CIBC:Documentation:SCIRun:ReleaseNotes:4.0

Program: SCIRun 4.0 Date: 11-18-2008

Overview

SCIRun 4.0 is the latest stable version of the SCIRun Problem Solving Environment.

Release cycle:

SCIRun 4.0 is distributed in a different fashion in comparison to previous SCIRun releases. We will be updating and releasing new SCIRun binaries once a week to improve feedback to the users of our binary release. With each binary release we will also release new tar/zip files with the code, for people who want to contribute to the development of SCIRun.

These updated releases are intended to quickly ship bug fixes.

Supported platforms:

1. Windows: SCIRun 4.0 currently runs on both Windows Vista and Windows XP. Currently only 32bit version is available, but a 64bit version is under development and is nearly finished. Please upgrade to the latest service packs of both Vista or XP before installing SCIRun.
2. OSX: SCIRun 4.0 supports both OSX 10.4.9 and higher and OSX 10.5.4 and higher. Currently both a 32bit and a 64bit version are available. The 64bit version is only available for OSX 10.5. Please note that SCIRun requires the X11 package to be installed from the installation disk. Note that some of the latest releases of the X11.pkg (2.3.1) contain bugs that prevent SCIRun from running properly when compiled with 2.3.1 X11 libraries. We use X11.pkg version 2.2.0 which has been verified to work correctly with SCIRun.
3. Linux: SCIRun 4.0 supports most flavors of Linux, but requires the user to compile SCIRun from scratch. ATI graphics cards do not work with SCIRun's volume renderer, and are unsupported. On Linux, we recommend NVIDIA graphics cards, which are known to have better compatibility with SCIRun. Although SCIRun is shipped with most third party software, compilation tools like gcc, svn and cmake need to be installed on the machine separately.

OpenGL requirement:

On old systems OpenGL often is version 1.2 or 1.1. However for SCIRun to work one needs an OpenGL library of version 2.0 or higher. Currently most Linux and OSX systems have a recent enough OpenGL library. Older Windows XP versions do not have a newer OpenGL library; please update OpenGL drivers on those systems before running SCIRun.

Binary versions:

• Binary versions are available for Windows XP, Windows Vista, OS X 10.4, and OS X 10.5.

Source code:

• SCIRun is open source software available under the terms of the MIT License. Use subversion to track the latest developments:

 svn checkout --username anonymous https://code.sci.utah.edu/svn/SCIRun/cibc/trunk/

Limitations of this version:

1. We have upgraded all the modules that take in code to evaluate functions. Please check the documentation of the modules to upgrade the functions. All old compiled modules are automatically upgraded but not all code inside the modules is updated automatically. Please follow documentation.
2. The Insight package and derived functionality is not available in SCIRun 4.0. Due to many issues with this package it will not be available in this version. Better and improved ITK support will follow later in SCIRun 4.1.

Documentation:

• Unfortunately SCIRun4.0 has no new or updated documentation. As we are developing a new documentation system for our software, new tutorials and instructional movies will become available this fall. We apologize for not having up to date documentation at this point. Questions regarding SCIRun can always be posted to scirun-users@sci.utah.edu, and we will be organizing a workshop for more 'hands on' assistance at the start of the winter season.

Known bugs:

1. 2D Colormap editor crashes SCIRun when it is deleted.
2. GenerateStreamLines currently only works for the cell walking, the integrating methods need to be fixed.

New features:

1. Binary release for Windows and OSX. Dynamic compilation has been removed from all of SCIRun to allow the distribution of binary versions.
2. Full 64bit support for Matrices and Fields, allowing both to be larger than 2Gb. Internally the 64bit version of SCIRun now use 64bit indices to support ever growing models.
3. Support for periodic FE models, support for floating electrodes. New modules are available to insert knowns into the FE matrix system and to merge the FE equations at the boundaries of a domain.
4. Added support for Leopard 32bit and Leopard 64bit. OSX Leopard is now properly supported by SCIRun.
5. Added module for importing environment variables into SCIRun.
6. Added support for specifying environment variables on the command line, e.g. specify +VAR=value on the commandline to set VAR to value.
7. Removed dynamic compilation, so SCIRun does not require a compiler anymore.
8. Simplified Volume Rendering pipeline: new FieldToTextureConverter will generate 2D histogram automatically.
9. Modules do not generate mapping matrix if it is not needed. If a matrix output port is not connected the mapping matrix will not be generated in the newer modules to safe memory.
10. Geometry tables will now be precomputed in parallel to improve efficiency. Field data types rely heavily on precomputing tables to speed up geometry computations. These computations are now done in parallel to improve performance on multi-core architectures.
11. Internally most function calls are now virtual so modules work on a wider range of mesh types and field types. Instead using the class name of a field to select whether an algorithm will work, we use the properties of the meshes and fields. This allows modules to work more broadly and less conversion modules are needed in the networks.
12. Modules like SetFieldData will automatically convert basis types as well as data types, allowing pipes to be connected more flexibly.
13. Most modules will do an automatic unstructure of the data if needed to make it easier for the user to link up modules.
14. Modules now report errors more thoroughly. Connecting a wrong input will not cause SCIRun to crash anymore.
15. The SCIRun look has been upgraded to look more modern. All GUIs have been updated.
16. Modules in the editor look smaller to support a better overview of what is going on in a module.
17. The network editor now supports editing networks while running a network.
18. Added a new smaller network overview to the lower part of the network editor.
19. All the menus of the ViewScene module have been upgraded to be better accessible.
20. Improved the box widget: it is now easier to rotate this widget and to restrict its movements.
21. Parser code upgrade. Code is no longer parsed through the compiler, but a high-performance parser was integrated, which runs in parallel and outperforms the old dynamically compiled versions.
22. Better support for backwards compatibility is integrated, upon loading networks modules are automatically converted to the new versions.
23. Most options from the .scirunrc are now available in the SCIRun network editor and are accessible through the menu.
24. New license dialog allows showing licenses of packages that are compiled into SCIRun binaries to give credit to external development.
25. New modules for mapping data onto a mesh that compute gradients, gradient norms, and fluxes. The module contains a lot of filters for averaging out data over the volume of an element.
26. Added new Clipping modules, one for clipping using meshes, multiple for clipping based on a function that is made up of fields and matrices.
27. LinearSolver now has MINRES solver for better performance.
28. Added modules for extracting structure of a labelfield. This one works with multi materials as well.
29. Added modules to split up a mesh based on a label (SplitFieldByDomain), and split up a mesh based on whether they are physically connected (SplitFieldByConnectedRegion).
30. Added a new interface to the InterFaceWithTetGen module that is more user friendly.
31. All file IO menus are now using the same underlying engine, for more consistency.
32. Added an option to display text in front of the generated geometry.
33. All fields now have options to find closest node and elements and project a point onto a mesh using lookup tables.
34. New RefineMesh module was added that does mesh refinement on quads, hexes, tris, and tets.
35. The pipelines in the SCIRun network editor now work properly when they are stretched over larger distances.
36. SCIRun now supports drawing networks in a small mode and a large mode. The small is intended for the larger networks and to allow more space for visualization of data.
37. SCIRunData paths and User data paths can now be edited from the network editor.
38. Code was added to maintain the .scirunrc file and automatically update an environment variable when it is changed.
39. Bases classes like Point, Vector and BBox are reintegrated into SCIRun and no longer are derived from the classes in the SLIVR library.
40. All file readers and writers for external file formats have been upgraded. They are more flexible now and do not require an additional system call to external programs.
41. Forced Teem code to be executed single threaded. The third party library 'Teem' has a series of useful functionality, but is not thread safe.
42. Added a new data type called FieldArray, to store time data. Although it has not been fully integrated into SCIRun yet, a first series of modules is available.
43. Added a tool to improve visualization of phase data. ApplyTriSurfPhaseFilter will extract phase jumps from the data and reconstruct where phase discontinuities are located.
44. Added a module for a polar projection of a surface onto a plane using a widget to define the transformation.
45. Added a new module for filtering Eigen vector data by doing a median filter on the main angle of the vector and its neightbors.
46. Added postread and presave instructions to Module class to help integrating backwards compatibility and to save status of the module before it is written to disk.
47. Fixed a series of memory leaks due to uninitialized reference counters and missing virtual destructors for classes with virtual methods.
48. Added a debug system for tracking object creation and destruction. If the number of created objects does not balance number of deleted objects over a SCIRun session, objects are being leaked into memory. This system tracks these and warns of possible memory leaks.
49. Added an option to script image generation. Like the regression system saves out images the new option '-I' does the same but does not restrict the size of the image.
50. New ViewScene windows have the dimension of the parent window.
51. SCIRun system no longer needs stubs for modules that are dependent on optional libraries. In the XML file one can now specify 'optional="true"'. This will suppress warnings if the code for the module cannot be found.
52. Added version tracking to modules to ensure better backwards compatibility in the future.
53. The loading system that automatically upgrades module names and records these changes, so the module can query them and upgrade module state if needed.
54. The revision number is now compiled into the SCIRun binary and is shown at the top right corner of the network editor to make it easier to track which version people are using.
55. Added a simple system to highlight modules in the program based on a word from the name of the module. At the top of the editor an entry box is present to search for a module.