https://snicdocs.nsc.liu.se/w/api.php?action=feedcontributions&user=Rossen+Apostolov+%28PDC%29&feedformat=atomSNIC Documentation - User contributions [en]2024-03-29T15:08:36ZUser contributionsMediaWiki 1.31.10https://snicdocs.nsc.liu.se/w/index.php?title=User:Rossen_Apostolov_(PDC)&diff=5833User:Rossen Apostolov (PDC)2014-05-14T09:33:33Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{{application expert info<br />
|first name=Rossen<br />
|last name=Apostolov<br />
|centre=PDC<br />
|fte=100<br />
|snic ae financing=100<br />
|other ae financing=<br />
|financing=SNIC<br />
|fields=Molecular dynamics<br />
|other activities=<br />
|image=Rossen.jpg<br />
|office=PDC, KTH;Teknikringen 14, 4F;SE-100 44 STOCKHOLM;SWEDEN<br />
|phone=<br />
}}<br />
<br />
== Quick facts ==<br />
* Working at PDC since 2010 <br />
* Ph.D. 2008 in Computational Biophysics<br />
* Working on Gromacs development<br />
* Involved in [http://www.scalalife.eu/ ScalaLife]<br />
<br />
== Expertise ==<br />
* [[expertise::Gromacs]]<br />
* [[expertise::Molecular Dynamics]]<br />
<br />
== General Responsibilities ==<br />
* Expert support to the end-users of MD applications<br />
* Maintenance/benchmarking/performance analysis of MD simulations software on SNIC resources<br />
<br />
== Projects ==<br />
* New format, library and API for efficient storage of binary trajectory data.<br />
* Multi-level MD - hybrid-QM/MM simulations of membrane systems.<br />
* Automated systems for multi-scale molecular simulations.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Rossen_Apostolov_(PDC)&diff=5473User:Rossen Apostolov (PDC)2013-10-17T09:14:15Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{{application expert info<br />
|first name=Rossen<br />
|last name=Apostolov<br />
|centre=PDC<br />
|fte=50<br />
|snic ae financing=50<br />
|other ae financing=<br />
|financing=SNIC<br />
|fields=Molecular dynamics<br />
|other activities=Technical Director for ScalaLife EU Project (50% financed)<br />
|image=Rossen.jpg<br />
|office=PDC, KTH;Teknikringen 14, 4F;SE-100 44 STOCKHOLM;SWEDEN<br />
|phone=<br />
}}<br />
<br />
== Quick facts ==<br />
* Working at PDC since 2010 <br />
* Ph.D. 2008 in Computational Biophysics<br />
* Working on Gromacs development<br />
* Involved in [http://www.scalalife.eu/ ScalaLife]<br />
<br />
== Expertise ==<br />
* [[expertise::Gromacs]]<br />
* [[expertise::Molecular Dynamics]]<br />
<br />
== General Responsibilities ==<br />
* Expert support to the end-users of MD applications<br />
* Maintenance/benchmarking/performance analysis of MD simulations software on SNIC resources<br />
<br />
== Projects ==<br />
* New format, library and API for efficient storage of binary trajectory data.<br />
* Multi-level MD - hybrid-QM/MM simulations of membrane systems.<br />
* Automated systems for multi-scale molecular simulations.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Rossen_Apostolov_(PDC)&diff=1919User:Rossen Apostolov (PDC)2011-09-07T14:13:46Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{{application expert info<br />
|first name=Rossen<br />
|last name=Apostolov<br />
|centre=PDC<br />
|fields=Molecular dynamics<br />
|other activities=Technical Director for ScalaLife.<br />
|image=Rossen.jpg<br />
|office=PDC, KTH;Teknikringen 14, 4F;SE-100 44 STOCKHOLM;SWEDEN<br />
|phone=<br />
}}<br />
<br />
== Quick facts ==<br />
* Working at PDC since 2010 <br />
* Ph.D. 2008 in Computational Biophysics<br />
* Working on Gromacs development<br />
* Involved in [http://www.scalalife.eu/ ScalaLife]<br />
<br />
== Expertise ==<br />
* [[expertise::Gromacs]]<br />
* [[expertise::GPGPU computing]]</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Rossen_Apostolov_(PDC)&diff=1910User:Rossen Apostolov (PDC)2011-09-07T13:04:11Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{{application expert info<br />
|first name=Rossen<br />
|last name=Apostolov<br />
|centre=PDC<br />
|fields=Molecular dynamics<br />
|other activities=Technical Director for ScalaLife.<br />
|image=Rossen.jpg<br />
|office=PDC, KTH;Teknikringen 14, 4F;SE-100 44 STOCKHOLM;SWEDEN<br />
|phone=+46-700-242-545<br />
}}<br />
<br />
== Quick facts ==<br />
* Working at PDC since 2010 <br />
* Ph.D. 2008 in Computational Biophysics<br />
* Working on Gromacs development<br />
* Involved in [http://www.scalalife.eu/ ScalaLife]<br />
<br />
== Expertise ==<br />
* [[expertise::Gromacs]]<br />
* [[expertise::GPGPU computing]]</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Rossen_Apostolov_(PDC)&diff=1904User:Rossen Apostolov (PDC)2011-09-07T12:18:14Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{{application expert info<br />
|first name=Rossen<br />
|last name=Apostolov<br />
|centre=PDC<br />
|fields=Molecular dynamics<br />
|other activities=Work 50% as technical director for ScalaLife.<br />
|image=Rossen.jpg<br />
|office=PDC, KTH;Teknikringen 14, 4F;SE-100 44 STOCKHOLM;SWEDEN<br />
|phone=+46-700-242-545<br />
}}<br />
<br />
== Quick facts ==<br />
* Working at PDC since 2010 <br />
* Ph.D. 2008 in Computational Biophysics<br />
* Working on Gromacs development<br />
* Involved in [http://www.scalalife.eu/ ScalaLife]<br />
<br />
== Expertise ==<br />
* [[expertise::Gromacs]]<br />
* [[expertise::GPGPU computing]]</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Rossen_Apostolov_(PDC)&diff=1902User:Rossen Apostolov (PDC)2011-09-07T12:14:10Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{{application expert info<br />
|first name=Rossen<br />
|last name=Apostolov<br />
|centre=PDC<br />
|fields=Molecular dynamics<br />
|other activities=Work 50% as technical director for ScalaLife.<br />
|image=Rossen.jpg<br />
|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored<br />
|phone=Semicolon separated phone numbers (with optional <br />
explanation), newlines are ignored<br />
}}<br />
<br />
== Quick facts ==<br />
* Working at PDC since 2010 <br />
* Ph.D. 2008 in Computational Biophysics<br />
* Working on Gromacs development<br />
* Involved in [http://www.scalalife.eu/ ScalaLife]<br />
<br />
== Expertise ==<br />
* [[expertise::Gromacs]]<br />
* [[expertise::GPGPU computing]]</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Application_Experts&diff=323Application Experts2011-03-23T10:57:16Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>===Torben Rasmussen, NSC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:Torben_small.jpg|frame|left|Torben Rasmussen]]<br />
|<br />
*Application expert in computational chemistry<br />
*Work at NSC since 2008<br />
*Handle user relations, general support, software installations, etc.<br />
*Ph.D. in 2001<br />
*Five years of postdoctoral experience in the field covering applications within organic chemistry, biochemistry, and life science<br />
*Have used [[Gaussian]] and Jaguar extensively<br />
*Experience with parametrization of molecular mechanics force fields<br />
|}<br />
<br />
===Chandan Basu, NSC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:chandan.jpg|frame|left|Chandan Basu]]<br />
|<br />
*Ph.D in computational Physics<br />
*Working at NSC since 2009<br />
*Working on benchmarking, optimization, scaling issues <br />
*Working on EU projects, e.g., IS-ENES, PRACE and also with SMHI<br />
|}<br />
<br />
===Johan Raber, NSC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:JohanR.png|frame|left|Johan Raber]]<br />
|<br />
*E-science coordinator<br />
*Work at NSC for two years as a Systems Expert<br />
*Handle user relations, general support etc.<br />
*PhD in Biophysics in 2007 at Uppsala University<br />
*MSc in Molecular Biotechnology Engineering<br />
*Long experience using Gaussian<br />
*Experience using GROMACS and Gaussian for QM/MD simulations<br />
|}<br />
<br />
===Joel Hedlund, NSC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:Joel_small.jpg|frame|left|Joel Hedlund]]<br />
|<br />
*Application expert in bioinformatics.<br />
*Work at NSC since 2011.<br />
*Ph.D. in 2010.<br />
*Main scientific work in the field of sequence analysis and bioinformatic protein family characterisation.<br />
*Have used [[HMMER]], [[BLAST]] and [[MSA]] extensively.<br />
|}<br />
<br />
===Jonathan Vincent, PDC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:|frame|left|Jonathan Vincent]]<br />
|<br />
*Application expert<br />
*Work at PDC since 2009<br />
*Handle advanced user support, software installations, etc.<br />
*Ph.D. 2000 in Semiconductor Physics, Postdoctoral experience in semiconductor physics and classical and quantum dynamics<br />
*Working on Benchmarking, code optimisation<br />
*Keywords : Cray XT6, Cray XE6, MPI, Benchmarking, Optimisation<br />
|}<br />
<br />
===Rossen Apostolov, PDC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:Rossen.jpg|frame|left|Rossen Apostolov]]<br />
|<br />
*Application expert in Molecular Dynamics simulations<br />
*Working at PDC since 2010<br />
*Ph.D. 2008 in Computational Biophysics<br />
*Working on [[Gromacs]] development<br />
*Keywords : Molecular Dynamics, Gromacs, GPGPU computing<br />
|}</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=File:Rossen.jpg&diff=322File:Rossen.jpg2011-03-23T10:55:58Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div></div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Application_Experts&diff=321Application Experts2011-03-23T10:49:08Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>===Torben Rasmussen, NSC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:Torben_small.jpg|frame|left|Torben Rasmussen]]<br />
|<br />
*Application expert in computational chemistry<br />
*Work at NSC since 2008<br />
*Handle user relations, general support, software installations, etc.<br />
*Ph.D. in 2001<br />
*Five years of postdoctoral experience in the field covering applications within organic chemistry, biochemistry, and life science<br />
*Have used [[Gaussian]] and Jaguar extensively<br />
*Experience with parametrization of molecular mechanics force fields<br />
|}<br />
<br />
===Chandan Basu, NSC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:chandan.jpg|frame|left|Chandan Basu]]<br />
|<br />
*Ph.D in computational Physics<br />
*Working at NSC since 2009<br />
*Working on benchmarking, optimization, scaling issues <br />
*Working on EU projects, e.g., IS-ENES, PRACE and also with SMHI<br />
|}<br />
<br />
===Johan Raber, NSC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:JohanR.png|frame|left|Johan Raber]]<br />
|<br />
*E-science coordinator<br />
*Work at NSC for two years as a Systems Expert<br />
*Handle user relations, general support etc.<br />
*PhD in Biophysics in 2007 at Uppsala University<br />
*MSc in Molecular Biotechnology Engineering<br />
*Long experience using Gaussian<br />
*Experience using GROMACS and Gaussian for QM/MD simulations<br />
|}<br />
<br />
===Joel Hedlund, NSC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:Joel_small.jpg|frame|left|Joel Hedlund]]<br />
|<br />
*Application expert in bioinformatics.<br />
*Work at NSC since 2011.<br />
*Ph.D. in 2010.<br />
*Main scientific work in the field of sequence analysis and bioinformatic protein family characterisation.<br />
*Have used [[HMMER]], [[BLAST]] and [[MSA]] extensively.<br />
|}<br />
<br />
===Jonathan Vincent, PDC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:|frame|left|Jonathan Vincent]]<br />
|<br />
*Application expert<br />
*Work at PDC since 2009<br />
*Handle advanced user support, software installations, etc.<br />
*Ph.D. 2000 in Semiconductor Physics, Postdoctoral experience in semiconductor physics and classical and quantum dynamics<br />
*Working on Benchmarking, code optimisation<br />
*Keywords : Cray XT6, Cray XE6, MPI, Benchmarking, Optimisation<br />
|}<br />
<br />
===Rossen Apostolov, PDC===<br />
{|<br />
|- valign="top"<br />
|<br />
[[image:|frame|left|Rossen Apostolov]]<br />
|<br />
*Application expert in Molecular Dynamics simulations<br />
*Working at PDC since 2010<br />
*Ph.D. 2008 in Computational Biophysics<br />
*Working on [[Gromacs]] development<br />
*Keywords : Molecular Dynamics, Gromacs, GPGPU computing<br />
|}</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=320Main Page2011-03-23T10:43:33Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{| cellspacing="10" <br />
|- valign="bottom"<br />
|<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
|[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]<br />
|}<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey; padding: 15px 15px 15px 15px;"><br />
'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''<br />
</blockquote><br />
<br />
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. <br />
<br />
<u>We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address:</u><br><br />
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. <br />
<br />
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. <br />
<br />
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.<br />
<br />
<u>Discussion pages:</u><br><br />
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.<br />
<br />
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.<br />
<br />
<br />
=[[Application Experts]]=<br />
*[[Application_Experts#Rossen Apostolov, PDC|Rossen Apostolov, PDC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Jerry Eriksson, HPC2N<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*Mats Nylén, HPC2N<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]], Computational Chemistry<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Mikael Rännar, HPC2N<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
*#[[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.<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
====Fluid simulations====<br />
* [[Edge]] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.<br />
* [[Fluent]]<br />
* [[OpenFOAM]]<br />
* [[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.<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
* Neurobiology<br />
** [[MUSIC]] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
* [[Gnuplot|Gnuplot]]<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
==[[SGUSI]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=319Main Page2011-03-23T10:43:12Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{| cellspacing="10" <br />
|- valign="bottom"<br />
|<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
|[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]<br />
|}<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey; padding: 15px 15px 15px 15px;"><br />
'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''<br />
</blockquote><br />
<br />
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. <br />
<br />
<u>We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address:</u><br><br />
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. <br />
<br />
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. <br />
<br />
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.<br />
<br />
<u>Discussion pages:</u><br><br />
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.<br />
<br />
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.<br />
<br />
<br />
=[[Application Experts]]=<br />
*[[Application_Experts#Rossen Apostolov, PDC|Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Jerry Eriksson, HPC2N<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*Mats Nylén, HPC2N<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]], Computational Chemistry<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Mikael Rännar, HPC2N<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
*#[[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.<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
====Fluid simulations====<br />
* [[Edge]] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.<br />
* [[Fluent]]<br />
* [[OpenFOAM]]<br />
* [[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.<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
* Neurobiology<br />
** [[MUSIC]] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
* [[Gnuplot|Gnuplot]]<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
==[[SGUSI]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=MUSIC&diff=318MUSIC2011-03-23T10:39:48Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
[[http://software.incf.org/software/music Project page]]<br />
<br />
Purpose<br />
<br />
MUSIC allows spike events and continuous time series to be communicated between applications in a cluster computer. The typical usage cases are connecting models developed for different simulators and connecting a parallel simulator to a post-processing tool.<br />
<br />
License: GNU General Public License<br />
<br />
Prerequirements: MPI<br />
<br />
Ease of Use: Intermediate<br />
<br />
Maturity:Intermediate<br />
<br />
Operating system: Unix-like</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=MUSIC&diff=317MUSIC2011-03-23T10:39:02Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
[[http://software.incf.org/software/music Project page]]<br />
<br />
Purpose<br />
<br />
MUSIC allows spike events and continuous time series to be communicated between applications in a cluster computer. The typical usage cases are connecting models developed for different simulators and connecting a parallel simulator to a post-processing tool.<br />
<br />
License: GNU General Public License<br />
Prerequirements: MPI<br />
Ease of Use: Intermediate<br />
Maturity:Intermediate<br />
Operating system: Unix-like</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=MUSIC&diff=316MUSIC2011-03-23T10:36:32Z<p>Rossen Apostolov (PDC): Created page with "C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime. Project page http://software.incf.org/software/music Pu..."</p>
<hr />
<div>C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
Project page<br />
<br />
[[http://software.incf.org/software/music]]<br />
Purpose<br />
<br />
MUSIC allows spike events and continuous time series to be communicated between applications in a cluster computer. The typical usage cases are connecting models developed for different simulators and connecting a parallel simulator to a post-processing tool.<br />
License<br />
<br />
GNU General Public License<br />
Prerequirements<br />
<br />
MPI<br />
Ease of Use<br />
<br />
Intermediate<br />
Maturity<br />
<br />
Intermediate<br />
Operating system<br />
Unix-like</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=315Main Page2011-03-23T10:35:50Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{| cellspacing="10" <br />
|- valign="bottom"<br />
|<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
|[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]<br />
|}<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey; padding: 15px 15px 15px 15px;"><br />
'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''<br />
</blockquote><br />
<br />
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. <br />
<br />
<u>We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address:</u><br><br />
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. <br />
<br />
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. <br />
<br />
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.<br />
<br />
<u>Discussion pages:</u><br><br />
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.<br />
<br />
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.<br />
<br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Jerry Eriksson, HPC2N<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*Mats Nylén, HPC2N<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]], Computational Chemistry<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Mikael Rännar, HPC2N<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
*#[[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.<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
====Fluid simulations====<br />
* [[Edge]] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.<br />
* [[Fluent]]<br />
* [[OpenFOAM]]<br />
* [[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.<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
* Neurobiology<br />
** [[MUSIC]] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
* [[Gnuplot|Gnuplot]]<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
==[[SGUSI]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Simson&diff=314Simson2011-03-23T10:35:19Z<p>Rossen Apostolov (PDC): Created page with "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."</p>
<hr />
<div>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.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Edge&diff=313Edge2011-03-23T10:34:43Z<p>Rossen Apostolov (PDC): Created page with "Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency (Totalförsvarets forskningsinstitut) (FOI) since 1997. The code is fully RANS capable, and fe..."</p>
<hr />
<div>Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency (Totalförsvarets forskningsinstitut) (FOI) since 1997. The code is fully RANS capable, and features several turbulence models from algebraic to state-of-the-art two-equation models. Furthermore the code also includes LES and DES models and the ability to run in "Euler" and laminar mode. Time-accurate and aeroelastic simulations are also possible.<br />
<br />
The Edge flow solver is based on a node-centered finite volume scheme. For steady flows, the equations are integrated towards steady state with an explicit multi-stage Runge-Kutta scheme. To accelerate convergence, residual smoothing and a multi-grid technique can be employed. Low Mach-number preconditioning is also available. Time-accurate computations are implemented using dual time-stepping: implicit time marching with explicit sub-iterations.<br />
<br />
The copyright holder is FOI. All rights to Edge are reserved by FOI. An idividual user-based written agreement with FOI is required to get access to the code. Edge or parts of Edge may not be sold, distributed or in any other way made available to third parties without a written permission from FOI.<br />
<br />
Website: [http://www.foi.se/edge Edge homepage].<br />
<br />
Documentation: [http://www.foi.se/upload/projects/edge/documentation-latest/edge-user.pdf edge-user.pdf]</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=312Main Page2011-03-23T10:32:56Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{| cellspacing="10" <br />
|- valign="bottom"<br />
|<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
|[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]<br />
|}<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey; padding: 15px 15px 15px 15px;"><br />
'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''<br />
</blockquote><br />
<br />
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. <br />
<br />
<u>We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address:</u><br><br />
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. <br />
<br />
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. <br />
<br />
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.<br />
<br />
<u>Discussion pages:</u><br><br />
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.<br />
<br />
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.<br />
<br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Jerry Eriksson, HPC2N<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*Mats Nylén, HPC2N<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]], Computational Chemistry<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Mikael Rännar, HPC2N<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
*#[[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.<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
====Fluid simulations====<br />
* [[Edge]] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.<br />
* [[Fluent]]<br />
* [[OpenFOAM]]<br />
* [[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.<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
* Neurobiology<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/36 MUSIC] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
* [[Gnuplot|Gnuplot]]<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
==[[SGUSI]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Dalton&diff=311Dalton2011-03-23T10:31:40Z<p>Rossen Apostolov (PDC): Created page with "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 theo..."</p>
<hr />
<div>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. At the release of Dalton 2.0 in March 2005, a total of 1208 licenses for Dalton 1.x had been issued. A new release is currently in preparation; Dalton 2011.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=310Main Page2011-03-23T10:31:09Z<p>Rossen Apostolov (PDC): </p>
<hr />
<div>{| cellspacing="10" <br />
|- valign="bottom"<br />
|<big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
|[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]<br />
|}<br />
<br />
<blockquote style="background-color: lightgrey; border: solid thin grey; padding: 15px 15px 15px 15px;"><br />
'''NOTE: This site is under constant development and is still in the very early days of it's existence!'''<br />
</blockquote><br />
<br />
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. <br />
<br />
<u>We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address:</u><br><br />
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. <br />
<br />
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. <br />
<br />
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.<br />
<br />
<u>Discussion pages:</u><br><br />
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.<br />
<br />
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.<br />
<br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Jerry Eriksson, HPC2N<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*Mats Nylén, HPC2N<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]], Computational Chemistry<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Mikael Rännar, HPC2N<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
*#[[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.<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
====Fluid simulations====<br />
* [http://dhcp-221-37.pdc.kth.se/drupal/node/29 Edge] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.<br />
* [http://dhcp-221-37.pdc.kth.se/drupal/node/31 Fluent]<br />
* [http://dhcp-221-37.pdc.kth.se/drupal/node/33 OpenFOAM]<br />
* [http://dhcp-221-37.pdc.kth.se/drupal/node/30 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.<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
* Neurobiology<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/36 MUSIC] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
* [[Gnuplot|Gnuplot]]<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
==[[SGUSI]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=236Main Page2011-03-02T10:36:18Z<p>Rossen Apostolov (PDC): /* Prominent Software */</p>
<hr />
<div><big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
<br />
NOTE: This site is under constant development and is still in the early days of it's existence! <br />
<br />
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. <br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]]<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
====Fluid simulations====<br />
* [http://dhcp-221-37.pdc.kth.se/drupal/node/29 Edge] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.<br />
* [http://dhcp-221-37.pdc.kth.se/drupal/node/31 Fluent]<br />
* [http://dhcp-221-37.pdc.kth.se/drupal/node/33 OpenFOAM]<br />
* [http://dhcp-221-37.pdc.kth.se/drupal/node/30 Sinsom] - 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.<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/14 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.<br />
* Neurobiology<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/36 MUSIC] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
*Gnuplot<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=235Main Page2011-03-02T10:35:23Z<p>Rossen Apostolov (PDC): /* Prominent software */</p>
<hr />
<div><big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
<br />
NOTE: This site is under constant development and is still in the early days of it's existence! <br />
<br />
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. <br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]]<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/14 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.<br />
* Neurobiology<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/36 MUSIC] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
*Gnuplot<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=234Main Page2011-03-02T10:15:22Z<p>Rossen Apostolov (PDC): /* Prominent software */</p>
<hr />
<div><big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
<br />
NOTE: This site is under constant development and is still in the early days of it's existence! <br />
<br />
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. <br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]]<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/14 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.<br />
* Neurobiology<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/36 MUSIC] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
* Fluid simulations<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/29 Edge] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/31 Fluent]<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/33 OpenFOAM]<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/30 Sinsom] - 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.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
*Gnuplot<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=233Main Page2011-03-02T10:11:53Z<p>Rossen Apostolov (PDC): /* Prominent software */</p>
<hr />
<div><big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
<br />
NOTE: This site is under constant development and is still in the early days of it's existence! <br />
<br />
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. <br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]]<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/14 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.<br />
* Neurobiology<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/36 MUSIC] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
*Gnuplot<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=232Main Page2011-03-02T10:10:47Z<p>Rossen Apostolov (PDC): /* Prominent software */</p>
<hr />
<div><big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
<br />
NOTE: This site is under constant development and is still in the early days of it's existence! <br />
<br />
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. <br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]]<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
* Neurobiology<br />
** [http://dhcp-221-37.pdc.kth.se/drupal/node/36 MUSIC] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
*Gnuplot<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=231Main Page2011-03-02T09:31:48Z<p>Rossen Apostolov (PDC): /* Application Experts */</p>
<hr />
<div><big>'''Welcome to the SNIC knowledge base and documentations site.'''</big><br />
<br />
NOTE: This site is under constant development and is still in the early days of it's existence! <br />
<br />
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. <br />
<br />
=[[Application Experts]]=<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/11 Rossen Apostolov, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/19 Lilit Axner, PDC]<br />
*[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC]<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br />
*Torgny Faxén, NSC<br />
*Anders Hast, Uppmax<br />
*[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br />
*Joachim Hein, Lunarc<br />
*Jonas Lindemann, Lunarc<br />
*[[Application_Experts#Johan Raber, NSC|Johan Raber, NSC]]<br />
*[[Application_Experts#Torben Rasmussen, NSC|Torben Rasmussen, NSC]], Computational Chemistry<br />
*Åke Sandgren, HPC2N<br />
*Mattias Slabanja, C3SE<br />
*Ola Spjuth, Uppmax<br />
*Daniel Spångberg, Uppmax<br />
*[http://dhcp-221-37.pdc.kth.se/drupal/node/24 Olav Vahtras, PDC]<br />
*[[Application_Experts#Jonathan Vincent, PDC|Jonathan Vincent, PDC]]<br />
<br />
=[[System Experts]]=<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
===Prominent Software===<br />
*Quantum Chemistry<br />
*#[[Gaussian]]<br />
*#[[NWChem]]<br />
<br />
*Molecular Dynamics<br />
*#[[GROMACS]]<br />
*#Namd<br />
*#Amber<br />
<br />
*Monte Carlo Thermodynamics<br />
*QSAR<br />
<br />
==Computational Physics==<br />
<br />
===Prominent Software===<br />
<br />
====Condensed Matter====<br />
*VASP<br />
<br />
====Astrophysics====<br />
<br />
== Bioinformatics ==<br />
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].<br />
=== Prominent software ===<br />
* Sequence analysis<br />
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.<br />
** [[HMMER]] - pattern recognition for protein families or domains.<br />
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.<br />
* Computational evolutionary biology<br />
** [[PHYLIP]] - Phylogeny.<br />
** [[MrBayes]] - MCMC prediction of phylogenetic trees.<br />
* Molecular Modeling<br />
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.<br />
<br />
==Meteorology and Climatology==<br />
<br />
*ECEARTH<br />
*RCA<br />
*RCO<br />
*NEMO<br />
<br />
==Visualization and post-processing==<br />
*Grace<br />
*Gnuplot<br />
<br />
==Software Development==<br />
*Compilers and Libraries<br />
*#Intel, PGI, GNU Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<br />
*#Intel trace analyzer<br />
<br />
=Grid information (SweGrid/Swestore)=<br />
<br />
==[[SweGrid User's Guide]]==<br />
<br />
==[[Swestore]]==<br />
<br />
=Using This Wiki=<br />
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].<br />
<br />
Please do '''not''' upload or otherwise publish copyrighted material on this wiki.</div>Rossen Apostolov (PDC)