HPC User Wiki 2016

Documentation for High-Performance Computing at the University Oldenburg

This is the HPC User Wiki for the HPC clusters CARL and EDDY. If you would like to contribute please contact Scientific Computing!

The old wiki for HERO and FLOW is found here.

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 HPC Cluster Overview Account creation Login File System Software and Environment Basic Job Submission Frequently Asked Questions	Login to the HPC cluster Usage of module Software Environments and their Differences Installed Application Software and Libraries File system and Data Management Migrate GPFS Data from Flow to Eddy 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 Parallel Jobs with MPI Interactive Jobs GPU Usage Best Practice

Application Software and Libraries

Compiler and Development Tools	Quantum Chemistry	Biology	Computational Fluid Dynamics	Mathematics/Scripting	Visualisation	Libraries
GNU Compiler Intel Compiler PGI Compiler OpenACC MPI Libraries Toolchains	Gaussian GaussView ORCA CP2K NBO pDynamo GROMACS NAMD PLUMED	BCFtools Beast BEDTools BLAST BLAT BamTools BioPerl Biopython Bowtie 1/Bowtie 2 Burrows-Wheeler Aligner CD-HIT cutadapt FASTX-Toolkit FastQC IGV and IGVTools Lighter Lumpy NextGenMap Picard SAMtools SOAPdenovo2 Stacks Trinity VCFTools ViennaRNA TopHat GATK Trimmomatic	OpenFOAM PALM THETA WRF/WPS	MATLAB Configuration MDCS Basic Examples MDCS Advanced Examples MDCS MDCS with GPUs Python Anaconda R STATA Gurobi Maple CVX	NCL ncview paraview Caffe	BLAS and LAPACK EGSnrc FLUKA GEANT4 HDF5 LEDA NetCDF

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.

Courses and Workshops	Lectures	Tutorials
Introduction to the new HPC Clusters [pdf] (23.02.2017, 14-16pm c.t., W02 1-148) Introduction to the new HPC Clusters [pdf] (14.03.2017, 14-16pm c.t., W02 1-148) Introduction for EDDY users for migrating from FLOW [pdf] (01.03.2017 and 02.03.2017, 10-12am c.t.) OpenACC Workshop (28./29.3.2017, 10am-6pm, W01 0-008) Introduction to HPC (18./20.09.2017, 9am-5pm, W01 0-008) Introduction to HPC (19./21.03.2018, 10am-5pm, W01 0-008)	Introduction to High-Performance Computing	Matlab Tutorials Audio Data Processing Using the MEX Compiler

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