Difference between revisions of "Paraview"

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(Created page with "http://www.ks.uiuc.edu/Research/vmd/ VMD "is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemb...")
 
 
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[[http://www.ks.uiuc.edu/Research/vmd/ VMD]] "is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer."
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[[http://www.paraview.org ParaView]] "is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.
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ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation."
  
  
 
====Type of Data====
 
====Type of Data====
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Will accept multiple data types
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Unsurprisingly, most respondents use this software for molecular/atomic/protein visualisation.
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====Size of Data Set====
 
====Size of Data Set====
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Respondents have processed data sets of up to a few TB
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This varies widely. About half the respondents have data sets smaller than a few GB. Two had data sets of 40 and 50 GB. Otherwise they had 1,000 or 30,000 atoms.
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====Advantages====
 
====Advantages====
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*Good performance
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The most widely cited advantages are
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*Free
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*quality of output
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*range of supported file types
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*simple to use/script
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====Quality of Documentation/Tutorials====
 
====Quality of Documentation/Tutorials====
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Good/Excellent documentation
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Documentation was almost universally regarded as good or very good. One respondent stated it was difficult to navigate.
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====Range of Data Formats====
 
====Range of Data Formats====
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"the major formats can be read"
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Again, almost universally regarded as good, with two exceptions:
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*"temperamental with periodic images"
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*"no support for cif"
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====Level of Support Available====
 
====Level of Support Available====
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Good support is available.Tutorials and a user guide are available on the website. The developers also host a mailing list.
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A range of resources is used: mailing lists and online forum.
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====Performance====
 
====Performance====
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Performance is good, provided that sufficient memory is available for the data set - it can be run over multiple nodes to provide this.
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Performance generally regarded as good, especially on a desktop machine.
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====Limitations====
 
====Limitations====
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Remote connections with X system is slow.
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*"Needs a good graphics card"
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*"TCL scripting is limited"
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*"Slow to load large data sets"
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*"Some additional analysis tools are unstable"
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*"Some representations not appropriate for periodic boundary conditions"
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*"Cannot interpret bond types"
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====Comments====
 
====Comments====
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The comments only reitereted points made previously: it is free and open source
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The tools are free and open source
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Latest revision as of 12:59, 24 November 2014

[ParaView] "is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView’s batch processing capabilities.

ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of petascale size as well as on laptops for smaller data, has become an integral tool in many national laboratories, universities and industry, and has won several awards related to high performance computation."


Type of Data

Will accept multiple data types

Size of Data Set

Respondents have processed data sets of up to a few TB

Advantages

  • Good performance
  • Free

Quality of Documentation/Tutorials

Good/Excellent documentation

Range of Data Formats

"the major formats can be read"

Level of Support Available

Good support is available.Tutorials and a user guide are available on the website. The developers also host a mailing list.

Performance

Performance is good, provided that sufficient memory is available for the data set - it can be run over multiple nodes to provide this.

Limitations

Remote connections with X system is slow.

Comments

The comments only reitereted points made previously: it is free and open source

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