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	HPC Cluster Overview Login to the HPC cluster File System Software and Environment Basic Job Submission Partitions	Usage of module File system and Data Management Shares under Windows Shares under Linux License servers	Overview Submitting Jobs Information on sbatch-options Documentation

Application Software and Libraries

Compiler and Development Tools	Quantum Chemistry	Biology	Computational Fluid Dynamics	Mathematics/Scripting	Other Software	Visualisation	Libraries
debugging git GNU Compiler Intel Compiler Open64 Compiler PGI Compiler profiling scalasca subversion (svn) valgrind	Gaussian MOLCAS MOLPRO NBO 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 Intel MPI LEDA NetCDF OpenMPI

Courses and Tutorials

At the moment, there are no courses and tutorials planned. As soon as we are planning a new course you will be informed.

Contact

In case you need HPC support you can use the contacts listed below. The General HPC support and 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