Relax 1.3.14

Official relax releases

relax version 1.3.14
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Keywords	IO, memory, performance
Release type	Major bugfix
Release date	19 March 2012
The relax 1.3.14 user manual

Description

This is a major bug fix release focusing on memory usage, performance, and IO. The parallised model-free optimisation code (for running on clusters/grids using the multi-processor package) was causing relax to crash on 32-bit systems due to the system running out of virtual memory. The new version should only require about a third of the memory of relax 1.3.13. The parts of relax dealing with atomic or spin specific data (reading of spin systems from PDB files, reading and writing of spin specific data, etc.) have been rewritten for efficiency and should now be many orders of magnitude faster for certain work loads. There have also been large improvements to the multi-processor framework, specifically the creation of a public API and a reference implementation. In addition there are improvements for IO capture on both the uni-processor and mpi4py-processor fabrics for relaying slave messages back to the master, better integration with the GUI and compatibility with the logging and teeing command line flags. Other changes include expansion of the relax information print out, support for numpy data structures in save files, and the addition of the rdc.delete and pcs.delete user functions. Feel free to upgrade if you would like the benefits of this new version.

Download

The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).

CHANGES file

Version 1.3.14
(19 March 2012, from /1.3)
http://svn.gna.org/svn/relax/tags/1.3.14

Features

• An expanded system information printout (from 'relax -i').
• Improvements to the multi-processor implementation, including creation of a public API and a reference implementation.
• Overhaul of the multi-processor stream capture design - the slave IO streams are now properly redirected to the master processor and the master no longer overrides stream capture by the relax user interfaces.
• Numpy data structures are now supported in relax save files.
• Implemented the rdc.delete and pcs.delete user functions.
• Speed ups of a number of user functions involved in looping over atomic or spin specific data - this can be significant if a lot of structural operations are performed, or a large number of structures are required.
• Redesigned how spin parameters are handled in the specific analyses (which includes parameter name changes).

Changes

• The MS Windows text wrapping width has been changed from 80 to 79 - this now fits the cmd prompt.
• The program intro print out and prompt UI help system is using the new Status.text_width variable to wrap text.
• The model-free constraint matrix A is now of numpy.int8 type - this is to decrease virtual memory usage and increase the scaling efficiency on clusters.
• Changed all relax website links to http://www.nmr-relax.com for consistency.
• The setup.py script can now be imported for the epydoc API documentation system.
• The extern and minfx.scipy_subset relax packages are excluded form the API documentation.
• Added the ability to skip scripts in the package __all__ list unit test checks.
• Added some code to detect the bit version of MS Windows in the information print out (to better distinguish 32 vs. 64-bit versions).
• Added some documentation about master processors on Linux 2.6 eating 100% of one CPU core (in the mpi4py multi-processor fabric).
• Added a reference implementation to the multi-processor package - this is to demonstrate to users of the package how an implementation is created via the public API.
• Elimination of all relax dependencies from the multi-processor package.
• Added support for the memory size on MS Windows to the relax info print out.
• Updated the value.set user function unknown parameter error message to list the known ones.
• For Unix and GNU/Linux systems, the relax info printout now shows the ram and swap size.
• Expansion and improvement of the information printed out by 'relax --info'.
• Expansion of the multi-processor API documentation.
• Expansion of the multi-processor package documentation with a step by step usage guide - this should increase the usability of the package by clarifying how one should use it.
• Expansion and improvements to the multi-processor package and module docstrings.
• The finish button in the new analysis wizard has been renamed to "Start".
• Created a special Verbosity singleton for controlling the multi-processor package print outs.
• Future proofed the relax codebase by replacing all ''' with """ in the docstrings.
• Removed the unnecessary try statement in the model-free Slave_command.run() method as exception handling is correctly performed on the slave and master.
• Shifted the Memo object into its own module (multi package).
• Simplification and abstraction of the Slave_command.run() method to shift all exception handling into the package. Therefore program code no longer needs to handle the multi-processor specific errors.
• Created a new module 'multi.misc' for holding miscellaneous functions used throughout the multi package.
• Created a public API for the multi-processor package, available via multi.__init__.
• The load_multiprocessor() function is no longer a static method of the Processor base class. This function loads the correct Processor class, so doesn't need to be a method of the base class and operates cleanly and more clearly as a stand alone function.
• Clean up of the processor IO module (multi package).
• Eliminated all usage of sys.__stdout__ and sys.__stderr__ in the multi-processor package - this returns full control of IO streams to the parent program.
• The float arg checks now checks against all the numpy float types (float16, float32, float64, float128).
• Added value.write user function calls to the J(ω) mapping system test script.
• Added some value.write user functions to the J(ω) mapping sample script.
• Modified the J(ω) mapping test data to include relaxation values of None to trigger bug #19329.
• Speed up for the generic_fns.relax_re.search() function.
• More speed ups for the Selection.__contains_mol_res_spin_containers() method.
• Reordered the checks in Selection.__contains_mol_res_spin_containers() - this cuts the number of function calls down by avoiding relax_re.search() calls if residue or spin numbers match.
• Simplified the generic_fns.relax_re.search() function - this is to minimise the number of isinstance() calls when dealing with the relax mol-res-spin sequence data.
• Updates for Python 3.0 using 2to3.
• Removal of a number of debugging print out statements.
• Significant speed ups of the return_spin() and return_residue() functions.
• Added a print out for the diffusion_tensor.init user function to inform the user of an angle unit change - this is in response to bug #19323 to make it clearer that a parameter conversion has occurred.
• Created a special specific API object called SPIN_PARAMS - this will be used to handle all operations to do with model parameters. The object Param_list has methods for parameter initialisation and handling (where all info is specified such as Grace string, units, default value, etc) and for determining if a parameter exists.
• Mass conversion to the new GLOBAL_PARAMS and SPIN_PARAMS specific API data structures. The parameters are now all lowercase, for example ['S2', 'te', 'Rex'] is now ['s2', 'te', 'rex']. The follow parameters are now converted throughout relax: 'bond_length' to 'r', 'CSA' to 'csa', 'heteronucleus' to 'heteronuc_type', 'proton' to 'proton_type'.
• Created a new algorithm for finding the pivot of motion between different structural models - this is available through the structure.find_pivot user function.
• Added the validate_models() method to the structural API - this is used to check that the models are 100% consistent.
• Added the centroid argument to the structure.superimpose user function - this allows for the superimposition of structures assuming a pivoted motion.

Bugfixes

• Fix for the title of the analysis selection wizard GUI element.
• Fix for the MemoryError during the "final" run of d'Auvergne Protocol[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 2008b] affecting 32-bit systems (bug #19528).
• Epydoc docstring fixes for the API documentation.
• Bug fix for old numpy versions missing the float16 object.
• The relax prompt mode now prints the intro message to sys.stdout - this fixes this mode with the logging option or in the mpi4py multiprocessor mode.
• Fix for the storage of numpy data structures in the relax save files - if special structures are created by the user, these were not correctly stored. The precision was often too low (printed at the numpy default of a precision of 8), and if one dimension had more than 1000 elements, ellipses would be stored instead (the ellipses would cause the save file to be unreadable by relax).
• Created the SplitIO.flush() method so that a flush() call now works with the -t and -l command line args - this simply calls the flush() methods of both streams.
• The relax data store __repr__() method now prints out all objects within the base object.
• Fix for a rare bug in the model-free analysis for when relaxation data of None is encountered.
• Fixes for the Dasha system test for the bug #19332 fix.
• Fixes for the Dasha use functions for file creation and data extraction - this should now handle relaxation data values of None, and also set the parameter values of deselected spins using the DASHA output files.
• Big bugfix for the value.read user function - the wrong spin ID string was being used to set the parameter value so that all spins have the same value set for the parameter (bug #19332).
• Bug fix for the consistency testing analysis for when relaxation data of None is encountered.
• The spin is now deselected if there is really less than three data points, excluding data points of None (bug #19329).
• Bug fix for the arg_check.is_none() function - the RelaxNoneError was not imported!
• Fix for the numbering of the TER record and subsequence HETATM records in the PDB file creation. The structure.write_pdb user function now creates the correct TER record after the ATOM records, and the HETATM records are renumbered if needed.
• Bug fix for the compilation of the user manual. The molecule user function class used the temporary variable i, which was causing the fetch_docstrings script to fail.

Links

For reference, the following links are also part of the announcement for this release:

• Official release notes
• Gna! news item
• Mail archive
• Local archives
• MARC

Announcements

If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.

References

• [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. Mol. BioSyst., 3(7), 483-494. (DOI: 10.1039/b702202f)
• [*d'Auvergne and Gooley, 2008b] d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133. (DOI: 10.1007/s10858-007-9213-3)

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See also

• The relax 1.3 API documentation

• The combined release notes for all relax versions (warning, this is very large).
• The combined release descriptions for all relax versions.
• The combined release metadata for all relax versions.
• The combined release features for all relax versions.
• The combined release changes for all relax versions (warning, this is very large).
• The combined release bugfixes for all relax versions.
• The combined release announcement links for all relax versions.