SNIC Documentation - User contributions [en]

User:Daniel Spångberg (UPPMAX)

2013-09-10T08:43:23Z

Daniel Spångberg (UPPMAX):

{{application expert info
|first name=Daniel
|last name=Spångberg
|centre=UPPMAX
|fields=SNAC-WG
|fte=25

|general activities=Helps user with choice, installation, use, and writing of molecular simulation packages.

|image=daniels.jpg


}}

== Quick facts ==
* Work at UPPMAX since 2004
* Ph.D. in 2003
* User of [[Gaussian]], [[GAMESS]], [[Turbomole]], [[CRYSTAL]], [[VASP]], [[CPMD]]

== Expertise ==
* [[expertise::Gaussian]], [[expertise::GAMESS]]

GAMESS

2012-02-08T15:58:00Z

Daniel Spångberg (UPPMAX):

{{software info
|description=ab initio quantum chemistry
|license=free
|fields=Computational materials science; Computational chemistry
}}
[http://www.msg.ameslab.gov/gamess/ {{PAGENAME}}] a general ab initio quantum chemistry package, also known as GAMESS (US).
== Availability ==
{{list resources for software}}

== License ==
{{show license}}

The software is freely available but users should cite the [http://www.msg.ameslab.gov/gamess/references.html following references] in any publications using the code.

== Experts ==
{{list experts}}

== Links ==
* [http://www.pdc.kth.se/resources/software/installed-software/applications/gamess-us Instructions for using GAMESS at PDC]
* [http://www.uppmax.uu.se/support/user-guides/gamess-us Instructions for using GAMESS at UPPMAX]

Kalkyl

2012-02-08T15:56:32Z

Daniel Spångberg (UPPMAX):

{{resource info
|description=cluster resource of about 21 TFLOPS
|centre=UPPMAX
|software=Gaussian,GAMESS,ABySS,ab_wtp,ANFO,ANNOVAR,BclConverter,BEDTools,BioPerl,BioPython,bioscope,BLAST,BLAT,Bowtie,BWA,CASAVA,Concaterpillar,Cufflinks,EMBOSS,EMMAX,FastQC,FASTX,FreeBayes,GARLI,GATK,GCTA,GenomeTools,HMMER,Maq,matrix2png,MIRA,MOSAIK,mpiblast,MrBayes,MUMmer,Picard,RAxML,Ray,SAMtools,SOAPdenovo,SolexaQA,SplitSeek,Staden,Tophat,UNAFold,Velvet
}}

== Available software ==
{{list software at resource}}

== Links ==
* [http://www.uppmax.uu.se/systems/kalkyl Description of Kalkyl at UPPMAX web page]

User:Daniel Spångberg (UPPMAX)

2012-02-08T15:54:21Z

Daniel Spångberg (UPPMAX):

{{application expert info
|first name=Daniel
|last name=Spångberg
|centre=UPPMAX
|fields=Molecular dynamics
|fte=50

|general activities=Helps user with choice, installation, use, and writing of molecular simulation packages.

|image=daniels.jpg


}}

== Quick facts ==
* Work at UPPMAX since 2004
* Handle support, primarily of molecular dynamics simulations
* Develop software, mainly related to molecular simulations
* Ph.D. in 2003
* User of [[Gaussian]], [[GAMESS]], [[Turbomole]], [[CRYSTAL]], [[VASP]], [[CPMD]]

== Expertise ==
* [[expertise::Gaussian]], [[expertise::GAMESS]]

User:Daniel Spångberg (UPPMAX)

2012-02-08T15:43:31Z

Daniel Spångberg (UPPMAX):

Main Page

2011-04-07T15:24:42Z

Daniel Spångberg (UPPMAX):

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

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

The aim of this site is that you should be able to get information, help, tips-and-tricks, etc. regarding the most widely used computational tools and scientific applications.

We also have an [mailto:application-support@nsc.liu.se application-support] e-mail address: 
This mail address can be used if you have support questions that are not directly regarding how to run a given application on a specific SNIC HPC resource, but regarding how to use the application itself or how to solve an issue with the application that is not specific to running it on a certain resource.

The application-support queue is monitored by all the application experts, who are distributed over all the six SNIC HPC centers, so there is a good chance that someone who knows the given application will see the support request and help answer your questions or solve your issue.

If you don’t know whether or not to use the application-support address for your support request, then just send your request to the support address at the HPC center where you run your jobs. Then someone monitoring that support queue will in turn move your support request to the application-support queue if they find that your request is better handled there.

Discussion pages: 
All pages in the knowledge base have parallel discussion pages (follow the link Discussion in the top of each page) where anyone interested can discuss the original page; add comments, suggestions, their own tips, new links etc. All you need to do to be able to edit a discussion page is to create an account for this wiki ([[Special:UserLogin|Log in / create account]]). Creating an account only requires that you register a working e-mail address. Once you have an account, you can log in by following the link in the top right-hand corner of any page.

We strongly encourage all users to add comments etc. to the discussion pages, so we can improve the knowledge base and keep the provided information as fresh as possible.

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

=[[System Experts]]=

=Scientific Topics=

==Computational Chemistry==

===Prominent Software===
*Quantum Chemistry
*#[[Gaussian]]
*#[[NWChem]]
*#[[Dalton]] - Dalton is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory.

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

*Monte Carlo Thermodynamics
*QSAR

==Computational Physics==

===Prominent Software===

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

====Astrophysics====

====Fluid simulations====
* [[Edge]] - Edge is an unstructured CFD solver developed at the Swedish Defence Research Agency.
* [[Fluent]]
* [[OpenFOAM]]
* [[Simson]] - Simson is a software package that implements an efficient spectral integration technique to solve the Navier-Stokes equations for incompressible channel and boundary layer flows.

== Bioinformatics ==
Bioinformatics is the science of handling information in biology. See also the Bioinformatics [[:Category:Bioinformatics|category page]].
=== Prominent software ===
* Sequence analysis
** [[BLAST]], [[FASTA]] - sequence similarity search and pairwise local alignment.
** [[HMMER]] - pattern recognition for protein families or domains.
** [[Multiple sequence alignment]] - simultaneous alignment of multiple biological sequences.
* Computational evolutionary biology
** [[PHYLIP]] - Phylogeny.
** [[MrBayes]] - MCMC prediction of phylogenetic trees.
* Molecular Modeling
** [[GROMACS]] - molecular dynamics, Newtonian simulation of motion.
* Neurobiology
** [[MUSIC]] - C++ library implementing an API which allows large scale neuronal network simulators to exchange data during runtime.

==Meteorology and Climatology==

*ECEARTH
*RCA
*RCO
*NEMO

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

==Software Development==
*Compilers and Libraries
*#Intel, PGI, GNU Compilers
*#MPI
*#BLAS
*#MKL
*Profiling and Debugging
*#TotalView
*#Vampir
*#Valgrind
*#Intel trace analyzer

=Grid information (SweGrid/Swestore)=

==[[SweGrid User's Guide]]==

==[[Swestore]]==

==[[SGUSI]]==

=Using This Wiki=
Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. For formatting and mediawiki markup details see [http://www.mediawiki.org/wiki/Help:Formatting Formatting]. For adding links see [http://www.mediawiki.org/wiki/Help:Links Links]. Also have a look at the [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ].

Please do '''not''' upload or otherwise publish copyrighted material on this wiki.

File:Daniels.jpg

2011-04-07T15:22:47Z

Daniel Spångberg (UPPMAX):

Application Experts

2011-04-07T15:21:36Z

Daniel Spångberg (UPPMAX):

===Torben Rasmussen, NSC===
{|
|- valign="top"
|
[[image:Torben_small.jpg|frame|left|Torben Rasmussen]]
|
*Application expert in computational chemistry
*Work at NSC since 2008
*Handle user relations, general support, software installations, etc.
*Ph.D. in 2001
*Five years of postdoctoral experience in the field covering applications within organic chemistry, biochemistry, and life science
*Have used [[Gaussian]] and Jaguar extensively
*Experience with parametrization of molecular mechanics force fields
|}

===Chandan Basu, NSC===
{|
|- valign="top"
|
[[image:chandan.jpg|frame|left|Chandan Basu]]
|
*Ph.D in computational Physics
*Working at NSC since 2009
*Working on benchmarking, optimization, scaling issues
*Working on EU projects, e.g., IS-ENES, PRACE and also with SMHI
|}

===Johan Raber, NSC===
{|
|- valign="top"
|
[[image:JohanR.png|frame|left|Johan Raber]]
|
*E-science coordinator
*Work at NSC for two years as a Systems Expert
*Handle user relations, general support etc.
*PhD in Biophysics in 2007 at Uppsala University
*MSc in Molecular Biotechnology Engineering
*Long experience using Gaussian
*Experience using GROMACS and Gaussian for QM/MD simulations
|}

===Joel Hedlund, NSC===
{|
|- valign="top"
|
[[image:Joel_small.jpg|frame|left|Joel Hedlund]]
|
*Application expert in bioinformatics.
*Work at NSC since 2011.
*Ph.D. in 2010.
*Main scientific work in the field of sequence analysis and bioinformatic protein family characterisation.
*Have used [[HMMER]], [[BLAST]] and [[MSA]] extensively.
|}

===Jonathan Vincent, PDC===
{|
|- valign="top"
|
[[image:|frame|left|Jonathan Vincent]]
|
*Application expert
*Work at PDC since 2009
*Handle advanced user support, software installations, etc.
*Ph.D. 2000 in Semiconductor Physics, Postdoctoral experience in semiconductor physics and classical and quantum dynamics
*Working on Benchmarking, code optimisation
*Keywords : Cray XT6, Cray XE6, MPI, Benchmarking, Optimisation
|}

===Rossen Apostolov, PDC===
{|
|- valign="top"
|
[[image:Rossen.jpg|frame|left|Rossen Apostolov]]
|
*Application expert in Molecular Dynamics simulations
*Working at PDC since 2010
*Ph.D. 2008 in Computational Biophysics
*Working on [[GROMACS|Gromacs]] development
*Keywords : Molecular Dynamics, Gromacs, GPGPU computing
|}

===Lilit Axner, PDC/KTH===
{|
|- valign="top"
|
[[image:lilit.jpg|frame|left|Lilit Axner]]
|
*Application expert in Computational Fluid Dynamics as well as Project manager for EU projects
*Works at PDC since 2010
*Ph.D. in Computer Science (2007)
*Previously worked at Dutch National Supercomputer Center (SARA)
*Experience in Lattice Boltzmann method, domain decomposition, load balancing, performance benchmarking, parallelization, mesh generation.
*Managing the following projects [http://www.prace-ri.eu/ Prace], [http://www.deisa.eu/ Deisa], [http://www.scalalife.eu/ ScalaLife]
**Assisting applicants of these projects
|}

===Daniel Spångberg, UPPMAX===
{|
|- valign="top"
|
[[image:daniels.jpg|frame|left|Daniel Spångberg]]
|
*Application expert in molecular dynamics
*Works at UPPMAX since 2004
*Handles support, primarily of molecular dynamics simulations
*Develops software, mainly related to molecular simulations
*Ph.D. in 2003
*User of [[Gaussian]], [[GAMESS]], [[Turbomole]], [[CRYSTAL]], [[VASP]], [[CPMD]]
|}