http://docs.snic.se/w/api.php?action=feedcontributions&feedformat=atom&user=Mikael+R%C3%A4nnar+%28HPC2N%29 2026-05-04T13:40:55Z User contributions MediaWiki 1.31.10 http://docs.snic.se/w/index.php?title=Introduction_to_Shared_Memory_Programming_and_OpenMP_(HPC2N,_May_28,_2015)&diff=6110 2015-05-12T14:58:37Z

<p>Mikael Rännar (HPC2N): Created page with &quot;{{training event info |description=Introduction to Shared Memory Programming and OpenMP |fields=Scientific computing |event type=Course |location=Umeå |start date=2015-05-28 |en...&quot;</p> <hr /> <div>{{training event info<br /> |description=Introduction to Shared Memory Programming and OpenMP<br /> |fields=Scientific computing<br /> |event type=Course<br /> |location=Umeå<br /> |start date=2015-05-28<br /> |end date=2015-05-28<br /> }}<br /> <br /> == Seminar Location ==<br /> MIT building, Umeå Universitet (Room to be announced later.)<br /> <br /> == Seminar overview ==<br /> This full-day course gives a short introduction to shard memory programming, with a focus on OpenMP. There will be a hands-on, where the participants get to compile and run small OpenMP programs on a cluster at HPC2N.<br /> <br /> == Trainer ==<br /> The course is delivered by HPC2N Staff<br /> <br /> == Seminar web page and registration ==<br /> <br /> <br /> https://www.hpc2n.umu.se/intro-openmp-2015</div>

Mikael Rännar (HPC2N) http://docs.snic.se/w/index.php?title=Introduction_to_Linux_and_Abisko_(HPC2N,_May_27)&diff=6109 2015-05-12T14:54:10Z

<p>Mikael Rännar (HPC2N): Created page with &quot;{{training event info |description=Introduction to Linux and Abisko |fields=Scientific computing |event type=Course |location=Umeå |start date=2015-05-27 |end date=2015-05-27 }}...&quot;</p> <hr /> <div>{{training event info<br /> |description=Introduction to Linux and Abisko<br /> |fields=Scientific computing<br /> |event type=Course<br /> |location=Umeå<br /> |start date=2015-05-27<br /> |end date=2015-05-27<br /> }}<br /> <br /> == Seminar Location ==<br /> MIT building, Umeå Universitet (Room to be announced later.)<br /> <br /> == Seminar overview ==<br /> This is a half-day course centered on how to use the systems that HPC2N is providing, and is a good starting point for people that are unfamiliar with how computer clusters work.<br /> <br /> The course will be divided into 2 parts finishing with a short hands-on session. The first part of the course will cover basic Linux commands and tools, while the second part will focus on the Abisko supercomputer (applying for HPC2N resources and acquire accounts, how to login to Abisko, how to run software, etc.).<br /> <br /> == Trainer ==<br /> The course is delivered by HPC2N Staff<br /> <br /> == Seminar web page and registration ==<br /> <br /> https://www.hpc2n.umu.se/intro-linux-abisko-may-2015</div>

Mikael Rännar (HPC2N) http://docs.snic.se/w/index.php?title=Introduction_to_Distributed_Memory_Programming_and_MPI_(HPC2N,_April_23,_2015)&diff=6075 2015-04-08T14:05:00Z

<p>Mikael Rännar (HPC2N): Created page with &quot;{{training event info |description=Introduction to Distributed Memory Programming and MPI |fields=Scientific computing |event type=Course |location=Umeå |start date=2015-04-23 |...&quot;</p> <hr /> <div>{{training event info<br /> |description=Introduction to Distributed Memory Programming and MPI<br /> |fields=Scientific computing<br /> |event type=Course<br /> |location=Umeå<br /> |start date=2015-04-23<br /> |end date=2015-04-23<br /> }}<br /> <br /> == Seminar Location ==<br /> MIT building, Umeå Universitet (Room to be announced later.)<br /> <br /> == Seminar overview ==<br /> This full-day course gives a short introduction to distributed memory programming, with a focus on MPI. There will be a hands-on, where the participants get to compile and run small MPI programs on a cluster at HPC2N.<br /> <br /> == Trainer ==<br /> The course is delivered by HPC2N Staff<br /> <br /> == Seminar web page and registration ==<br /> <br /> https://www.hpc2n.umu.se/intro-mpi-2015</div>

Mikael Rännar (HPC2N) http://docs.snic.se/w/index.php?title=Introduction_to_Linux_and_Abisko_(HPC2N,_April_22)&diff=6074 2015-04-08T13:56:33Z

<p>Mikael Rännar (HPC2N): </p> <hr /> <div>{{training event info<br /> |description=Introduction to Linux and Abisko<br /> |fields=Scientific computing<br /> |event type=Course<br /> |location=Umeå<br /> |start date=2015-04-22<br /> |end date=2015-04-22<br /> }}<br /> <br /> == Seminar Location ==<br /> MIT building, Umeå Universitet (Room to be announced later.)<br /> <br /> == Seminar overview ==<br /> This is a half-day course centered on how to use the systems that HPC2N is providing, and is a good starting point for people that are unfamiliar with how computer clusters work.<br /> <br /> The course will be divided into 2 parts finishing with a short hands-on session. The first part of the course will cover basic Linux commands and tools, while the second part will focus on the Abisko supercomputer (applying for HPC2N resources and acquire accounts, how to login to Abisko, how to run software, etc.).<br /> <br /> == Trainer ==<br /> The course is delivered by HPC2N Staff<br /> <br /> == Seminar web page and registration ==<br /> <br /> https://www.hpc2n.umu.se/intro-linux-abisko-2015</div>

Mikael Rännar (HPC2N) http://docs.snic.se/w/index.php?title=Introduction_to_Linux_and_Abisko_(HPC2N,_April_22)&diff=6073 2015-04-08T13:55:06Z

<p>Mikael Rännar (HPC2N): Created page with &quot;{{training event info |description=Introduction to Linux and Abisko |fields=Scientific computing |event type=Course |location=Stockholm |start date=2015-04-22 |end date=2015-04-2...&quot;</p> <hr /> <div>{{training event info<br /> |description=Introduction to Linux and Abisko<br /> |fields=Scientific computing<br /> |event type=Course<br /> |location=Stockholm<br /> |start date=2015-04-22<br /> |end date=2015-04-22<br /> }}<br /> <br /> == Seminar Location ==<br /> MIT building, Umeå Universitet (Room to be announced later.)<br /> <br /> == Seminar overview ==<br /> This is a half-day course centered on how to use the systems that HPC2N is providing, and is a good starting point for people that are unfamiliar with how computer clusters work.<br /> <br /> The course will be divided into 2 parts finishing with a short hands-on session. The first part of the course will cover basic Linux commands and tools, while the second part will focus on the Abisko supercomputer (applying for HPC2N resources and acquire accounts, how to login to Abisko, how to run software, etc.).<br /> <br /> == Trainer ==<br /> The course is delivered by HPC2N Staff<br /> <br /> == Seminar web page and registration ==<br /> <br /> https://www.hpc2n.umu.se/intro-linux-abisko-2015</div>

Mikael Rännar (HPC2N) http://docs.snic.se/w/index.php?title=MATLAB_using_SNIC_clusters_(HPC2N_September_2014)&diff=5921 2014-09-19T11:36:07Z

<p>Mikael Rännar (HPC2N): Created page with &quot;{{training event info |description=Speeding up MATLAB Computations using SNIC Clusters |fields=Scientific computing |event type=Seminar |location=Umeå |start date=2014-09-30 |e...&quot;</p> <hr /> <div>{{training event info<br /> |description=Speeding up MATLAB Computations using SNIC Clusters <br /> |fields=Scientific computing<br /> |event type=Seminar<br /> |location=Umeå<br /> |start date=2014-09-30<br /> |end date=2014-09-30<br /> }}<br /> == Seminar overview ==<br /> Join us for this seminar to see how you can get access to the resources already available to you, and speed up your computations in [[MATLAB]] on your computer and on large clusters. The Swedish National Infrastructure for Computing (SNIC) allows researchers to apply for usage of MATLAB Distributed Computing Server (MDCS) on their clusters to speed up massive MATLAB computations at no cost. We will go through how to get access to these systems and how to write MATLAB code to run on them.<br /> <br /> == Trainer ==<br /> The seminar is delivered by Daniel Armyr, Application Engineer at MathWorks.<br /> <br /> == Seminar web page and registration ==<br /> For more information and registration refer to the <br /> [https://go2.mathworks.com/speeding-up-matlab-computations-using-snic-clusters-sem-se-51719 Mathworks webpage]</div>

Mikael Rännar (HPC2N) http://docs.snic.se/w/index.php?title=User:Mikael_R%C3%A4nnar_(HPC2N)&diff=2566 2011-09-21T12:30:25Z

<p>Mikael Rännar (HPC2N): </p> <hr /> <div>{{application expert info<br /> |first name=Mikael<br /> |last name=Rännar<br /> |centre=HPC2N<br /> |fields=Computational science<br /> |fte=50<br /> |financing=PRACE<br /> |general activities=PRACE activities<br /> |other activities=<br /> &lt;!--|image=name of an uploaded image file--&gt;<br /> |office=Room E447 MIT building;<br /> Dept. of Computing Science;<br /> Umeå University;<br /> SE-90187 UMEÅ<br /> &lt;!--<br /> |phone=Semicolon separated phone numbers (with optional <br /> explanation), newlines are ignored<br /> --&gt;<br /> }}<br /> &lt;!--<br /> == Quick facts ==<br /> * Or any other heading. <br /> * This part is clear text and very much up to you.<br /> * Bullet lists are good <br /> * for the lazy<br /> <br /> == Expertise ==<br /> * [[expertise::Python]]<br /> * [[expertise::mass spectrometry]]<br /> * [[expertise::flux capacitor calibration]]<br /> --&gt;</div>

Mikael Rännar (HPC2N) http://docs.snic.se/w/index.php?title=User:Mikael_R%C3%A4nnar_(HPC2N)&diff=2565 2011-09-21T12:24:39Z

<p>Mikael Rännar (HPC2N): </p> <hr /> <div>{{application expert info<br /> |first name=Mikael<br /> |last name=Rännar<br /> |centre=HPC2N<br /> |fields=Computational science<br /> |fte=50<br /> |financing=PRACE<br /> |general activities=PRACE activities<br /> |other activities=<br /> &lt;!--|image=name of an uploaded image file--&gt;<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 /> &lt;!--<br /> == Quick facts ==<br /> * Or any other heading. <br /> * This part is clear text and very much up to you.<br /> * Bullet lists are good <br /> * for the lazy<br /> <br /> == Expertise ==<br /> * [[expertise::Python]]<br /> * [[expertise::mass spectrometry]]<br /> * [[expertise::flux capacitor calibration]]<br /> --&gt;</div>

Mikael Rännar (HPC2N) http://docs.snic.se/w/index.php?title=Main_Page&diff=437 2011-05-03T14:38:58Z

<p>Mikael Rännar (HPC2N): </p> <hr /> <div>{| cellspacing=&quot;10&quot; <br /> |- valign=&quot;bottom&quot;<br /> |&lt;big&gt;'''Welcome to the SNIC knowledge base and documentations site.'''&lt;/big&gt;<br /> |[[image:SNIClogo_half.png|link=http://www.snic.vr.se]]<br /> |}<br /> <br /> &lt;blockquote style=&quot;background-color: lightgrey; border: solid thin grey; padding: 15px 15px 15px 15px;&quot;&gt;<br /> '''NOTE: This site is under constant development and is still in the very early days of it's existence!'''<br /> &lt;/blockquote&gt;<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 /> &lt;u&gt;We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address:&lt;/u&gt;&lt;br&gt;<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 /> &lt;u&gt;Discussion pages:&lt;/u&gt;&lt;br&gt;<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]], Molecular Dynamics<br /> *[[Application_Experts#Lilit Axner, PDC/KTH|Lilit Axner, PDC/KTH]], Computational Fluid Dynamics<br /> *[[Application_Experts#Chandan Basu, NSC|Chandan Basu, NSC]], Computational Science<br /> *[http://dhcp-221-37.pdc.kth.se/drupal/node/21 Mattias Chevalier, PDC], Computational Fluid Dynamics<br /> *[[Application_Experts#Martin Dahlö, UPPMAX|Martin Dahlö, UPPMAX]]<br /> *[http://dhcp-221-37.pdc.kth.se/drupal/node/23 Michael Djurfeldt, PDC]<br /> *Jerry Eriksson, HPC2N<br /> *Torgny Faxén, NSC<br /> *[[Application_Experts#Anders Hast, UPPMAX|Anders Hast, UPPMAX]], Scientific Visualization<br /> *[[Application_Experts#Joel Hedlund, NSC|Joel Hedlund, NSC]], Bioinformatics<br /> *[[Application_Experts#Joachim Hein, Lunarc|Joachim Hein, Lunarc]], Parallel Programming, Performance Analysis<br /> *[[Application_Experts#Hans Karlsson, UPPMAX|Hans Karlsson, UPPMAX]], Computational Quantum Mechanics<br /> *Jonas Lindemann, Lunarc, Grid Computing, SGUSI<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 /> *[[Application_Experts#Elias Rudberg, UPPMAX|Elias Rudberg, UPPMAX]], Code and Algorithm Development<br /> *Mikael Rännar, HPC2N, Computing Science<br /> *Åke Sandgren, HPC2N<br /> *[[Application_Experts#Biplab Sanyal, UPPMAX|Biplab Sanyal, UPPMAX]], Theoretical Material Physics<br /> *[[Application_Experts#Mattias Slabanja, C3SE|Mattias Slabanja, C3SE]], Computational Materials Science<br /> *[[Application_Experts#Ola Spjuth, UPPMAX|Ola Spjuth, UPPMAX]], Bioinformatics<br /> *[[Application_Experts#Daniel Spångberg, UPPMAX|Daniel Spångberg, UPPMAX]], Molecular Dynamics<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 /> For an index over the pages related to Computational Chemistry, please visit the [[:Category:Computational_Chemistry|category page]].<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 /> For an index over the pages related to Fluid simulations, please visit the [[:Category:Computational_Fluid_Dynamics|category page]]. <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>

Mikael Rännar (HPC2N)