HPC User Wiki 2016

Documentation for High-Performance Computing at the University Oldenburg

This HPC User Wiki is for the new HPC cluster and is still under heavy construction!

For editors: the old Wiki should be stored in the current state, i.e. pages from the old Wiki should only be used if they don't need to be changed (minor changes are ok). In case substantial changes are need a new page should be created. In case of a naming conflict add "2016" to page name and use text links. Example:

Page name in old Wiki: Some Old Page
Page name in new Wiki: Some Old Page 2016
Link in old Wiki: [[Some Old Page]]
Link in new Wiki: [[Some Old Page 2016|Some Old Page]]

General Information

HPC Facilities	Quickstart Guide	User environment	Job Management (Queueing) System
Overview CARL EDDY HPC Policies Groups Acknowledging CARL/EDDY User Meetings	Quickstart Guide Login HPC Cluster Overview File System Software and Environment Basic Job Submission	Login to the HPC cluster Usage of module File system and Data Management Local Mounting of File Systems Shares under Windows Shares under Linux License servers	Overview Submitting Jobs Partitions Information on sbatch-options Documentation Information on used Resources

Application Software and Libraries

Compiler and Development Tools	Quantum Chemistry	Biology	Computational Fluid Dynamics	Mathematics/Scripting	Visualisation	Libraries
GNU Compiler Intel Compiler PGI Compiler MPI Libraries Toolchains	Gaussian ORCA CP2K	BCFtools BEDTools BLAST BLAT BamTools BioPerl Biopython Bowtie 1/Bowtie 2 CD-HIT FASTX-Toolkit FastQC IGV and IGVTools Lighter SAMtools Trinity ViennaRNA cutadapt	Ansys FOAMpro Nektar++ Nek 5000 OpenFOAM PALM STAR-CCM++ THETA WRF/WPS	MATLAB Configuration MDCS Basic Examples MDCS Tutorials MDCS Python R STATA Gurobi	iso99 NCL ncview paraview	BLAS and LAPACK EGSnrc FLUKA GEANT4 HDF5 LEDA LEDA

Courses and Tutorials

Below you can find a list of Courses and Tutorials for our HPC clusters. Currently, a short, two hour introduction for the new clusters CARL and EDDY is planned. During the summer semester a lecture "Introduction to HPC" is held (2h/week). If you are interested in attending or would like to request a course please contact Scientific Computing.

Introduction for CARL and EDDY	Introduction to HPC
Introduction to the new HPC Clusters [pdf] (23.02.2017, 14-16pm c.t.)	nothing planned yet

Contact

In case you need HPC support you can use the contacts listed below. The servicedesk of IT services can be contacted for all questions regarding HPC, and are recommended in particular when someone is absent (e.g. due to a vacation).

HPC Resource	Name	EMail
CARL and EDDY	General HPC Support and Servicedesk	servicedesk@uni-oldenburg.de
CARL	Stefan Harfst Julius Brunken	stefan.harfst@uni-oldenburg.de julius.brunken@uni-oldenburg.de
EDDY	Wilke Trei	wilke.trei@forwind.de

HPC Support Internal