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BwUniCluster3.0/Containers

P Schuhmacher — Thu, 06 Aug 2026 13:09:26 GMT

Start via Slurm

← Older revision		Revision as of 15:09, 6 August 2026
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	=== Start via Slurm ===		=== Start via Slurm ===
	Start existing Container:		Start existing Container:
	*<code>salloc -p dev_single -t 00:10:00 --container-name=ubuntu --container-mounts=/etc/slurm/task_prolog:/etc/slurm/task_prolog,/scratch:/scratch~~,/usr/lib64/slurm:/usr/lib64/slurm,/usr/lib64/libhwloc.so:/usr/lib64/libhwloc.so,/usr/lib64/libhwloc.so.15:/usr/lib64/libhwloc.so.15~~</code>		*<code>salloc -p dev_single -t 00:10:00 --container-name=ubuntu --container-mounts=/etc/slurm/task_prolog:/etc/slurm/task_prolog,/scratch:/scratch</code>

	Download and start Container via pyxis directly:		Download and start Container via pyxis directly:
	*<code>salloc -p dev_single -t 00:10:00 --container-image=ubuntu --container-name=ubuntu --container-mounts=/etc/slurm/task_prolog:/etc/slurm/task_prolog,/scratch:/scratch~~,/usr/lib64/slurm:/usr/lib64/slurm,/usr/lib64/libhwloc.so:/usr/lib64/libhwloc.so,/usr/lib64/libhwloc.so.15:/usr/lib64/libhwloc.so.15~~</code>		*<code>salloc -p dev_single -t 00:10:00 --container-image=ubuntu --container-name=ubuntu --container-mounts=/etc/slurm/task_prolog:/etc/slurm/task_prolog,/scratch:/scratch</code>
	In this case an enroot Container is created under ~./local/share/enroot/		In this case an enroot Container is created under ~./local/share/enroot/

	Note: <code>--container-mounts=/etc/slurm/task_prolog:/etc/slurm/task_prolog,/scratch:/scratch~~,/usr/lib64/slurm:/usr/lib64/slurm,/usr/lib64/libhwloc.so:/usr/lib64/libhwloc.so,/usr/lib64/libhwloc.so.15:/usr/lib64/libhwloc.so.15~~</code> is needed for the plugin to work!! The Container name has to start with pyxis_ for the Plugin to work. When using the second Method this is done automatically. Furthermore when specifying the container name in your slurm Job the pyxis_ has to be omitted.		Note: <code>--container-mounts=/etc/slurm/task_prolog:/etc/slurm/task_prolog,/scratch:/scratch</code> is needed for the plugin to work!! The Container name has to start with pyxis_ for the Plugin to work. When using the second Method this is done automatically. Furthermore when specifying the container name in your slurm Job the pyxis_ has to be omitted.

	All options usable for pyxis can be found via srun --help under "Options provided by plugins:"		All options usable for pyxis can be found via srun --help under "Options provided by plugins:"

File:Uc1 file cut 750.jpg

S Braun — Wed, 05 Aug 2026 12:41:15 GMT

S Braun deleted page File:Uc1 file cut 750.jpg

BwVideo test

S Braun — Wed, 05 Aug 2026 12:39:54 GMT

S Braun deleted page BwVideo test content before blanking was: " 1024px"

Start VNC Server - bwUniCluster

S Braun — Wed, 05 Aug 2026 12:38:13 GMT

S Braun deleted page Start VNC Server - bwUniCluster content before blanking was: "== Start a VNC Server on the bwUniCluster == To start a VNC Server on the bwUniCluster you must log into the cluster with your username and password as usual. You should not start the server on a login node but request an interactive job using for example the following command. $ msub -V -I -l nodes=1:ppn=1 -l walltime=0:02:00:00 On your assigned compute node start the VNC server with $ module load vis/tigervnc $ run_vncserver If you start a VNC server for th..."

2018-09-24: 5th bwHPC Symposium

S Braun — Wed, 05 Aug 2026 12:37:29 GMT

S Braun deleted page 2018-09-24: 5th bwHPC Symposium content before blanking was: "== Call for Participation in the 5th bwHPC Symposium == On behalf of the bwHPC initiative (www.bwhpc.de) we invite you to participate in the upcoming 5th bwHPC symposium on September 24/25, 2018 hosted at the University of Freiburg. The symposium provides the opportunity to present scientific projects, results or methods that have been carried out, achieved or developed with the support of bwHPC high performance computing resources. The symposium is free of cha..."

2017-10-04: 4th bwHPC Symposium

S Braun — Wed, 05 Aug 2026 12:37:14 GMT

S Braun deleted page 2017-10-04: 4th bwHPC Symposium content before blanking was: "Dear Sir or Madam, on behalf of the bwHPC-C5 project ([http://www.bwhpc-c5.de www.bwhpc-c5.de]) we invite you to participate in the upcoming 4th bwHPC symposium on '''October 4, 2017''' hosted at Eberhard Karls Universität Tübingen. The symposium focuses on the presentation of scientific computing projects as well as on the progress and the success stories of the bwHPC realization concept. The event offers an unique opportunity to engage in an active dialogu..."

BwUniCluster2.0/Software/R/terra (R 4.2.1)

S Braun — Wed, 05 Aug 2026 12:36:52 GMT

S Braun deleted page BwUniCluster2.0/Software/R/terra (R 4.2.1) content was: " Note that the instructions provided below refer to R 4.2.1 (but not R 4.3.3)! We are currently updating our guides for R 4.3.3. = General information = sf and terra allow to use the following tools for handling spatial structures in R * the 'Geospatial' Data Abstraction Library [https://gdal.org/ GDAL] * Projection/transformation opera...", and the only contributor was "K Kuck" (talk)

BwUniCluster2.0/Software/R/stringi

S Braun — Wed, 05 Aug 2026 12:36:43 GMT

S Braun deleted page BwUniCluster2.0/Software/R/stringi content was: "Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)! = General information = <code>stringi</code> is an <code>R</code> package for fast, portable, correct, consistent, and convenient string/text processing in any locale or character encoding. = Installation = Please enter the code, presented in the boxes below, di...", and the only contributor was "K Kuck" (talk)

BwUniCluster2.0/Software/R/cummeRbund

S Braun — Wed, 05 Aug 2026 12:36:36 GMT

S Braun deleted page BwUniCluster2.0/Software/R/cummeRbund content was: "= General information = [https://compbio.mit.edu/cummeRbund/ '''<code>CummeRbund</code>'''] is an <code>R</code> package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output. = Installation instructions = == Preparations == Installing <code>CummeRbund</code> involves compiling source code. Therefore, ensure that the following flags are set in <code>$HOME/...", and the only contributor was "K Kuck" (talk)

BwUniCluster2.0/Software/R/Rjags

S Braun — Wed, 05 Aug 2026 12:36:28 GMT

S Braun deleted page BwUniCluster2.0/Software/R/Rjags content was: "Note that the instructions provided below refer to R 4.2.1 (but not R 4.4.1)! We are currently updating our guides for R 4.4.1. = General information = rjags is a R interface to use JAGS, [https://mcmc-jags.sourceforge.io/ Just another Gibbs Sampler]. JAGS is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation rjags needs a JAGS installation on the side. We recommend to compile via Inte..."

BwUniCluster2.0/Software/R/Rgdal (R 4.2.1)

S Braun — Wed, 05 Aug 2026 12:36:20 GMT

S Braun deleted page BwUniCluster2.0/Software/R/Rgdal (R 4.2.1) content was: "Note that the instructions provided below refer to R 4.2.1 (but not R 4.4.1)! = General information = Note that rgdal and rgeos have been retired by their developers in 2023! Please find further information at [https://cran.r-project.org/web/packages/rgdal/index.html https://cran.r-project.org/web/packages/rgd...", and the only contributor was "K Kuck" (talk)

VNC Server - bwUniCluster 2.0

S Braun — Wed, 05 Aug 2026 12:33:11 GMT

S Braun deleted page VNC Server - bwUniCluster 2.0 content was: "== Start a VNC Server on the bwUniCluster 2.0 == To start a VNC Server on the bwUniCluster 2.0 you must log into the cluster with your username and password as usual. Please do not start the VNC Server on a login node but request an interactive job using for example the following command: $ salloc -p single -n 1 -t 120 --...", and the only contributor was "F Wagner" (talk)

UC2/arch

S Braun — Wed, 05 Aug 2026 12:32:44 GMT

S Braun deleted page UC2/arch content was: "''{{SUBPAGENAME}}'' is a subpage of {{BASEPAGENAME}} to demonstrate the subpage feature", and the only contributor was "R Barthel" (talk)

BwUniCluster2.0/Software/R

S Braun — Wed, 05 Aug 2026 12:32:13 GMT

S Braun deleted page BwUniCluster2.0/Software/R content was: "{{Softwarepage|math/R}} {| width=600px class="wikitable" |- ! Description !! Content |- | module load | math/R |- | License | GPL |- | Citing | n/a |- | Links | [http://www.r-project.org/ Homepage] | [http://cran.r-project.org/manuals.html Documentation] |- | Graphical Interface | No |- | Plugins | User dependent |} = Description = '''R''' is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and e..."

Category:BwUniCluster 2.0

S Braun — Wed, 05 Aug 2026 12:31:51 GMT

S Braun deleted page Category:BwUniCluster 2.0 content was: "This page lists all articles that are assigned to the high-performance computer '''bwUniCluster 2.0'''. <!-- {| style="width: 100%; border-spacing: 5px;" | style="text-align:center; color:#000;vertical-align:middle;font-size:75%;" | center|border|550px|Close-up of bwUniCluster by Simon Raffeiner, Copyright: KIT (SCC) |- | style="text-align:center; color:#000;vertical-align:middle;" |Close-up..."

UC2

S Braun — Wed, 05 Aug 2026 12:31:28 GMT

S Braun deleted page UC2 content was: "Main page testing subpage feature {{Special:PrefixIndex/UC2/}}"

UC2/access

S Braun — Wed, 05 Aug 2026 12:31:11 GMT

S Braun deleted page UC2/access content was: "''{{SUBPAGENAME}}'' is a subpage of {{BASEPAGENAME}} to demonstrate the subpage feature", and the only contributor was "R Barthel" (talk)

2017-01-24: bwUniCluster downtime

S Braun — Wed, 05 Aug 2026 12:30:47 GMT

S Braun deleted page 2017-01-24: bwUniCluster downtime content before blanking was: "To repair the damaged HOME file system of all non-KIT users we have scheduled a downtime for the three clusters for January 24, 2017. During the downtime there will be no access to the clusters and all jobs running at that time have to be cancelled. We will use the downtime to switch to the backup of the HOME file system and to upgrade the OS kernel. Update from 2017-01-24, 4 p.m.: The clusters bwUniCluster, ForHLR I and ForHLR II can now be used again. Please..."

BwUniCluster 2.0 Maintenance/2020-10/Software Issues

S Braun — Wed, 05 Aug 2026 12:30:13 GMT

S Braun deleted page BwUniCluster 2.0 Maintenance/2020-10/Software Issues content before blanking was: "After the last regular maintenance interval (from 06.10.2020 to 13.10.2020) the following issues with Intel MPI exist: * Intel MPI 2018 is incompatible with Red Hat 8.2. Any invocation, even a simple "Hello World" MPI program, will result in a crash. The ''mpi/impi/2018'' module has therefore been removed. * There is a bug in Intel MPI 2019.x which leads to crashes when multiple MPI applications which are linked against..."

BwUniCluster2.0/Jupyter (Deutsch)

S Braun — Wed, 05 Aug 2026 12:29:58 GMT

S Braun deleted page BwUniCluster2.0/Jupyter (Deutsch) content was: "{{Note|Foo}} Als Alternative zum Zugriff auf die HPC Ressourcen mittels SSH kann Jupyter verwendet werden. Hierfür ist lediglich ein Webbrowser nötig. Innerhalb der Website kann Quellcode verschiedener Programmiersprachen editiert und ausgeführt werden. Weiterhin stehen unterschiedliche Benutzerschnittstellen und Terminals zur Verfügung. <!-- * [https://uc2-jupyter.scc.kit...", and the only contributor was "S Braun" (talk)

BwUniCluster2.0/First Steps

S Braun — Wed, 05 Aug 2026 12:29:20 GMT

S Braun deleted page BwUniCluster2.0/First Steps content was: "<!-- == Command line interface == Any work is to be done via command line interface. A quick guide can be found [https://indico.scc.kit.edu/indico/event/278/material/slides/10.pdf '''here''']. == Software setup == Softwares provided by bwHPC have to be loaded according to your need via the '''Software Module System'''. == Computation == Any kind of computation on any HPC cluster is done as bwUniCluster_2.0_Slurm_common_Features|'''batch job..."

BwUniCluster2.0

S Braun — Wed, 05 Aug 2026 12:28:03 GMT

S Braun deleted page BwUniCluster2.0 content was: " <!--{| style="width: 100%; border-spacing: 5px;" | style="text-align:center; color:#000;vertical-align:middle;font-size:75%;" | center|border|550px|Close-up of bwUniCluster by Simon Raffeiner, Copyright: KIT (SCC) |- | style="text-align:center; color:#000;vertical-align:middle;" |Close-up of bwUniCluster © KIT (Simon Raffeiner/SCC) |} On 17.03.2020, the Sci..."

Helix/Software/Matlab

S Fischer — Mon, 03 Aug 2026 10:03:51 GMT

Compile MATLAB binaries with mcc

← Older revision		Revision as of 12:03, 3 August 2026
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	== Compile MATLAB binaries with mcc ==		== Compile MATLAB binaries with mcc ==

	~~MATLAB~~ on ~~Helix~~ ~~comes~~ ~~with~~ a compiler, <code>mcc</code>~~, that can be used~~ to create binaries from MATLAB-code.		If you have a MATLAB license that includes [https://de.mathworks.com/products/compiler.html MATLAB Compiler], e.g. on your local computer, you can use <code>mcc</code> to create binaries from MATLAB code.
	Stand-alone MATLAB programs compiled with <code>mcc</code> do not require any license tokens at runtime and you can start jobs in parallel without any risk of running out of licences.		Stand-alone MATLAB programs compiled with <code>mcc</code> do not require any license tokens at runtime and you can start jobs in parallel without any risk of running out of licences.