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 Managing your Group 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 & Medicine		Mathematics/Scripting
GNU Compiler Intel Compiler MPI Libraries Compiling with OpenMPI Compiling with Intel MPI PGI Compiler OpenACC ROS Singularity Spark Toolchains	Gaussian GaussView ORCA CP2K NBO pDynamo GROMACS NAMD PLUMED CRYSTAL	ANTs AUGUSTUS bam_to_mate_hist BCFtools Beast BEDTools bgc BLAST BLAT BamTools BioPerl Biopython Bowtie 1/Bowtie 2 BRAKER2 Burrows-Wheeler Aligner CD-HIT cutadapt Exonerate FASTX-Toolkit FastQC FreeSurfer FSL GeneMark-EX GffCompare gffread HISAT2	IGV and IGVTools jcvi KNIME Lighter lpsolve Lumpy MrBayes NextGenMap Parasail Picard RSEM Salmon SAMtools Sickle SNAP SNAP-HMM SOAPdenovo2 Stacks STAR StringTie TopHat Trinity VCFTools ViennaRNA TopHat GATK Trimmomatic	Julia MATLAB Advanced Examples MDCS Basic Examples MDCS Configuration MDCS CVX MDCS with GPUs IQMtools NEURON parallel Perl Python ScientificPython Anaconda TCL R STATA Gurobi Maple

Libraries	Physics	Machine Learning	Computational Fluid Dynamics	Visualisation
BLAS and LAPACK SuiteSparse	EGSnrc FLUKA GEANT4 GRAS GATE g4py FDTD Solutions HDF5 LEDA NetCDF PVMOS	Caffe TensorFlow Theano Keras	ESMF GMT PALM OpenFOAM THETA WRF/WPS	Mesa NCL ncview paraview

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	E-Mail
CARL and EDDY	General HPC Support and Servicedesk	hpcsupport@uni-oldenburg.de servicedesk@uni-oldenburg.de
CARL	Stefan Harfst Fynn Schwietzer	stefan.harfst@uni-oldenburg.de fynn.schwietzer1@uni-oldenburg.de
EDDY	Wilke Trei	wilke.trei@forwind.de

HPC Support Internal