amp;gt;&lt;br /&gt;
&amp;lt;span style=&amp;quot;font-weight:bold;font-size:115%;&amp;quot;&amp;gt;Response&amp;lt;/span&amp;gt; &lt;br /&gt;
# After submission the RV responsible will receive an email from ZAS--&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Roles in a RV ==&lt;br /&gt;
{| style=&amp;quot;width:100%;border:3px solid darkgray; margin: 1em auto 1em auto;&amp;quot;&lt;br /&gt;
|-&lt;br /&gt;
! style=&amp;quot;width:25%;padding:2px;margin:3px; background:#AAA; font-size:100%; font-weight:bold; border:1px solid #BBBBBB; text-align:left; color:#000; padding:0.2em 0.4em;&amp;quot;| Role&lt;br /&gt;
! style=&amp;quot;padding:2px;margin:3px; background:#AAA; font-size:100%; font-weight:bold; border:1px solid #BBBBBB; text-align:left; color:#000; padding:0.2em 0.4em;&amp;quot; | Explanation&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| RV responsible&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Registers the &#039;&#039;rechenvorhaben&#039;&#039; (RV), i.e. the planned compute activities. Can deactivate but also reactivate RV managers and coworkers. Can promote coworkers to mangers and vice versa.&lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| RV manager&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Defines a RV coworker with rights to deactivate and reactivate RV coworkers.  &lt;br /&gt;
|-&lt;br /&gt;
!scope=&amp;quot;column&amp;quot; {{Lightgray_small}}| RV coworker&lt;br /&gt;
|scope=&amp;quot;column&amp;quot; {{Tab element}} | Registers her/his membership via RV acronym and password.&lt;br /&gt;
|-&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
= Issueing bwForCluster entitlement =&lt;br /&gt;
&lt;br /&gt;
Each university issues the bwForCluster entitlement&lt;br /&gt;
&amp;lt;pre&amp;gt;http://bwidm.de/entitlement/bwForCluster&amp;lt;/pre&amp;gt;&lt;br /&gt;
only for their own members. &lt;br /&gt;
&lt;br /&gt;
The following unversities have already established a process to issue the bwForCluster entitlement:&lt;br /&gt;
* [http://www.scc.kit.edu/downloads/sdo/Antrag_Zugangsberechtigung_bwForCluster_v2.pdf KIT]&lt;br /&gt;
* [[BwForCluster User Access Members Uni Ulm|Ulm University]]&lt;br /&gt;
* [[BwForCluster User Access Members Uni Tübingen|Tübingen University]]&lt;br /&gt;
If you do not find your university in the list above, please contact your local service desk.&lt;br /&gt;
&lt;br /&gt;
= Personal registration at bwForCluster  = &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Once you have registered your own RV (&#039;&#039;rechenvorhaben&#039;&#039;) or a membership in an RV at ZAS, the cluster assignment team will provide you with information about your designated cluster. You will receive an email providing you with the website to finally register yourself for the this cluster.&lt;br /&gt;
&lt;br /&gt;
Please note, this step is different to your registration at ZAS since here you do not register your RV or your membership in an RV but yourself as a person. Only based on your personal credentials a user account can be generated. However, defined resource requests (compare your RV or RV membership registration) will be cross-checked with the resources consumed by you and your coworkers of the RV.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
After steps 1 and 2 (RV approval and bwForCluster entitlement) please visit the&lt;br /&gt;
&lt;br /&gt;
* &#039;&#039;Service provider&#039;&#039; cluster registration website (link to this website in email after RV approval):&lt;br /&gt;
*# Select your home organization from the list of organizations and click &#039;&#039;&#039;Proceed&#039;&#039;&#039;.&lt;br /&gt;
*# You will be redirected to the &#039;&#039;Identity Provider&#039;&#039; of your home organization.&lt;br /&gt;
*# Enter your home-organizational user ID (might be user name, email, ...) and password and click &#039;&#039;&#039;Login&#039;&#039;&#039; or &#039;&#039;&#039;Anmelden&#039;&#039;&#039;.&lt;br /&gt;
*# When doing this for the first time you need to accept that your personal data is transferred to the &#039;&#039;service provider&#039;&#039;.&lt;br /&gt;
*# You will be redirected back to the cluster registration website.&lt;br /&gt;
*# Select &#039;&#039;&#039;Service Description&#039;&#039;&#039; of the designated cluster.&lt;br /&gt;
*# Click on &#039;&#039;&#039;Register&#039;&#039;&#039; link to register for this cluster.&lt;br /&gt;
*# Read and accept the terms and conditions of use and click on button &#039;&#039;&#039;Register&#039;&#039;&#039;.&lt;br /&gt;
*# Finally you will receive an email with instructions how to login to the cluster (please wait ~15 minutes before trying).&lt;br /&gt;
*# Optionally but strongly recommended: Click on &#039;&#039;&#039;Set Service Password&#039;&#039;&#039; and set a password for this cluster.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
----&lt;br /&gt;
[[Category:Access|bwForCluster]][[Category:bwForCluster_Chemistry]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
	<entry>
		<id>https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster_2.0_User_Access&amp;diff=733</id>
		<title>BwUniCluster 2.0 User Access</title>
		<link rel="alternate" type="text/html" href="https://wiki.bwhpc.de/wiki/index.php?title=BwUniCluster_2.0_User_Access&amp;diff=733"/>
		<updated>2014-02-12T15:41:50Z</updated>

		<summary type="html">&lt;p&gt;M Dynowski: /* Step A: bwUniCluster entitlement for registration */&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{| style=&amp;quot;border-style: solid; border-width: 1px&amp;quot;&lt;br /&gt;
! Navigation: [[BwHPC_Best_Practices_Repository|bwHPC BPR]] / [[BwUniCluster_User_Guide|bwUniCluster]] &lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!--&amp;lt;span style=&amp;quot;color:red;font-size:105%;&amp;quot;&amp;gt;Important note: bwUniCluster is &#039;&#039;&#039;not&#039;&#039;&#039; in production mode yet.&amp;lt;/span&amp;gt;--&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&#039;&#039;bwUniCluster&#039;&#039;&#039;&#039;&#039; is Baden-Württemberg&#039;s general purpose tier 3 high performance computing (HPC)&lt;br /&gt;
cluster co-financed by Baden-Württemberg&#039;s ministry of science, research and arts and &lt;br /&gt;
the shareholders:&lt;br /&gt;
* Albert Ludwig University of Freiburg&lt;br /&gt;
* Eberhard Karls University, Tübingen&lt;br /&gt;
* Karlsruhe Institute of Technology (KIT)&lt;br /&gt;
* Ruprecht-Karls-Universität Heidelberg&lt;br /&gt;
* Ulm University&lt;br /&gt;
* University of Hohenheim&lt;br /&gt;
* University of Konstanz&lt;br /&gt;
* University of Mannheim&lt;br /&gt;
* University of Stuttgart&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
To log on &#039;&#039;&#039;&#039;&#039;bwUniCluster&#039;&#039;&#039;&#039;&#039; an user account is required. All members of  the shareholder&lt;br /&gt;
universities can apply for an account.&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
{| style=&amp;quot;width: 100%; border-spacing: 5px;&amp;quot;&lt;br /&gt;
| style=&amp;quot;text-align:left; color:#000;vertical-align:top;&amp;quot; |__TOC__ &lt;br /&gt;
|&amp;lt;br&amp;gt;&amp;lt;br&amp;gt;[[File:bwUniCluster_17Jan2014_p044-rot_t10.10.00.jpg|center|border|250px|bwUniCluster wiring by Holger Obermaier, copyright: KIT (SCC)]] &amp;lt;span style=&amp;quot;font-size:80%&amp;quot;&amp;gt;bwUniCluster wiring © KIT (SCC)&amp;lt;/span&amp;gt;&lt;br /&gt;
|}&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
= Registration =&lt;br /&gt;
&lt;br /&gt;
Granting access and issuing a user account for &#039;&#039;&#039;&#039;&#039;bwUniCluster&#039;&#039;&#039;&#039;&#039; requires the registration at the KIT service website [https://bwidm.scc.kit.edu/ https://bwidm.scc.kit.edu] (step B). However, this registration depends on the &#039;&#039;&#039;bwUniCluster entitlement&#039;&#039;&#039; issued by your university (step A).&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Step A: bwUniCluster entitlement for registration ==&lt;br /&gt;
Each university issues the bwUniCluster entitlement &#039;&#039;&#039;only&#039;&#039;&#039; for their own members. Details on the issuing process and/or the entitlement application forms are listed hereafter:  &lt;br /&gt;
* [https://www.bwhpc-c5.uni-freiburg.de/bwunicluster/freischaltung-uni-account Albert Ludwig University of Freiburg]&lt;br /&gt;
* [http://www.zdv.uni-tuebingen.de/dienstleistungen/computing/zugang-zu-den-ressourcen.html Eberhard Karls University of Tübingen]&lt;br /&gt;
* [http://www.scc.kit.edu/downloads/sdo/Antrag_Benutzernummer_bwUniCluster.pdf KIT]&lt;br /&gt;
* [[Media:unknown.pdf‎|Ruprecht-Karls-Universität Heidelberg]]&lt;br /&gt;
* [[BWUniCluster_User_Access_Members_Uni_Ulm|Ulm University]]&lt;br /&gt;
* [http://www.rz.uni-hohenheim.de/bwhpc University of Hohenheim]&lt;br /&gt;
* [[BWUniCluster_User_Access_Members_Uni_Konstanz|University of Konstanz]]&lt;br /&gt;
* [[Media:unknown.pdf‎|University of Mannheim]]&lt;br /&gt;
* [[Media:unknown.pdf‎|University of Stuttgart]]&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Step B: Web Registration ==&lt;br /&gt;
After step A, i.e., after issueing the bwUniCluster entitlement, please visit: &lt;br /&gt;
* [https://bwidm.scc.kit.edu/ https://bwidm.scc.kit.edu] &lt;br /&gt;
*# Select your home organization from the list and click &#039;&#039;&#039;Proceed&#039;&#039;&#039;&lt;br /&gt;
*# You will be directed to the &#039;&#039;Identity Provider&#039;&#039; of your home organisation  &lt;br /&gt;
*# Enter your home-organisational user ID / username  and your home-organisational password and click &#039;&#039;&#039;Login&#039;&#039;&#039; button&lt;br /&gt;
*# You will be redirected back to the registration website [https://bwidm.scc.kit.edu/ https://bwidm.scc.kit.edu/] &lt;br /&gt;
*# &amp;lt;div&amp;gt;Select &#039;&#039;&#039;bwUniCluster Service Description&#039;&#039;&#039; (on the left hand side)&amp;lt;br&amp;gt;[[File:bwUniCluster_registration_sidebar.png|center|border|]]&amp;lt;/div&amp;gt;&lt;br /&gt;
*# Click &#039;&#039;&#039;Register&#039;&#039;&#039;&lt;br /&gt;
*# Finally&lt;br /&gt;
*#* for all non-KIT members &#039;&#039;&#039;mandatorily&#039;&#039;&#039; set a service password for authentication on bwUniCluster&lt;br /&gt;
*#* for KIT members &#039;&#039;&#039;optionally&#039;&#039;&#039; set a service password for authentication on bwUniCluster&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&amp;lt;!-- old description&lt;br /&gt;
** login with your home-organizational user account and user password,&lt;br /&gt;
** select service &#039;&#039;&#039;&#039;&#039;bwUniCluster&#039;&#039;&#039;&#039;&#039; (on the left side) and &lt;br /&gt;
** follow the instructions to complete the registration.&lt;br /&gt;
--&amp;gt;&lt;br /&gt;
&amp;lt;br/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
== Changing Password ==&lt;br /&gt;
By default, for KIT members your bwUniCluster &#039;&#039;&#039;password&#039;&#039;&#039; to log on matches  that one of your KIT &lt;br /&gt;
account, while for all non-KIT members your bwUniCluster &#039;&#039;&#039;password&#039;&#039;&#039; is that one you saved during the web registration (compare step 7 of chapter 1.2). &lt;br /&gt;
At any time, you can set a new bwUniCluster password via the registration website [https://bwidm.scc.kit.edu/ https://bwidm.scc.kit.edu] by carrying out the following steps:&lt;br /&gt;
# visit [https://bwidm.scc.kit.edu/ https://bwidm.scc.kit.edu] and select your home organization &lt;br /&gt;
# authenticate yourself via your home-organizational user id / username and your home-organizational password&lt;br /&gt;
# find on the left side &#039;&#039;&#039;bwUniCluster&#039;&#039;&#039; and select &#039;&#039;&#039;Set Service Password&#039;&#039;&#039;&lt;br /&gt;
# set new service, i.e. bwUniCluster, password, repeat it and click &#039;&#039;&#039;Save&#039;&#039;&#039; button.&lt;br /&gt;
# the page answers e.g. &amp;quot;Das Passwort wurde bei dem Dienst geändert&amp;quot; (&amp;quot;password has been changed&amp;quot;)&lt;br /&gt;
# proceed to log in using the new password in the next step&lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==  Contact ==&lt;br /&gt;
If you have questions or problems concerning registration, please [[BwUniCluster_Contact_and_Support#Registration|contact your local hotline]]. &lt;br /&gt;
&amp;lt;br&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
= Login =&lt;br /&gt;
After finishing the web registration &#039;&#039;&#039;&#039;&#039;bwUniCluster&#039;&#039;&#039;&#039;&#039; is ready for your &#039;&#039;&#039;SSH&#039;&#039;&#039; based login.&lt;br /&gt;
&#039;&#039;&#039;&#039;&#039;bwUniCluster&#039;&#039;&#039;&#039;&#039; has two dedicated login nodes. The selection of the login node is done automatically and is based on a round-robin scheduling. Logging in another time the session might run &lt;br /&gt;
on the other login node.&lt;br /&gt;
&lt;br /&gt;
Only the secure shell &#039;&#039;&#039;SSH&#039;&#039;&#039; is allowed to login. Other protocols like &#039;&#039;&#039;telnet&#039;&#039;&#039; or &#039;&#039;&#039;rlogin&#039;&#039;&#039;&lt;br /&gt;
are not allowed for security reasons.&lt;br /&gt;
&lt;br /&gt;
A connection to &#039;&#039;&#039;&#039;&#039;bwUniCluster&#039;&#039;&#039;&#039;&#039; can be established by the command:&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ ssh &amp;lt;UserID&amp;gt;@bwunicluster.scc.kit.edu&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
If you are using &#039;&#039;&#039;OpenSSH&#039;&#039;&#039; (usually installed on Linux based systems) and you want to use a GUI-based application on &#039;&#039;&#039;&#039;&#039;bwUniCluster&#039;&#039;&#039;&#039;&#039; you should use the &lt;br /&gt;
&#039;&#039;ssh&#039;&#039; command with the option &#039;&#039;-X&#039;&#039;&lt;br /&gt;
&lt;br /&gt;
&amp;lt;pre&amp;gt;&lt;br /&gt;
$ ssh -X &amp;lt;UserID&amp;gt;@bwunicluster.scc.kit.edu&lt;br /&gt;
&amp;lt;/pre&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== About UserID / Username ==&lt;br /&gt;
&lt;br /&gt;
&#039;&#039;&#039;&amp;lt;UserID&amp;gt;&#039;&#039;&#039; of the ssh command is a placeholder for your &#039;&#039;&#039;&#039;&#039;username&#039;&#039;&#039;&#039;&#039; at your home &lt;br /&gt;
organization together with a &#039;&#039;&#039;&#039;&#039;prefix&#039;&#039;&#039;&#039;&#039; as followed:&lt;br /&gt;
&lt;br /&gt;
* Freiburg: &amp;lt;UserID&amp;gt; = fr_username&lt;br /&gt;
* Heidelberg: &amp;lt;UserID&amp;gt; = hd_username&lt;br /&gt;
* Hohenheim: &amp;lt;UserID&amp;gt; = ho_username&lt;br /&gt;
* KIT:  &amp;lt;UserID&amp;gt; = username &#039;&#039;(without any prefix)&#039;&#039;&lt;br /&gt;
* Konstanz: &amp;lt;UserID&amp;gt; = kn_username&lt;br /&gt;
* Mannheim: &amp;lt;UserID&amp;gt; = ma_username&lt;br /&gt;
* Stuttgart: &amp;lt;UserID&amp;gt; = st_username&lt;br /&gt;
* Tübingen: &amp;lt;UserID&amp;gt; = tu_username&lt;br /&gt;
* Ulm: &amp;lt;UserID&amp;gt; = ul_username&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Allowed activities on login nodes ==&lt;br /&gt;
&lt;br /&gt;
The login nodes of bwUniCluster are the access point to the compute system and to your bwUniCluster $HOME directory. The login nodes are shared with all the users of bwUniCluster. Therefore, your activities on the login nodes are limited to primarily set up your batch jobs. Your activities may also be:&lt;br /&gt;
* &#039;&#039;&#039;short&#039;&#039;&#039; compilation of your program code and&lt;br /&gt;
* &#039;&#039;&#039;short&#039;&#039;&#039; pre- and postprocessing of your batch jobs.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
To guarantee usability for all the users of bwUniCluster &amp;lt;span style=&amp;quot;color:red;font-size:100%;&amp;quot;&amp;gt;&#039;&#039;&#039;you must not run your compute jobs on the login nodes&#039;&#039;&#039;&amp;lt;/span&amp;gt;. Compute jobs must be submitted to the&lt;br /&gt;
[[bwUniCluster Batch Jobs|queueing system]]. Any compute job running on the login nodes will be terminated without any notice. Any long-running compilation or any long-running pre- or postprocessing of batch jobs must also be submitted to the [[bwUniCluster Batch Jobs|queueing system]].&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
= First steps on bwUniCluster =&lt;br /&gt;
&lt;br /&gt;
For setting up your environment to use compilers and installed software please visit:&lt;br /&gt;
* [[BwUniCluster_Environment_Modules|bwUniCluster user environment]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
For guides on how to submit compute jobs to bwUniCluster please visit:&lt;br /&gt;
* [[bwUniCluster Batch Jobs|bwUniCluster batch jobs]]  &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
----&lt;br /&gt;
&lt;br /&gt;
[[Category:bwHPC|Access bwUniCluster]]&lt;br /&gt;
[[Category:bwUniCluster|Access]]&lt;/div&gt;</summary>
		<author><name>M Dynowski</name></author>
	</entry>
</feed>