Difference between revisions of "HPC User Wiki 2016"

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{| style="background-color:#eeeeff;" cellpadding="10" border="1" cellspacing="0"  
{| style="background-color:#eeeeff;" cellpadding="10" border="1" cellspacing="0" align="center"
|- style="background-color:#ddddff;"
|- style="background-color:#ddddff;"
!Compiler and Development Tools
! scope="col" width="200px" | Compiler and Development Tools
!Quantum Chemistry
! scope="col" width="200px" | Quantum Chemistry
!Biology
! scope="col" width="200px" colspan="2" | Biology
!Computational Fluid Dynamics
! scope="col" width="200px" | Mathematics/Scripting
!Mathematics/Scripting
! scope="col" width="200px" | Visualisation
!Visualisation
!Libraries
|- valign="top"
|- valign="top"
|
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* [[PLUMED]]
* [[PLUMED]]
* [[CRYSTAL]]
* [[CRYSTAL]]
|  
|  
*[[AUGUSTUS 2016 | AUGUSTUS]]
*[[AUGUSTUS 2016 | AUGUSTUS]]
*[[bam_to_mate_hist 2016 | bam_to_mate_hist]]
*[[bam_to_mate_hist 2016 | bam_to_mate_hist]]
*[[BRAKER2 2016 | BRAKER2]]
*[[BCFtools]]
*[[BCFtools]]
*[[Beast]]
*[[Beast]]
*[[BEDTools]]
*[[BEDTools]]
*[[bgc 2016 | bgc]]
*[[BLAST]]
*[[BLAST]]
*[[BLAT]]
*[[BLAT]]
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*[[Biopython]]
*[[Biopython]]
*[[Bowtie 1/Bowtie 2]]
*[[Bowtie 1/Bowtie 2]]
*[[BRAKER2 2016 | BRAKER2]]
*[[Burrows-Wheeler Aligner]]
*[[Burrows-Wheeler Aligner]]
*[[CD-HIT]]
*[[CD-HIT]]
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*[[IGV and IGVTools]]
*[[IGV and IGVTools]]
*[[jcvi 2016 | jcvi]]
*[[jcvi 2016 | jcvi]]
|
*[[Lighter]]
*[[Lighter]]
*[[lpsolve 2016 | lpsolve]]
*[[lpsolve 2016 | lpsolve]]
*[[Lumpy]]Biopython
*[[Lumpy]]
*[[NextGenMap]]
*[[NextGenMap]]
*[[Picard]]
*[[Picard]]
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*[[GATK]]
*[[GATK]]
*[[Trimmomatic]]
*[[Trimmomatic]]
|
* [[ESMF 2016 | ESMF]]
* [[GMT 2016 | GMT]]
* [[Install PALM on Eddy | PALM]]
* [[OpenFOAM_2016 | OpenFOAM]]
* [[THETA_2016 | THETA]]
* [[WRF/WPS_2016 | WRF/WPS]]
|  
|  
* [[Julia 2016 | Julia]]
* [[Julia 2016 | Julia]]
* [[MATLAB 2016 | MATLAB]]   
* [[MATLAB 2016 | MATLAB]]   
** [[Advanced Examples MDCS 2016 | Advanced Examples MDCS]]
** [[Basic Examples MDCS 2016 | Basic Examples MDCS]]
** [[Configuration MDCS 2016 | Configuration MDCS]]
** [[Configuration MDCS 2016 | Configuration MDCS]]
** [[Basic Examples MDCS 2016 | Basic Examples MDCS]]
** [[CVX]]
** [[Advanced Examples MDCS 2016 | Advanced Examples MDCS]]
** [[MDCS with GPUs]]
** [[MDCS with GPUs]]
** [[IQMtools]]
** [[IQMtools]]
*[[bgc 2016 | bgc]]
* [[Python 2016 | Python]]
* [[Python 2016 | Python]]
** [[Anaconda 2016 | Anaconda]]
** [[Anaconda 2016 | Anaconda]]
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* [[Gurobi 2016 | Gurobi]]
* [[Gurobi 2016 | Gurobi]]
* [[Maple 2016 | Maple]]
* [[Maple 2016 | Maple]]
* [[CVX]]
 
|  
|  
<!--* [[iso99]]-->
* [[Mesa 2016 | Mesa]]
* [[Mesa 2016 | Mesa]]
* [[NCL]]
* [[NCL]]
* [[ncview]]
* [[ncview]]
* [[paraview]]
* [[paraview]]
* [[Caffe]]
|-
|  
{| style="background-color:#eeeeff;" cellpadding="10" border="1" cellspacing="0"
|- style="background-color:#ddddff;"
! scope="col" width="200px" | Libraries
! scope="col" width="200px" | Physics
! scope="col" width="312px" | Machine Learning
! scope="col" width="200px" | Computational Fluid Dynamics
! scope="col" width="200px" | Languages
|- valign="top"
|
* [[BLAS and LAPACK 2016 | BLAS and LAPACK]]
* [[BLAS and LAPACK 2016 | BLAS and LAPACK]]
|
* [[EGSnrc 2016 | EGSnrc]]
* [[EGSnrc 2016 | EGSnrc]]
* [[FLUKA 2016 | FLUKA]]
* [[FLUKA 2016 | FLUKA]]
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** [[GEANT4 2016#GRAS | GRAS]]
** [[GEANT4 2016#GRAS | GRAS]]
** [[GEANT4 2016#GATE | GATE]]
** [[GEANT4 2016#GATE | GATE]]
* [[FDTD_Solutions 2016 | FDTD_Solutions]]
* [[FDTD_Solutions 2016 | FDTD Solutions]]
* [[HDF5 2016 | HDF5]]
* [[HDF5 2016 | HDF5]]
* [[LEDA  2016 | LEDA]]
* [[LEDA  2016 | LEDA]]
* [[NetCDF 2016 | NetCDF]]
* [[NetCDF 2016 | NetCDF]]
|-
|
 
* [[Caffe]]
|
* [[ESMF 2016 | ESMF]]
* [[GMT 2016 | GMT]]
* [[Install PALM on Eddy | PALM]]
* [[OpenFOAM_2016 | OpenFOAM]]
* [[THETA_2016 | THETA]]
* [[WRF/WPS_2016 | WRF/WPS]]
|
*Anaconda                                                                     
*Bison
*Bison                     
*[[Gurobi 2016|Gurobi]]
*flex
*Java
*[[Julia 2016 | Julia]]
*nodejs
*Perl
*[[Python 2016 |Python]]
*[[R 2016| R]]
*ScientificPython
*Tcl
*Yasm
|}
|}
|}
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== Courses and Tutorials ==
== Courses and Tutorials ==

Revision as of 10:39, 25 October 2018

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

Application Software and Libraries

Compiler and Development Tools Quantum Chemistry Biology Mathematics/Scripting Visualisation
Libraries Physics Machine Learning Computational Fluid Dynamics Languages

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)

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 		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

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