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!

General Information

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HPC Facilities	Quickstart Guide	User environment	Job Management (Queueing) System
Overview CARL EDDY HPC Policies Cost Sharing Scientific Computing Groups Managing your Group Acknowledging CARL/EDDY User Meetings Not directly administered by our University: GOLD HLRN	Quickstart Guide HPC Cluster Overview Account creation Login File System Software and Environment Basic Job Submission Frequently Asked Questions	Login to the HPC cluster Remote Desktop Connection Using SSH Keys VPN: Connect from Home Usage of module Software Environments and their Differences Installed Application Software and Libraries File system and Data Management Local Mounting of File Systems Shares under Windows Shares under Linux Mounting a Directory on Nextcloud 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

----------------------  What's installed and what's new? ----------------------

Compiler and Development Tools	Quantum Chemistry	Biology & Medicine		Mathematics, Statistics & Scripting
ALE GNU Compiler Go Ghostscript Intel Compiler Intel Tools Threading Building Blocks (TBB) Inspector VTune Advisor MPI Libraries Compiling with OpenMPI Compiling with Intel MPI PGI Compiler OpenACC Qt ROS Singularity Spark Toolchains	CP2K CRYSTAL Gaussian GaussView GROMACS MOLGW NAMD NBO ORCA pDynamo PLUMED	ANTs AUGUSTUS bam_to_mate_hist bwa-mem2 BCFtools Beast BEDTools bgc BLAST BLAT BamTools BBMap BioPerl Biopython Bowtie 1/Bowtie 2 BRAKER2 Burrows-Wheeler Aligner canu CD-HIT cutadapt Exonerate FASTX-Toolkit FastQC FreeSurfer FSL GATK GATE GeneMark-EX GenomeTools GffCompare gffread HISAT2 IGV and IGVTools ipyrad ITK jcvi Lighter	MAFFT minimap2 MUSCLE lpsolve Lumpy medaka MIRTK MrBayes MultiQC NextGenMap NiBabel PEST++ Pychopper picard Pilon Picard QUAST / QUAST-LG Racon RepeatModeler REPET RSEM Salmon SAMtools Sickle Mindboggle SNAP SNAP-HMM SOAPdenovo2 Stacks STAR StringTie TopHat Trinity TopHat Trimmomatic VCFTools ViennaRNA wtdbg2 Fiji/Unet	dakota Gurobi Julia Maple MATLAB Configuration MDCS Basic Examples MDCS Advanced Examples MDCS MDCS Troubleshooting CVX MDCS with GPUs IQMtools NEURON parallel Perl Python ScientificPython Anaconda R R-bundle-Bioconductor RStan STATA TCL

Libraries	Physics	Machine Learning	Computational Fluid Dynamics	Visualisation
BLAS and LAPACK MariaDB PyTables SuiteSparse	EGSnrc FLUKA FDTD Solutions / Lumerical GEANT4 GRAS GATE g4py HDF5 LEDA NetCDF Octopus PVMOS SCUFF-EM Yambo	Caffe Keras TensorFlow Theano KNIME PyTorch	ESMF GMT PALM OpenFOAM THETA WRF/WPS	Ghostscript 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) Workshop Nvidia HPC SDK (06.07.2021, 10am-1pm, online) Introduction to HPC (three day course) upcoming or most recent course (15.03-17.03.2021) all course	Introduction to High-Performance Computing	HPC Video Lectures Matlab Tutorials Audio Data Processing Using the MEX Compiler R Tutorial

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

The old wiki for HERO and FLOW is found here.

HPC Support Internal

Globus Data Transfer