Difference between revisions of "HPC User Wiki 2016"
From HPC users
Jump to navigationJump to search
Schwietzer (talk | contribs) |
|||
| (53 intermediate revisions by 2 users not shown) | |||
| Line 3: | Line 3: | ||
<!-- Table of Contents von der Startseite entfernen--> | <!-- Table of Contents von der Startseite entfernen--> | ||
__NOTOC__ | __NOTOC__ | ||
This is the HPC User Wiki for the HPC clusters CARL and EDDY. If you would like to contribute please contact {{sc}}! | |||
{{warningbox| | {{warningbox| | ||
The current wiki for the HPC cluster ROSA and STORM/MOUSE can be found [https://hpcwiki.uol.de/ 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 :) | |||
}} | }} | ||
| Line 34: | Line 36: | ||
** [[Group Tools|Managing your Group]] | ** [[Group Tools|Managing your Group]] | ||
* [[Acknowledging_the_HPC_facilities 2016| Acknowledging CARL/EDDY]] | * [[Acknowledging_the_HPC_facilities 2016| Acknowledging CARL/EDDY]] | ||
* [[User Meetings]] | * [[User Meetings | User Meetings / User Representatives]] | ||
'' | ''Other HPC resources:'' | ||
* [[HPC Facilities of the University of Oldenburg 2016#GOLD| GOLD]] | * [[HPC Facilities of the University of Oldenburg 2016#GOLD| GOLD]] | ||
* [[ HLRN 2016 | HLRN ]] | * [[ HLRN 2016 | HLRN ]] | ||
| Line 51: | Line 53: | ||
| | | | ||
* [[Login | Login to the HPC cluster]] | * [[Login | Login to the HPC cluster]] | ||
** [[Login#HPC_Account | Getting an HPC account]] | |||
** [[Login#Connect to CARL/EDDY using the Remote Desktop Protocol | Remote Desktop Connection]] | ** [[Login#Connect to CARL/EDDY using the Remote Desktop Protocol | Remote Desktop Connection]] | ||
** [[Login#Using SSH Keys for login | Using SSH Keys]] | ** [[Login#Using SSH Keys for login | Using SSH Keys]] | ||
| Line 74: | Line 77: | ||
* [[Interactive Jobs]] | * [[Interactive Jobs]] | ||
* [[GPU Usage]] | * [[GPU Usage]] | ||
* [[Best Practice]] | * [[Best Practice]] | ||
** [[How to Manage Many Jobs]] | |||
|- | |- | ||
|} | |} | ||
| Line 92: | Line 96: | ||
| | | | ||
* [[ALE 2016 | ALE ]] | * [[ALE 2016 | ALE ]] | ||
* [[CMake 2016 | CMake]] | |||
* [[GNU Compiler 2016 | GNU Compiler]] | * [[GNU Compiler 2016 | GNU Compiler]] | ||
* [[Go 2016 | Go]] | * [[Go 2016 | Go]] | ||
* [[Intel Compiler 2016 | Intel Compiler]] | * [[Intel Compiler 2016 | Intel Compiler]] | ||
* [[Intel Tools]] | * [[Intel Tools]] | ||
| Line 101: | Line 105: | ||
** [[VTune]] | ** [[VTune]] | ||
** [[Advisor]] | ** [[Advisor]] | ||
* [[Lua 2016 | Lua]] | |||
* [[MPI Libraries | MPI Libraries ]] | * [[MPI Libraries | MPI Libraries ]] | ||
** [[MPI Libraries#Compiling with OpenMPI | Compiling with OpenMPI]] | ** [[MPI Libraries#Compiling with OpenMPI | Compiling with OpenMPI]] | ||
| Line 106: | Line 111: | ||
* [[PGI Compiler 2016 | PGI Compiler]] | * [[PGI Compiler 2016 | PGI Compiler]] | ||
** [[OpenACC]] | ** [[OpenACC]] | ||
*[[Parallel 2016 | parallel]] | |||
* [[Qt 2016 | Qt]] | * [[Qt 2016 | Qt]] | ||
* [[ROS 2016 | ROS]] | * [[ROS 2016 | ROS]] | ||
| Line 112: | Line 118: | ||
* [[Toolchains | Toolchains]] | * [[Toolchains | Toolchains]] | ||
| | | | ||
* [[AIMAll 2016 | AIMAll]] | |||
* [[CP2K 2016 | CP2K]] | * [[CP2K 2016 | CP2K]] | ||
* [[CRYSTAL]] | * [[CRYSTAL]] | ||
* [[DIAMOND 2016 | DIAMOND]] | |||
* [[Gaussian 2016 | Gaussian]] | * [[Gaussian 2016 | Gaussian]] | ||
** [[GaussView]] | ** [[GaussView]] | ||
| Line 123: | Line 131: | ||
* [[pDynamo]] | * [[pDynamo]] | ||
* [[PLUMED]] | * [[PLUMED]] | ||
| | * [[QuantumESPRESSO 2016 | QuantumESPRESSO]] | ||
| | |||
*[[angsd 2016 | angsd]] | |||
*[[ANTs 2016 | ANTs]] | *[[ANTs 2016 | ANTs]] | ||
*[[AUGUSTUS 2016 | AUGUSTUS]] | *[[AUGUSTUS 2016 | AUGUSTUS]] | ||
| Line 142: | Line 152: | ||
*[[Burrows-Wheeler Aligner]] | *[[Burrows-Wheeler Aligner]] | ||
*[[canu 2016 | canu]] | *[[canu 2016 | canu]] | ||
*[[cdbfasta 2016 | cdbfasta]] | |||
*[[CD-HIT]] | *[[CD-HIT]] | ||
*[[CellRanger 2016 | CellRanger]] | |||
*[[cutadapt]] | *[[cutadapt]] | ||
*[[discovardenovo 2016 | discovardenovo]] | |||
*[[Exonerate 2016 | Exonerate]] | *[[Exonerate 2016 | Exonerate]] | ||
*[[FastANI 2016 | FastANI]] | |||
*[[FASTX-Toolkit]] | *[[FASTX-Toolkit]] | ||
*[[FastQC]] | *[[FastQC]] | ||
| Line 151: | Line 165: | ||
*[[GATK]] | *[[GATK]] | ||
*[[GATE 2016 | GATE]] | *[[GATE 2016 | GATE]] | ||
*[[GenomeThreader 2016 | GenomeThreader]] | |||
*[[GeneMark-EX 2016 | GeneMark-EX]] | *[[GeneMark-EX 2016 | GeneMark-EX]] | ||
*[[GenomeTools 2016 | GenomeTools]] | |||
*[[GffCompare 2016 | GffCompare]] | *[[GffCompare 2016 | GffCompare]] | ||
*[[gffread 2016 | gffread]] | *[[gffread 2016 | gffread]] | ||
*[[hapflk 2016 |hapflk]] | |||
*[[HISAT2 2016 | HISAT2]] | *[[HISAT2 2016 | HISAT2]] | ||
*[[IGV and IGVTools]] | *[[IGV and IGVTools]] | ||
*[[IQ-TREE 2016 | IQ-TREE]] | |||
*[[ipyrad]] | *[[ipyrad]] | ||
*[[ ITK 2016 | ITK ]] | *[[ ITK 2016 | ITK ]] | ||
*[[jcvi 2016 | jcvi]] | *[[jcvi 2016 | jcvi]] | ||
*[[Kraken 2016 | Kraken]] | |||
*[[Kaldi 2016 | Kaldi]] | |||
*[[Kaiju 2016 | Kaiju]] | |||
| | |||
*[[Lighter]] | *[[Lighter]] | ||
| | *[[MAFFT 2016 | MAFFT]] | ||
*[[minimap2 2016 | minimap2]] | *[[minimap2 2016 | minimap2]] | ||
*[[MUSCLE 2016 | MUSCLE]] | *[[MUSCLE 2016 | MUSCLE]] | ||
*[[lpsolve 2016 | lpsolve]] | *[[lpsolve 2016 | lpsolve]] | ||
*[[Lumpy]] | *[[Lumpy]] | ||
*[[MCScanX 2016 | MCScanX]] | |||
*[[medaka 2016 | medaka]] | *[[medaka 2016 | medaka]] | ||
*[[MIRTK 2016 | MIRTK]] | *[[MIRTK 2016 | MIRTK]] | ||
| Line 171: | Line 194: | ||
*[[NextGenMap]] | *[[NextGenMap]] | ||
*[[NiBabel 2016 | NiBabel]] | *[[NiBabel 2016 | NiBabel]] | ||
*[[nQuire 2016 | nQuire]] | |||
*[[OrthoFinder 2016 | OrthoFinder]] | |||
*[[OMA 2016 | OMA]] | |||
*[[PEST++ 2016 | PEST++]] | *[[PEST++ 2016 | PEST++]] | ||
*[[Pychopper 2016 | Pychopper]] | *[[Pychopper 2016 | Pychopper]] | ||
| Line 183: | Line 209: | ||
*[[Salmon 2016 | Salmon]] | *[[Salmon 2016 | Salmon]] | ||
*[[SAMtools]] | *[[SAMtools]] | ||
*[[SHAPEIT4 2016 | SHAPEIT4]] | |||
*[[Sickle 2016 | Sickle]] | *[[Sickle 2016 | Sickle]] | ||
*[[SPAdes 2016 | SPAdes]] | |||
*[[spaln 2016 | spaln]] | |||
*[[Mindboggle 2016 | Mindboggle]] | *[[Mindboggle 2016 | Mindboggle]] | ||
*[[SNAP 2016 | SNAP]] | *[[SNAP 2016 | SNAP]] | ||
| Line 192: | Line 221: | ||
*[[StringTie 2016 | StringTie]] | *[[StringTie 2016 | StringTie]] | ||
*[[TopHat 2016 | TopHat]] | *[[TopHat 2016 | TopHat]] | ||
*[[TransDecoder 2016 | TransDecoder 2016]] | |||
*[[Trinity]] | *[[Trinity]] | ||
*[[TopHat]] | *[[TopHat]] | ||
| Line 197: | Line 227: | ||
*[[VCFTools]] | *[[VCFTools]] | ||
*[[ViennaRNA]] | *[[ViennaRNA]] | ||
*[[wtdbg 2016 | wtdbg2 ]] | |||
*[[Fiji/Unet 2016 | Fiji/Unet]] | *[[Fiji/Unet 2016 | Fiji/Unet]] | ||
| | | | ||
| Line 211: | Line 242: | ||
** [[MDCS with GPUs]] | ** [[MDCS with GPUs]] | ||
** [[IQMtools]] | ** [[IQMtools]] | ||
* [[Mmg 2016 | Mmg]] | |||
* [[NEURON 2016 | NEURON]] | * [[NEURON 2016 | NEURON]] | ||
*[[osrm-backend 2016 | osrm]] | |||
*[[parallel 2016 | parallel]] | *[[parallel 2016 | parallel]] | ||
* [[Perl 2016 | Perl]] | * [[Perl 2016 | Perl]] | ||
* [[Python 2016 | Python]] | * [[Python 2016 | Python]] | ||
** [[JupyterLab]] | |||
* ScientificPython | * ScientificPython | ||
** [[Anaconda 2016 | | ** [[Anaconda 2016 | Anaconda3 / Miniconda3]] | ||
* [[R 2016 | R]] | * [[R 2016 | R]] | ||
** R-bundle-Bioconductor | ** R-bundle-Bioconductor | ||
** [[RStudio 2016 | RStudio]] | |||
* [[RStan 2016 | RStan]] | * [[RStan 2016 | RStan]] | ||
*[[SALOME 2016 | SALOME ]] | |||
* [[STATA 2016 | STATA]] | * [[STATA 2016 | STATA]] | ||
* [[TCL 2016 | TCL]] | * [[TCL 2016 | TCL]] | ||
| Line 233: | Line 269: | ||
| | | | ||
* [[BLAS and LAPACK 2016 | BLAS and LAPACK]] | * [[BLAS and LAPACK 2016 | BLAS and LAPACK]] | ||
* [[FLAC 2016 | FLAC]] | |||
* [[libsamplerate 2016 | libsamplerate]] | |||
* [[MariaDB 2016 | MariaDB]] | * [[MariaDB 2016 | MariaDB]] | ||
* [[PyTables 2016 | PyTables]] | * [[PyTables 2016 | PyTables]] | ||
| Line 239: | Line 277: | ||
| | | | ||
* [[EGSnrc 2016 | EGSnrc]] | * [[EGSnrc 2016 | EGSnrc]] | ||
* [[ElmerFEM 2016 | ElmerFEM]] | |||
* [[FLUKA 2016 | FLUKA]] | * [[FLUKA 2016 | FLUKA]] | ||
* [[fluka.cern | fluka.cern]] | |||
* [[FDTD_Solutions / Lumerical 2016 | FDTD Solutions / Lumerical]] | * [[FDTD_Solutions / Lumerical 2016 | FDTD Solutions / Lumerical]] | ||
* [[GEANT4 2016| GEANT4]] | * [[GEANT4 2016| GEANT4]] | ||
| Line 247: | Line 287: | ||
* [[HDF5 2016 | HDF5]] | * [[HDF5 2016 | HDF5]] | ||
* [[LEDA 2016 | LEDA]] | * [[LEDA 2016 | LEDA]] | ||
* [[mumax 2016 | mumax]] | |||
* [[NetCDF 2016 | NetCDF]] | * [[NetCDF 2016 | NetCDF]] | ||
* [[Octopus 2016 | Octopus ]] | * [[Octopus 2016 | Octopus ]] | ||
* [[PVMOS 2016 | PVMOS]] | * [[PVMOS 2016 | PVMOS]] | ||
* [[SCUFF-EM 2016 | SCUFF-EM]] | * [[SCUFF-EM 2016 | SCUFF-EM]] | ||
* [[libsamplerate 2016 | sndfile-tools]] | |||
* [[VASP 2016 | VASP]] | |||
** [[p4vasp 2016 | p4vasp]] | |||
* [[Yambo 2016 | Yambo]] | * [[Yambo 2016 | Yambo]] | ||
| | | | ||
| Line 272: | Line 316: | ||
* [[ncview]] | * [[ncview]] | ||
* [[paraview]] | * [[paraview]] | ||
* [[PCL 2016 | PCL]] | |||
|} | |} | ||
|} | |} | ||
| Line 290: | Line 335: | ||
* Introduction for EDDY users for migrating from FLOW [[media:Eddy_Introduction.pdf|[pdf]]]<br>(01.03.2017 and 02.03.2017, 10-12am c.t.) | * Introduction for EDDY users for migrating from FLOW [[media:Eddy_Introduction.pdf|[pdf]]]<br>(01.03.2017 and 02.03.2017, 10-12am c.t.) | ||
* [[OpenACC Workshop]]<br>(28./29.3.2017, 10am-6pm, W01 0-008) | * [[OpenACC Workshop]]<br>(28./29.3.2017, 10am-6pm, W01 0-008) | ||
* [[Workshop Nvidia HPC SDK]]<br>(06.07.2021, 10am-1pm, online) | |||
* [[Workshop How to AMD]]<br>(04./05.04.2023, 14pm-17pm, online) | |||
* [[HPC Introduction | Introduction to HPC (three day course)]] | * [[HPC Introduction | Introduction to HPC (three day course)]] | ||
** [[HPC Introduction 03/ | ** [[HPC Introduction 03/2023 | upcoming or most recent course]]<br>(27.03-29.03.2023) | ||
** [[HPC Introduction | all course]] | ** [[HPC Introduction | all course]] | ||
| | | | ||
| Line 331: | Line 378: | ||
|} | |} | ||
</center> | </center> | ||
<br/> | |||
---------------- [[Migration|Migration to the new HPC clusters]] ---------------- | |||
The old wiki for HERO and FLOW is found [[Welcome to the HPC User Wiki of the University of Oldenburg | here]].<br><br> | The old wiki for HERO and FLOW is found [[Welcome to the HPC User Wiki of the University of Oldenburg | here]].<br><br> | ||
<span style="color: green">[[HPC Support Internal]]</span> <br><br> | <span style="color: green">[[HPC Support Internal]]</span> <br> | ||
[[Intel CPU Bug]]<br> | |||
[[Globus Data Transfer]] | [[Globus Data Transfer]] | ||
Latest revision as of 08:06, 27 June 2024
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 |
|---|---|---|---|
|
|
Application Software and Libraries
---------------------- What's installed and what's new? ----------------------
| Compiler and Development Tools | Quantum Chemistry | Biology & Medicine | Mathematics, Statistics & Scripting | |
|---|---|---|---|---|
|
|
|||
| Libraries | Physics | Machine Learning | Computational Fluid Dynamics | Visualisation |
|---|---|---|---|---|
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 |
|---|---|---|
|
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 | |
|---|---|---|
| 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
