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 current wiki for the HPC cluster ROSA and STORM/MOUSE can be found here. Unfortunately, the new wiki is far from complete so you may need to adapt some information from this wiki still. We are working on it :)

General Information

---------------- FAQ - Frequently Asked Questions ---------------- 

 ------------- Want to stay in contact with the HPC support and other users? Join our Mattermost group! -------------

------------------ Tired of reading long wiki articles? ------------------ 
------------- Check out our new HPC Video Lectures! -------------

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 / User Representatives Other HPC resources: 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 Getting an HPC account 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 How to Manage Many Jobs

Application Software and Libraries

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

Compiler and Development Tools	Quantum Chemistry	Biology & Medicine		Mathematics, Statistics & Scripting
ALE CMake GNU Compiler Go Intel Compiler Intel Tools Threading Building Blocks (TBB) Inspector VTune Advisor Lua MPI Libraries Compiling with OpenMPI Compiling with Intel MPI PGI Compiler OpenACC parallel Qt ROS Singularity Spark Toolchains	AIMAll CP2K CRYSTAL DIAMOND Gaussian GaussView GROMACS MOLGW NAMD NBO ORCA pDynamo PLUMED QuantumESPRESSO	angsd 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 cdbfasta CD-HIT CellRanger cutadapt discovardenovo Exonerate FastANI FASTX-Toolkit FastQC FreeSurfer FSL GATK GATE GenomeThreader GeneMark-EX GenomeTools GffCompare gffread hapflk HISAT2 IGV and IGVTools IQ-TREE ipyrad ITK jcvi Kraken Kaldi Kaiju	Lighter MAFFT minimap2 MUSCLE lpsolve Lumpy MCScanX medaka MIRTK MrBayes MultiQC NextGenMap NiBabel nQuire OrthoFinder OMA PEST++ Pychopper picard Pilon Picard QUAST / QUAST-LG Racon RepeatModeler REPET RSEM Salmon SAMtools SHAPEIT4 Sickle SPAdes spaln Mindboggle SNAP SNAP-HMM SOAPdenovo2 Stacks STAR StringTie TopHat TransDecoder 2016 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 Mmg NEURON osrm parallel Perl Python JupyterLab ScientificPython Anaconda3 / Miniconda3 R R-bundle-Bioconductor RStudio RStan SALOME STATA TCL

Libraries	Physics	Machine Learning	Computational Fluid Dynamics	Visualisation
BLAS and LAPACK FLAC libsamplerate MariaDB PyTables SuiteSparse	EGSnrc ElmerFEM FLUKA fluka.cern FDTD Solutions / Lumerical GEANT4 GRAS GATE g4py HDF5 LEDA mumax NetCDF Octopus PVMOS SCUFF-EM sndfile-tools VASP p4vasp Yambo	Caffe Keras TensorFlow Theano KNIME PyTorch	ESMF GMT PALM OpenFOAM THETA WRF/WPS	Ghostscript Mesa NCL ncview paraview PCL

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) Workshop How to AMD (04./05.04.2023, 14pm-17pm, online) Introduction to HPC (three day course) upcoming or most recent course (27.03-29.03.2023) 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

---------------- Migration to the new HPC clusters ---------------- 

The old wiki for HERO and FLOW is found here.

HPC Support Internal
Intel CPU Bug
Globus Data Transfer