https://snicdocs.nsc.liu.se/w/api.php?action=feedcontributions&user=Johan+Raber+%28NSC%29&feedformat=atomSNIC Documentation - User contributions [en]2024-03-29T02:18:27ZUser contributionsMediaWiki 1.31.10https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=7467User:Johan Raber (NSC)2020-04-01T11:34:09Z<p>Johan Raber (NSC): /* Projects */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=50<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as an Application Expert at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Maintain large portions of the Computational Chemistry software stack at NSC<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::NWChem]]<br />
* [[expertise::Gnuplot]]<br />
* [[expertise::R]]<br />
* [[expertise::CP2K]]<br />
* [[expertise::GROMACS]]<br />
<br />
== Projects ==<br />
<!--<br />
* [[project::NSC GPU and Accelerator Pilot]]<br />
* [[project::PRACE WP12: Network topology analysis and efficient collective design]]<br />
* [[project::Parallelization of a materials science code]]<br />
--></div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=7466User:Johan Raber (NSC)2020-04-01T11:28:40Z<p>Johan Raber (NSC): /* Expertise */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=50<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as an Application Expert at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Maintain large portions of the Computational Chemistry software stack at NSC<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::NWChem]]<br />
* [[expertise::Gnuplot]]<br />
* [[expertise::R]]<br />
* [[expertise::CP2K]]<br />
* [[expertise::GROMACS]]<br />
<br />
== Projects ==<br />
* [[project::NSC GPU and Accelerator Pilot]]<br />
* [[project::PRACE WP12: Network topology analysis and efficient collective design]]<br />
* [[project::Parallelization of a materials science code]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=7465User:Johan Raber (NSC)2020-04-01T11:27:48Z<p>Johan Raber (NSC): /* Quick facts */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=50<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as an Application Expert at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Maintain large portions of the Computational Chemistry software stack at NSC<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::NWChem]]<br />
* [[expertise::Gnuplot]]<br />
* [[expertise::R]]<br />
<br />
== Projects ==<br />
* [[project::NSC GPU and Accelerator Pilot]]<br />
* [[project::PRACE WP12: Network topology analysis and efficient collective design]]<br />
* [[project::Parallelization of a materials science code]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=5286User:Johan Raber (NSC)2013-09-06T10:20:04Z<p>Johan Raber (NSC): /* Expertise */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=50<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as the e-science coordinator at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Experience using [[GROMACS]] and [[Gaussian]] for QM/MD simulations<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::NWChem]]<br />
* [[expertise::Gnuplot]]<br />
* [[expertise::R]]<br />
<br />
== Projects ==<br />
* [[project::NSC GPU and Accelerator Pilot]]<br />
* [[project::PRACE WP12: Network topology analysis and efficient collective design]]<br />
* [[project::Parallelization of a materials science code]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=5285User:Johan Raber (NSC)2013-09-06T10:19:16Z<p>Johan Raber (NSC): /* Expertise */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=50<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as the e-science coordinator at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Experience using [[GROMACS]] and [[Gaussian]] for QM/MD simulations<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::Gnuplot]]<br />
* [[expertise::R]]<br />
<br />
== Projects ==<br />
* [[project::NSC GPU and Accelerator Pilot]]<br />
* [[project::PRACE WP12: Network topology analysis and efficient collective design]]<br />
* [[project::Parallelization of a materials science code]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Xds&diff=5229Xds2013-06-04T07:13:19Z<p>Johan Raber (NSC): Created page with "{{software info |description=X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. |license=free |fields=Structura..."</p>
<hr />
<div>{{software info<br />
|description=X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method.<br />
|license=free<br />
|fields=Structural biology<br />
}}<br />
[http://xds.mpimf-heidelberg.mpg.de/ {{PAGENAME}}] {{#show: {{PAGENAME}} |?description}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://xds.mpimf-heidelberg.mpg.de/ Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Shelx&diff=5228Shelx2013-06-04T07:10:28Z<p>Johan Raber (NSC): Created page with "{{software info |description=is a set of programs for the determination of small (SM) and macromolecular (MM) crystal structures by single crystal X-ray and neutron diffraction. ..."</p>
<hr />
<div>{{software info<br />
|description=is a set of programs for the determination of small (SM) and macromolecular (MM) crystal structures by single crystal X-ray and neutron diffraction.<br />
|license=free<br />
|fields=Structural biology<br />
}}<br />
[http://shelx.uni-ac.gwdg.de/SHELX/ {{PAGENAME}}] {{#show: {{PAGENAME}} |?description}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://pingu.com Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Shake_n_bake&diff=5227Shake n bake2013-06-04T07:08:06Z<p>Johan Raber (NSC): Created page with "{{software info |description=is a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data. ..."</p>
<hr />
<div>{{software info<br />
|description=is a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data.<br />
|license=free<br />
|fields=Structural biology<br />
}}<br />
[http://www.hwi.buffalo.edu/SnB/ {{PAGENAME}}] {{#show: {{PAGENAME}} |?description}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.hwi.buffalo.edu/SnB/ Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Coot&diff=5226Coot2013-06-04T07:03:03Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{software info<br />
|description=software for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data<br />
|license=free<br />
|fields=Structural biology; Visualisation<br />
}}<br />
[http://lmb.bioch.ox.ac.uk/coot/ {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://lmb.bioch.ox.ac.uk/coot/ Offical website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Pymol&diff=5225Pymol2013-06-04T07:01:51Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{software info<br />
|description=is a molecular visualization system.<br />
|license=free<br />
|fields=Structural biology;Visualisation;Computational chemistry<br />
}}<br />
[http://pymol.org {{PAGENAME}}] {{#show: {{PAGENAME}} |?description}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://pymol.org Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Pymol&diff=5224Pymol2013-06-04T07:01:08Z<p>Johan Raber (NSC): Created page with "{{software info |description=is a molecular visualization system. |license=free |fields=Structural biology, Visualisation, Computational chemistry }} [http://pymol.org {{PAGENAME..."</p>
<hr />
<div>{{software info<br />
|description=is a molecular visualization system.<br />
|license=free<br />
|fields=Structural biology, Visualisation, Computational chemistry<br />
}}<br />
[http://pymol.org {{PAGENAME}}] {{#show: {{PAGENAME}} |?description}}<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://pymol.org Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Phenix&diff=5223Phenix2013-06-04T06:56:20Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{software info<br />
|description=is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods<br />
|license=free<br />
|fields=Structural biology<br />
}}<br />
[http://www.phenix-online.org {{PAGENAME}}] (Python-based Hierarchical<br />
ENvironment for Integrated Xtallography) {{#show:<br />
{{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.phenix-online.org/ Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Phenix&diff=5222Phenix2013-06-04T06:55:57Z<p>Johan Raber (NSC): Created page with "{{software info |description=is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods |license=free |fields=..."</p>
<hr />
<div>{{software info<br />
|description=is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods<br />
|license=free<br />
|fields=Structural biology<br />
}}<br />
[http://www.phenix-online.org {{PAGENAME}}] (Python-based Hierarchical<br />
ENvironment for Integrated Xtallography) is a software package for {{#show:<br />
{{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.phenix-online.org/ Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Hkl2map&diff=5221Hkl2map2013-06-04T06:51:20Z<p>Johan Raber (NSC): Created page with "{{software info |description=is a graphical user-interface for macromolecular phasing |license=free |fields=Structural biology }} [http://example.com {{PAGENAME}}] {{#show: {{PAG..."</p>
<hr />
<div>{{software info<br />
|description=is a graphical user-interface for macromolecular phasing<br />
|license=free<br />
|fields=Structural biology<br />
}}<br />
[http://example.com {{PAGENAME}}] {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://webapps.embl-hamburg.de/hkl2map/ Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Ccp4&diff=5220Ccp42013-06-04T06:45:27Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{software info<br />
|description=determining macromolecular structures by X-ray<br />
crystallography<br />
|license=free<br />
|fields=Structural biology;Visualisation<br />
}}<br />
[http://www.ccp4.ac.uk {{PAGENAME}}] (Collaborative Computational Project No. 4) is a software package for {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.ccp4.ac.uk/ Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Ccp4&diff=5219Ccp42013-06-04T06:44:36Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{software info<br />
|description=software for determining macromolecular structures by X-ray<br />
crystallography<br />
|license=free<br />
|fields=Structural biology;Visualisation<br />
}}<br />
[http://www.ccp4.ac.uk {{PAGENAME}}] (Collaborative Computational Project No. 4) is a software package for {{#show: {{PAGENAME}} |?description}}, which is motivated by this dependent clause.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.ccp4.ac.uk/ Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Ccp4&diff=5218Ccp42013-06-04T06:43:44Z<p>Johan Raber (NSC): Created page with "{{software info |description=software for determining macromolecular structures by X-ray crystallography |license=free |fields=Structural biology;Visualisation }} [http://www.ccp..."</p>
<hr />
<div>{{software info<br />
|description=software for determining macromolecular structures by X-ray<br />
crystallography<br />
|license=free<br />
|fields=Structural biology;Visualisation<br />
}}<br />
[http://www.ccp4.ac.uk {{PAGENAME}}] (abbreviation explained) is a software package for {{#show: {{PAGENAME}} |?description}}, which is motivated by this dependent clause.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://www.ccp4.ac.uk/ Official website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Triolith&diff=5217Triolith2013-06-04T06:31:42Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{resource info<br />
|description=Capability cluster with 338 TFLOPS peak and 1:2 Infiniband fat-tree<br />
|production=yes<br />
|commissioning date=July 2012<br />
|decommissioning date=July 2016<br />
|resource type=compute<br />
|centre=NSC<br />
|software=ansys,ARC<br />
client,Blast,clustalw,comsol,CPMD,CP2K,Coot,EMTO,EMTOx,exciting-code,<br />
elk,Fluent,gaussian,gnuplot,grace,gromacs,hmmer,Inspector,Intel compiler<br />
suite,Intel<br />
MPI,lammps,mathematica,matlab,mkl,molden,openmpi,p4vasp,povray,R,rosetta,ruby,sam,schrodinger,siesta,swig,totalview,Trace<br />
analyzer and collector,vasp,vmd,VTune Amplifier,WIEN2k,Yambo,Shake n bake,<br />
ccp4, amber, cdo,cif2cell, cmake, code_saturne, dl_poly, fasta, ferret,<br />
gamess-us, gaussview, gcc, graphviz, grib_api, gribex, hdf5, hkl2map, namd,<br />
ncl, nco, ncview, netcdf, nwchem, octopus, openbabel, orca, phenix, phonopy,<br />
pymol, qdalton, scalasca, shelx, tau, trilinos, vesta,<br />
xcrysden, xds, yambo<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
More information about available software on Triolith will be published soon.<br />
<br />
== Links ==<br />
* [http://www.nsc.liu.se/systems/triolith/ Triolith User Guide at NSC]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Triolith&diff=5215Triolith2013-06-04T06:29:03Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{resource info<br />
|description=Capability cluster with 338 TFLOPS peak and 1:2 Infiniband fat-tree<br />
|production=yes<br />
|commissioning date=July 2012<br />
|decommissioning date=July 2016<br />
|resource type=compute<br />
|centre=NSC<br />
|software=ansys,ARC<br />
client,Blast,clustalw,comsol,CPMD,CP2K,Coot,EMTO,EMTOx,exciting-code,<br />
elk,Fluent,gaussian,gnuplot,grace,gromacs,hmmer,Inspector,Intel compiler<br />
suite,Intel<br />
MPI,lammps,mathematica,matlab,mkl,molden,openmpi,p4vasp,povray,R,rosetta,ruby,sam,schrodinger,siesta,swig,totalview,Trace<br />
analyzer and collector,vasp,vmd,VTune Amplifier,WIEN2k,Yambo,Shake n bake,<br />
ccp4, amber, cdo,cif2cell, cmake, code_saturne, dl_poly, fasta, ferret,<br />
gamess-us, gaussview, gcc, graphviz, grib_api, gribex, hdf5, hkl2map, namd,<br />
ncl, nco, ncview, netcdf, nwchem, octopus, openbabel, orca, phenix, phonopy,<br />
pymol, qdalton, scalasca, Schrödinger suite, shelx, tau, trilinos, vesta,<br />
xcrysden, xds, yambo<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
More information about available software on Triolith will be published soon.<br />
<br />
== Links ==<br />
* [http://www.nsc.liu.se/systems/triolith/ Triolith User Guide at NSC]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Matter&diff=5209Matter2013-06-03T12:53:07Z<p>Johan Raber (NSC): /* Available software */</p>
<hr />
<div>{{resource info<br />
|description=cluster resource of 37 TFLOPS dedicated to materials science<br />
|resource type=compute<br />
|centre=NSC<br />
|production=yes<br />
|commissioning date=October 2010<br />
|decommissioning date=<br />
|software=ansys,ARC client,Blast,clustalw,comsol,cpmd,CS-Rosetta,dalton,edge,EMTO,EMTOx,exciting-code, Elk,Fluent,gaussian,gnuplot,grace,Greens,gromacs,hmmer,Inspector,Intel compiler suite,Intel MPI,lammps,mafft,mathematica,matlab,mkl,molden,muscle,mvapich2,NMRPipe,octave,openmpi,p4vasp,paraview,pgi,povray,R,rosetta,ruby,sam,schrodinger,siesta,swig,totalview,Trace analyzer and collector,vasp,vmd,VTune Amplifier,WIEN2k,Yambo<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.nsc.liu.se/systems/snic/ NSC SNIC resource user guide]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Kappa&diff=5208Kappa2013-06-03T12:52:41Z<p>Johan Raber (NSC): /* Available software */</p>
<hr />
<div>{{resource info<br />
|description=throughput cluster resource of 26 TFLOPS<br />
|resource type=compute<br />
|centre=NSC<br />
|production=yes<br />
|commissioning date=April 2010<br />
|decommissioning date=June 2013<br />
|software=ansys,ARC client,Blast,clustalw,comsol,CPMD,CS-Rosetta,dalton,edge,EMTO,EMTOx,exciting-code, elk,Fluent,gaussian,gnuplot,grace,Greens,gromacs,hmmer,Inspector,Intel compiler suite,Intel MPI,lammps,mafft,mathematica,matlab,mkl,molden,muscle,mvapich2,NMRPipe,octave,openmpi,p4vasp,paraview,pgi,povray,R,rosetta,ruby,sam,schrodinger,siesta,swig,totalview,Trace analyzer and collector,vasp,vmd,VTune Amplifier,WIEN2k,Yambo<br />
}}<br />
{{set list|software||sep=,|quiet=true}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
== Links ==<br />
* [http://www.nsc.liu.se/systems/snic/ NSC user guide for SNIC resources]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Triolith&diff=5207Triolith2013-06-03T12:51:49Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{resource info<br />
|description=Capability cluster with 338 TFLOPS peak and 1:2 Infiniband fat-tree<br />
|production=yes<br />
|commissioning date=July 2012<br />
|decommissioning date=July 2016<br />
|resource type=compute<br />
|centre=NSC<br />
|software=ansys,ARC client,Blast,clustalw,comsol,CPMD,CP2K,Coot,EMTO,EMTOx,exciting-code, elk,Fluent,gaussian,gnuplot,grace,gromacs,hmmer,Inspector,Intel compiler suite,Intel MPI,lammps,mathematica,matlab,mkl,molden,openmpi,p4vasp,povray,R,rosetta,ruby,sam,schrodinger,siesta,swig,totalview,Trace analyzer and collector,vasp,vmd,VTune Amplifier,WIEN2k,Yambo<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
More information about available software on Triolith will be published soon.<br />
<br />
== Links ==<br />
* [http://www.nsc.liu.se/systems/triolith/ Triolith User Guide at NSC]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Triolith&diff=5206Triolith2013-06-03T12:51:18Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{resource info<br />
|description=Capability cluster with 338 TFLOPS peak and 1:2 Infiniband fat-tree<br />
|production=yes<br />
|commissioning date=July 2012<br />
|decommissioning date=July 2016<br />
|resource type=compute<br />
|centre=NSC<br />
|software=ansys,ARC client,Blast,clustalw,comsol,CPMD,CP2K,EMTO,EMTOx,exciting-code, elk,Fluent,gaussian,gnuplot,grace,gromacs,hmmer,Inspector,Intel compiler suite,Intel MPI,lammps,mathematica,matlab,mkl,molden,openmpi,p4vasp,povray,R,rosetta,ruby,sam,schrodinger,siesta,swig,totalview,Trace analyzer and collector,vasp,vmd,VTune Amplifier,WIEN2k,Yambo<br />
}}<br />
<br />
== Available software ==<br />
{{list software at resource}}<br />
<br />
More information about available software on Triolith will be published soon.<br />
<br />
== Links ==<br />
* [http://www.nsc.liu.se/systems/triolith/ Triolith User Guide at NSC]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Coot&diff=5205Coot2013-06-03T12:46:00Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{software info<br />
|description=software for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data<br />
|license=free<br />
|fields=Structural biology<br />
}}<br />
[http://lmb.bioch.ox.ac.uk/coot/ {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://lmb.bioch.ox.ac.uk/coot/ Offical website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Coot&diff=5204Coot2013-06-03T12:45:40Z<p>Johan Raber (NSC): Created page with "{{software info |description=software for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data |license=fr..."</p>
<hr />
<div>{{software info<br />
|description=software for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data<br />
|license=free<br />
|fields=Structural biology<br />
}}<br />
[http://lmb.bioch.ox.ac.uk/coot/ {{PAGENAME}}] is a {{#show: {{PAGENAME}} |?description}}.<br />
<br />
== Availability ==<br />
{{list resources for software}}<br />
<br />
== Tips and tricks ==<br />
Describe general tips and tricks for using the software here, eg. compilation trickery, general workflow design to get better performance... <br />
<br />
== License ==<br />
{{show license}}<br />
<br />
== Experts ==<br />
{{list experts}}<br />
<br />
== Links ==<br />
* [http://lmb.bioch.ox.ac.uk/coot/ Offical website]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=4899User:Johan Raber (NSC)2013-04-19T06:45:44Z<p>Johan Raber (NSC): /* Expertise */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=50<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as the e-science coordinator at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Experience using [[GROMACS]] and [[Gaussian]] for QM/MD simulations<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::Gnuplot]]<br />
<br />
<!-- == Projects == --><br />
{{#set:project=[[NSC_GPU_and_Accelerator_Pilot]]}}</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=4898User:Johan Raber (NSC)2013-04-19T06:45:14Z<p>Johan Raber (NSC): </p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=50<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as the e-science coordinator at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Experience using [[GROMACS]] and [[Gaussian]] for QM/MD simulations<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::Gnuplot]]<br />
* [[expertise::POV-Ray]]<br />
<br />
<!-- == Projects == --><br />
{{#set:project=[[NSC_GPU_and_Accelerator_Pilot]]}}</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=3289User:Johan Raber (NSC)2012-01-25T10:57:10Z<p>Johan Raber (NSC): /* Expertise */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=25<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as the e-science coordinator at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Experience using [[GROMACS]] and [[Gaussian]] for QM/MD simulations<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::Gnuplot]]<br />
* [[expertise::POV-Ray]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=3288User:Johan Raber (NSC)2012-01-25T10:56:20Z<p>Johan Raber (NSC): /* Expertise */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=25<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as the e-science coordinator at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Experience using [[GROMACS]] and [[Gaussian]] for QM/MD simulations<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]<br />
* [[expertise::Gnuplot]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=User:Johan_Raber_(NSC)&diff=3287User:Johan Raber (NSC)2012-01-25T10:55:02Z<p>Johan Raber (NSC): /* Quick facts */</p>
<hr />
<div>{{application expert info<br />
|first name=Johan<br />
|last name=Raber<br />
|centre=NSC<br />
|fields=Computational chemistry<br />
|fte=25<br />
|snic ae financing=25<br />
|other ae financing=<br />
|financing=SNIC<br />
<!--|general activities=Semicolon separated list of things you do as an application expert.; If you feel it is necessary.; Use minimal *but complete* sentences.--><br />
|other activities=E-science coordinator at NSC.<br />
|image=JohanR.png<br />
<!--|office=Semicolon separated lines; of visiting address; newlines<br />
are ignored; Provide this only if you want to.--><br />
<!--|phone=Semicolon separated phone numbers (with optional <br />
explanation); newlines are ignored; only add this if you want users to phone you constantly.--><br />
}}<br />
<br />
== Quick facts ==<br />
* Worked at NSC as a Systems Expert, 2008-2010<br />
* Since 2010 I work as the e-science coordinator at NSC <br />
* Handled user relations, general support etc. <br />
* Ph.D. in Biophysics in 2007 at Uppsala University<br />
** Research Topic: Quantum chemical studies of an anti-cancer drug<br />
** Tools: Gaussian, NWChem and GROMACS<br />
* M.Sc. in Molecular Biotechnology Engineering <br />
* Experience using [[GROMACS]] and [[Gaussian]] for QM/MD simulations<br />
<br />
== Expertise ==<br />
* [[expertise::Gaussian]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Gnuplot&diff=269Gnuplot2011-03-08T15:03:57Z<p>Johan Raber (NSC): Created page with "=Gnuplot="</p>
<hr />
<div>=Gnuplot=</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=268Main Page2011-03-08T15:03:34Z<p>Johan Raber (NSC): /* Visualization and post-processing */</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 />
*#[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 />
<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>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=243Main Page2011-03-03T12:37:54Z<p>Johan Raber (NSC): /* Fluid simulations */</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]], Computational Chemistry<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 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 />
** [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 />
==[[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>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=242Main Page2011-03-03T12:36:28Z<p>Johan Raber (NSC): /* 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]], Computational Chemistry<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 />
==[[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>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Application_Experts&diff=86Application Experts2010-12-02T09:00:10Z<p>Johan Raber (NSC): /* Johan raber, NSC */</p>
<hr />
<div>===Torben Rasmussen, NSC===<br />
{|<br />
|-<br />
|<br />
[[image:Torben_small.jpg|frame|left|Torben Rasmussen]]<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 />
|-<br />
|<br />
[[image:chandan.jpg|frame|left|Chandan Basu]]<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 />
|-<br />
|<br />
[[image:JohanR.png|frame|left|Johan Raber]]<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 />
|}</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Application_Experts&diff=85Application Experts2010-12-02T08:59:56Z<p>Johan Raber (NSC): /* Johan raber, NSC */</p>
<hr />
<div>===Torben Rasmussen, NSC===<br />
{|<br />
|-<br />
|<br />
[[image:Torben_small.jpg|frame|left|Torben Rasmussen]]<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 />
|-<br />
|<br />
[[image:chandan.jpg|frame|left|Chandan Basu]]<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 />
|-<br />
|<br />
[[image:JohanR.png|frame|left|Johan Raber]]<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 />
|}</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=File:JohanR.png&diff=84File:JohanR.png2010-12-02T08:59:28Z<p>Johan Raber (NSC): </p>
<hr />
<div></div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=FAQ&diff=52FAQ2010-11-26T12:15:46Z<p>Johan Raber (NSC): </p>
<hr />
<div>In this FAQ you will find an wide assortment of answers to questions commonly asked, either in this forum or in the RT system.<br />
<br />
=====Q: Why, Oh Why?=====<br />
A: Because</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Application_Experts&diff=51Application Experts2010-11-26T12:14:40Z<p>Johan Raber (NSC): Created page with 'Experts scmexperts'</p>
<hr />
<div>Experts scmexperts</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=50Main Page2010-11-26T11:54:28Z<p>Johan Raber (NSC): /* For testing purposes (will be REMOVED!) */</p>
<hr />
<div><big>'''Welcome to the SNIC Application Experts Wiki.'''</big><br />
<br />
The aim of this page is that you should be able to get the information you need by a single click. Completely unrealistic we know, but when you aim for the stars you may reach the tree tops. If you have any questions you might find them answered in the [[FAQ]].<br />
<br />
=[[Application Experts]]=<br />
*Torben Rasmussen, NSC<br />
*Johan Raber, NSC<br />
*Chandan Basu, NSC<br />
*<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
Computational Chemistry is the tool of choice when studying aspects of chemical and thermodynamical phenomena not easily studied by experimental means. Examples include ...<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 />
* Condensed Matter<br />
* Astrophysics<br />
<br />
==Bioinformatics==<br />
<br />
* Sequence analysis<br />
* Computational evolutionary biology<br />
* Docking<br />
* Molecular Modeling<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 Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<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.<br />
<br />
=For testing purposes (will be REMOVED!)=<br />
<br />
Upload [[media:test.pdf|test]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=49Main Page2010-11-26T11:53:26Z<p>Johan Raber (NSC): /* Using This Wiki */</p>
<hr />
<div><big>'''Welcome to the SNIC Application Experts Wiki.'''</big><br />
<br />
The aim of this page is that you should be able to get the information you need by a single click. Completely unrealistic we know, but when you aim for the stars you may reach the tree tops. If you have any questions you might find them answered in the [[FAQ]].<br />
<br />
=[[Application Experts]]=<br />
*Torben Rasmussen, NSC<br />
*Johan Raber, NSC<br />
*Chandan Basu, NSC<br />
*<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
Computational Chemistry is the tool of choice when studying aspects of chemical and thermodynamical phenomena not easily studied by experimental means. Examples include ...<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 />
* Condensed Matter<br />
* Astrophysics<br />
<br />
==Bioinformatics==<br />
<br />
* Sequence analysis<br />
* Computational evolutionary biology<br />
* Docking<br />
* Molecular Modeling<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 Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<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.<br />
<br />
=For testing purposes (will be REMOVED!)=<br />
<br />
[[media:test.pdf]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=48Main Page2010-11-26T11:52:55Z<p>Johan Raber (NSC): /* Using This Wiki */</p>
<hr />
<div><big>'''Welcome to the SNIC Application Experts Wiki.'''</big><br />
<br />
The aim of this page is that you should be able to get the information you need by a single click. Completely unrealistic we know, but when you aim for the stars you may reach the tree tops. If you have any questions you might find them answered in the [[FAQ]].<br />
<br />
=[[Application Experts]]=<br />
*Torben Rasmussen, NSC<br />
*Johan Raber, NSC<br />
*Chandan Basu, NSC<br />
*<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
Computational Chemistry is the tool of choice when studying aspects of chemical and thermodynamical phenomena not easily studied by experimental means. Examples include ...<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 />
* Condensed Matter<br />
* Astrophysics<br />
<br />
==Bioinformatics==<br />
<br />
* Sequence analysis<br />
* Computational evolutionary biology<br />
* Docking<br />
* Molecular Modeling<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 Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<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.<br />
<br />
=For testing purposes (will be REMOVED!)=<br />
<br />
[[media:test.pdf]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=47Main Page2010-11-26T11:52:40Z<p>Johan Raber (NSC): /* Using This Wiki */</p>
<hr />
<div><big>'''Welcome to the SNIC Application Experts Wiki.'''</big><br />
<br />
The aim of this page is that you should be able to get the information you need by a single click. Completely unrealistic we know, but when you aim for the stars you may reach the tree tops. If you have any questions you might find them answered in the [[FAQ]].<br />
<br />
=[[Application Experts]]=<br />
*Torben Rasmussen, NSC<br />
*Johan Raber, NSC<br />
*Chandan Basu, NSC<br />
*<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
Computational Chemistry is the tool of choice when studying aspects of chemical and thermodynamical phenomena not easily studied by experimental means. Examples include ...<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 />
* Condensed Matter<br />
* Astrophysics<br />
<br />
==Bioinformatics==<br />
<br />
* Sequence analysis<br />
* Computational evolutionary biology<br />
* Docking<br />
* Molecular Modeling<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 Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<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.<br />
<br />
=For testing purposes (will be REMOVED!)=<br />
<br />
[[media:test.pdf]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=46Main Page2010-11-26T11:52:23Z<p>Johan Raber (NSC): /* Using This Wiki */</p>
<hr />
<div><big>'''Welcome to the SNIC Application Experts Wiki.'''</big><br />
<br />
The aim of this page is that you should be able to get the information you need by a single click. Completely unrealistic we know, but when you aim for the stars you may reach the tree tops. If you have any questions you might find them answered in the [[FAQ]].<br />
<br />
=[[Application Experts]]=<br />
*Torben Rasmussen, NSC<br />
*Johan Raber, NSC<br />
*Chandan Basu, NSC<br />
*<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
Computational Chemistry is the tool of choice when studying aspects of chemical and thermodynamical phenomena not easily studied by experimental means. Examples include ...<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 />
* Condensed Matter<br />
* Astrophysics<br />
<br />
==Bioinformatics==<br />
<br />
* Sequence analysis<br />
* Computational evolutionary biology<br />
* Docking<br />
* Molecular Modeling<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 Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<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.<br />
<br />
=For testing purposes (will be REMOVED!)=<br />
<br />
[[media:test.pdf]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=File:Test.pdf&diff=45File:Test.pdf2010-11-26T11:50:39Z<p>Johan Raber (NSC): </p>
<hr />
<div></div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=Main_Page&diff=44Main Page2010-11-26T11:50:08Z<p>Johan Raber (NSC): /* For testing purposes (will be REMOVED!) */</p>
<hr />
<div><big>'''Welcome to the SNIC Application Experts Wiki.'''</big><br />
<br />
The aim of this page is that you should be able to get the information you need by a single click. Completely unrealistic we know, but when you aim for the stars you may reach the tree tops. If you have any questions you might find them answered in the [[FAQ]].<br />
<br />
=[[Application Experts]]=<br />
*Torben Rasmussen, NSC<br />
*Johan Raber, NSC<br />
*Chandan Basu, NSC<br />
*<br />
<br />
=Scientific Topics=<br />
<br />
==Computational Chemistry==<br />
<br />
Computational Chemistry is the tool of choice when studying aspects of chemical and thermodynamical phenomena not easily studied by experimental means. Examples include ...<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 />
* Condensed Matter<br />
* Astrophysics<br />
<br />
==Bioinformatics==<br />
<br />
* Sequence analysis<br />
* Computational evolutionary biology<br />
* Docking<br />
* Molecular Modeling<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 Compilers<br />
*#MPI<br />
*#BLAS<br />
*#MKL<br />
*Profiling and Debugging<br />
*#TotalView<br />
*#Vampir<br />
*#Valgrind<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 />
=For testing purposes (will be REMOVED!)=<br />
<br />
[[media:test.pdf]]</div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=File:MARS_space_usage.pdf&diff=42File:MARS space usage.pdf2010-11-26T11:36:40Z<p>Johan Raber (NSC): </p>
<hr />
<div></div>Johan Raber (NSC)https://snicdocs.nsc.liu.se/w/index.php?title=File:Marsdb_master_SU.svg&diff=37File:Marsdb master SU.svg2010-11-26T10:58:25Z<p>Johan Raber (NSC): </p>
<hr />
<div></div>Johan Raber (NSC)