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<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big>
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'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''
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NOTE: This site is under constant development and is still in the early days of it's existence!
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{| cellspacing="10"
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[[image:SNIClogo_150.png|link=http://www.snic.se]]
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[[image:kb_docu_450.png|link=]]
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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.  
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Welcome to the general SNIC knowledge base and documentations site.
  
=[[Application Experts]]=
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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.
*Rossen Apostolov, PDC
 
*Lilit Axner, PDC
 
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]
 
*Mattias Chevalier, PDC
 
*Michael Djurfeldt, PDC
 
*Torgny Faxén, NSC
 
*Anders Hast, Uppmax
 
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics
 
*Joachim Hein, Lunarc
 
*Jonas Lindemann, Lunarc
 
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]]
 
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry
 
*Åke Sandgren, HPC2N
 
*Mattias Slabanja, C3SE
 
*Ola Spjuth, Uppmax
 
*Daniel Spångberg, Uppmax
 
*Olav Vahtras, PDC
 
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]
 
  
=[[System Experts]]=
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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.
  
=Scientific Topics=
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;[[Software]]
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:Overview of all the software articles.
  
==Computational Chemistry==
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;[https://docs.swestore.se/ Swestore]
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:Documentation regarding the Swedish storage initiative.
  
===Prominent Software===
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;[[Projects]]
*Quantum Chemistry
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:Overview of ongoing and past projects.
*#[[Gaussian]]
 
*#[[NWChem]]
 
  
*Molecular Dynamics
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;[[Support]]
*#[[GROMACS]]
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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.
*#Namd
 
*#Amber
 
  
*Monte Carlo Thermodynamics
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;People
*QSAR
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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.
  
==Computational Physics==
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===== Discussion pages =====
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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.
  
===Prominent Software===
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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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====Condensed Matter====
 
*VASP
 
 
 
====Astrophysics====
 
 
 
== Bioinformatics ==
 
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].
 
=== Prominent software ===
 
* Sequence analysis
 
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.
 
** [[HMMER]] - pattern recognition for protein families or domains.
 
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.
 
* Computational evolutionary biology
 
** [[PHYLIP]] - Phylogeny.
 
** [[MrBayes]] - MCMC prediction of phylogenetic trees.
 
* Molecular Modeling
 
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.
 
 
 
==Meteorology and Climatology==
 
 
 
*ECEARTH
 
*RCA
 
*RCO
 
*NEMO
 
 
 
==Visualization and post-processing==
 
*Grace
 
*Gnuplot
 
 
 
==Software Development==
 
*Compilers and Libraries
 
*#Intel, PGI, GNU Compilers
 
*#MPI
 
*#BLAS
 
*#MKL
 
*Profiling and Debugging
 
*#TotalView
 
*#Vampir
 
*#Valgrind
 
*#Intel trace analyzer
 
 
 
=Grid information (SweGrid/Swestore)=
 
 
 
==[[SweGrid User's Guide]]==
 
 
 
==[[Swestore]]==
 
 
 
=Using This Wiki=
 
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].
 
 
 
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.
 

Latest revision as of 13:19, 8 February 2023


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.
Swestore
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.