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|<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big>
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|[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]
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'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''
'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''
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The aim of this site is that you should be able to get information, help, tips-and-tricks, etc. regarding the most widely used computational tools and scientific applications.  
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<u>We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address:</u><br>
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Welcome to the general SNIC knowledge base and documentations site.
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This mail address can be used if you have support questions that are not directly regarding how to run a given application on a specific SNIC HPC resource, but regarding how to use the application itself or how to solve an issue with the application that is not specific to running it on a certain resource.  
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The application-support queue is monitored by all the application experts, who are distributed over all the six SNIC HPC centers, so there is a good chance that someone who knows the given application will see the support request and help answer your questions or solve your issue.  
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The aim of this site is that you should be able to get information, help, tips-and-tricks, etc. regarding the most widely used computational tools and scientific applications. The site also aims to provide general documentation related to the SNIC HPC-centres and various SNIC initiatives.
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If you don’t know whether or not to use the application-support address for your support request, then just send your request to the support address at the HPC center where you run your jobs. Then someone monitoring that support queue will in turn move your support request to the application-support queue if they find that your request is better handled there.
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;[[Research areas]]
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:Articles on this site are generally marked as relevant for one or more research areas. On this page you see a list of the research areas for which at least one relevant article exists.
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:On the page for a specific research area, you find a list of the software articles that have been marked as relevant for that research area. Here you also find a list of the application experts that are associated with the given research area.
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<u>Discussion pages:</u><br>
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;[[Software]]
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All pages in the knowledge base have parallel discussion pages (follow the link Discussion in the top of each page) where anyone interested can discuss the original page; add comments, suggestions, their own tips, new links etc. All you need to do to be able to edit a discussion page is to create an account for this wiki ([[Special:UserLogin|Log in / create account]]). Creating an account only requires that you register a working e-mail address. Once you have an account, you can log in by following the link in the top right-hand corner of any page.
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:Overview of all the software articles.
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We strongly encourage all users to add comments etc. to the discussion pages, so we can improve the knowledge base and keep the provided information as fresh as possible.
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;[[SweGrid]]
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:Documentation for using the grid-resources provided by SweGrid.  
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;[[SNIC storage]]
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:Documentation regarding the Swedish storage initiative.
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=[[Application Experts]]=
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;[[Projects]]
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*[[Application_Experts#Rossen Apostolov, PDC|Rossen Apostolov, PDC]], Molecular Dynamics
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:Overview of ongoing and past projects.
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*[[Application_Experts#Lilit Axner, PDC/KTH|Lilit Axner, PDC/KTH]], Computational Fluid Dynamics
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*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]], Computational Science
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*[[Application_Experts#Mattias Chevalier, PDC|Mattias Chevalier, PDC]], Computational Fluid Dynamics
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*[[Application_Experts#Martin Dahlö, UPPMAX|Martin Dahlö, UPPMAX]]
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*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]
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*Jerry Eriksson, HPC2N
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*Torgny Faxén, NSC
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*[[Application_Experts#Anders Hast, UPPMAX|Anders Hast, UPPMAX]], Scientific Visualization
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*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics
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*[[Application_Experts#Joachim Hein, Lunarc|Joachim Hein, Lunarc]], Parallel Programming, Performance Analysis
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*[[Application_Experts#Hans Karlsson, UPPMAX|Hans Karlsson, UPPMAX]], Computational Quantum Mechanics
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*[[Application_Experts#Soon-Heum "Jeff" Ko, NSC|Soon-Heum "Jeff" Ko, NSC]], Computational Fluid Dynamics
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*Peter Larsson, NSC, Computational Material Science
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*Jonas Lindemann, Lunarc, Grid Computing, SGUSI
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*Mats Nylén, HPC2N
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*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]], Computational Chemistry
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*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry
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*[[Application_Experts#Elias Rudberg, UPPMAX|Elias Rudberg, UPPMAX]], Code and Algorithm Development
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*Mikael Rännar, HPC2N, Computing Science
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*Åke Sandgren, HPC2N
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*[[Application_Experts#Biplab Sanyal, UPPMAX|Biplab Sanyal, UPPMAX]], Theoretical Material Physics
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*[[Application_Experts#Mattias Slabanja, C3SE|Mattias Slabanja, C3SE]], Computational Materials Science
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*[[Application_Experts#Ola Spjuth, UPPMAX|Ola Spjuth, UPPMAX]], Bioinformatics
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*[[Application_Experts#Daniel Spångberg, UPPMAX|Daniel Spångberg, UPPMAX]], Molecular Dynamics
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*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]
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*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]
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=[[System Experts]]=
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;[[Support]]
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:Overview of all the support e-mail addresses available for requesting support along with a description of what type of requests that the address is meant to handle.
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=Scientific Topics=
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;People
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:Presentations of all the authors that contribute to the site.
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:[[Application experts]] are SNIC personnel that to some extent are available for advanced application support through this site and the [mailto:application-support@snic.se application-support] address.
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:[[Systems experts]] are SNIC personnel that maintain and develop the various resources and provide help and support for using the resources, both through this site and the various HPC-centre web sites and support addresses.
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==Computational Chemistry==
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<!--
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For an index over the pages related to Computational Chemistry, please visit the [[:Category:Computational_Chemistry|category page]].
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===== Discussion pages =====
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===Prominent Software===
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All pages on this site have parallel discussion pages (follow the link Discussion in the top of each page) where anyone interested can discuss the original page; add comments, suggestions, their own tips, new links etc. All you need to do to be able to edit a discussion page is to create an account for this wiki ([[Special:UserLogin|Log in / create account]]). Creating an account only requires that you register a working e-mail address. Once you have an account, you can log in by following the link in the top right-hand corner of any page.
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*Quantum Chemistry
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*#[[Gaussian]]
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*#[[NWChem]]
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*#[[Dalton]] - Dalton is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory.
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*Molecular Dynamics
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We strongly encourage all users to add comments etc. to the discussion pages, so we can improve the knowledge base and keep the provided information as fresh as possible.
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*#[[GROMACS]]
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-->
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*#Namd
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*#Amber
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*Monte Carlo Thermodynamics
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*QSAR
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==Computational Physics==
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===Prominent Software===
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====Condensed Matter====
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*[[VASP]]
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====Astrophysics====
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====Fluid simulations====
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For an index over the pages related to Fluid simulations, please visit the [[:Category:Computational_Fluid_Dynamics|category page]].  
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* [[Edge]] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.
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* [[Fluent]] - FLUENT is a popular commercial computational fluid dynamics (CFD) package which is developed by ANSYS Inc.
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* [[OpenFOAM]] - OpenFOAM (Open Field Operation and Manipulation) is a free, open source CFD software package produced by OpenCFD Ltd.
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* [[Simson]] - Simson is a software package that implements an efficient spectral integration technique to solve the Navier-Stokes equations for incompressible channel and boundary layer flows.
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== Bioinformatics ==
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Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].
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=== Prominent software ===
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* Sequence analysis
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** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.
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** [[HMMER]] - pattern recognition for protein families or domains.
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** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.
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* Computational evolutionary biology
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** [[PHYLIP]] - Phylogeny.
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** [[MrBayes]] - MCMC prediction of phylogenetic trees.
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* Molecular Modeling
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** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.
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* Neurobiology
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** [[MUSIC]] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.
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==Meteorology and Climatology==
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*ECEARTH
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*RCA
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*RCO
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*NEMO
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==Visualization and post-processing==
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*Grace
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* [[Gnuplot|Gnuplot]]
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==Software Development==
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*Compilers and Libraries
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*#Intel, PathScale, PGI, GNU Compilers
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*#MPI
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*#BLAS
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*#MKL
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*Profiling and Debugging
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*#TotalView
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*#Vampir
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*#Valgrind
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*#Intel trace analyzer
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=Grid information (SweGrid/Swestore)=
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==[[SweGrid User's Guide]]==
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==[[Swestore]]==
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==[[SGUSI]]==
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=Using This Wiki=
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Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. For formatting and mediawiki markup details see [http://www.mediawiki.org/wiki/Help:Formatting Formatting]. For adding links see [http://www.mediawiki.org/wiki/Help:Links Links]. Also have a look at the [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ].
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Please do '''not''' upload or otherwise publish copyrighted material on this wiki.
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Latest revision as of 13:04, 23 January 2018


SNIClogo 150.png

Kb docu 450.png

Welcome to the general SNIC knowledge base and documentations site.

The aim of this site is that you should be able to get information, help, tips-and-tricks, etc. regarding the most widely used computational tools and scientific applications. The site also aims to provide general documentation related to the SNIC HPC-centres and various SNIC initiatives.

Research areas
Articles on this site are generally marked as relevant for one or more research areas. On this page you see a list of the research areas for which at least one relevant article exists.
On the page for a specific research area, you find a list of the software articles that have been marked as relevant for that research area. Here you also find a list of the application experts that are associated with the given research area.
Software
Overview of all the software articles.
SweGrid
Documentation for using the grid-resources provided by SweGrid.
SNIC storage
Documentation regarding the Swedish storage initiative.
Projects
Overview of ongoing and past projects.
Support
Overview of all the support e-mail addresses available for requesting support along with a description of what type of requests that the address is meant to handle.
People
Presentations of all the authors that contribute to the site.
Application experts are SNIC personnel that to some extent are available for advanced application support through this site and the application-support address.
Systems experts are SNIC personnel that maintain and develop the various resources and provide help and support for using the resources, both through this site and the various HPC-centre web sites and support addresses.


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