SNIC Documentation - User contributions [en]

Main Page

2011-04-19T10:20:29Z

Lennart Karlsson (UPPMAX):

{| cellspacing="10"
|- valign="bottom"
|<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big>
|[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]
|}

<blockquote style="background-color: lightgrey; border: solid thin grey; padding: 15px 15px 15px 15px;">
'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''
</blockquote>

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.

We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address: 
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.

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.

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.

Discussion pages: 
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.

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.

=[[Application Experts]]=
*[[Application_Experts#Rossen Apostolov, PDC|Rossen Apostolov, PDC]]
*[[Application_Experts#Lilit Axner, PDC|Lilit Axner, PDC/KTH]]
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]
*[[Application_Experts#Martin Dahlö, UPPMAX|Martin Dahlö, UPPMAX]]
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]
*Jerry Eriksson, HPC2N
*Torgny Faxén, NSC
*[[Application_Experts#Anders Hast, UPPMAX|Anders Hast, UPPMAX]], Scientific Visualization
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics
*Joachim Hein, Lunarc
*[[Application_Experts#Hans Karlsson, UPPMAX|Hans Karlsson, UPPMAX]], Computational Quantum Mechanics
*Jonas Lindemann, Lunarc
*Mats Nylén, HPC2N
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]], Computational Chemistry
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry
*[[Application_Experts#Elias Rudberg, UPPMAX|Elias Rudberg, UPPMAX]], Code and Algorithm Development
*Mikael Rännar, HPC2N
*Åke Sandgren, HPC2N
*[[Application_Experts#Biplab Sanyal, UPPMAX|Biplab Sanyal, UPPMAX]], Theoretical Material Physics
*Mattias Slabanja, C3SE
*[[Application_Experts#Ola Spjuth, UPPMAX|Ola Spjuth, UPPMAX]]
*[[Application_Experts#Daniel Spångberg, UPPMAX|Daniel Spångberg, UPPMAX]], Molecular Dynamics
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]

=[[System Experts]]=

=Scientific Topics=

==Computational Chemistry==

===Prominent Software===
*Quantum Chemistry
*#[[Gaussian]]
*#[[NWChem]]
*#[[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.

*Molecular Dynamics
*#[[GROMACS]]
*#Namd
*#Amber

*Monte Carlo Thermodynamics
*QSAR

==Computational Physics==

===Prominent Software===

====Condensed Matter====
*VASP

====Astrophysics====

====Fluid simulations====
* [[Edge]] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.
* [[Fluent]]
* [[OpenFOAM]]
* [[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.

== 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.
* Neurobiology
** [[MUSIC]] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.

==Meteorology and Climatology==

*ECEARTH
*RCA
*RCO
*NEMO

==Visualization and post-processing==
*Grace
* [[Gnuplot|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]]==

==[[SGUSI]]==

=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.

Main Page

2011-04-19T10:12:10Z

Lennart Karlsson (UPPMAX):

{| cellspacing="10"
|- valign="bottom"
|<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big>
|[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]
|}

<blockquote style="background-color: lightgrey; border: solid thin grey; padding: 15px 15px 15px 15px;">
'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''
</blockquote>

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.

We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address: 
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.

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.

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.

Discussion pages: 
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.

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.

=[[Application Experts]]=
*[[Application_Experts#Rossen Apostolov, PDC|Rossen Apostolov, PDC]]
*[[Application_Experts#Lilit Axner, PDC|Lilit Axner, PDC/KTH]]
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]
*Jerry Eriksson, HPC2N
*Torgny Faxén, NSC
*Anders Hast, UPPMAX
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics
*Joachim Hein, Lunarc
*Jonas Lindemann, Lunarc
*Mats Nylén, HPC2N
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]], Computational Chemistry
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry
*[[Application_Experts#Elias Rudberg, UPPMAX|Elias Rudberg, UPPMAX]]
*Mikael Rännar, HPC2N
*Åke Sandgren, HPC2N
*Mattias Slabanja, C3SE
*Ola Spjuth, UPPMAX
*[[Application_Experts#Daniel Spångberg, UPPMAX|Daniel Spångberg, UPPMAX]]
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]

=[[System Experts]]=

=Scientific Topics=

==Computational Chemistry==

===Prominent Software===
*Quantum Chemistry
*#[[Gaussian]]
*#[[NWChem]]
*#[[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.

*Molecular Dynamics
*#[[GROMACS]]
*#Namd
*#Amber

*Monte Carlo Thermodynamics
*QSAR

==Computational Physics==

===Prominent Software===

====Condensed Matter====
*VASP

====Astrophysics====

====Fluid simulations====
* [[Edge]] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.
* [[Fluent]]
* [[OpenFOAM]]
* [[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.

== 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.
* Neurobiology
** [[MUSIC]] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.

==Meteorology and Climatology==

*ECEARTH
*RCA
*RCO
*NEMO

==Visualization and post-processing==
*Grace
* [[Gnuplot|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]]==

==[[SGUSI]]==

=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.