helprelax - Support: sr #3118, Optimization for faster reading of...

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sr #3118: Optimization for faster reading of state files

Submitted by:  Troels E. Linnet <tlinnet>
Submitted on:  Fri Feb 14 09:25:22 2014  
Category: NonePriority: 5 - Normal
Severity: 1 - WishStatus: Postponed
Assigned to: NoneOpen/Closed: Closed
Operating System: None

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Tue Jun 17 18:40:02 2014, comment #1:

For large amount of pipes and data, just save these as individual states.

Troels E. Linnet <tlinnet>
Project Member
Fri Feb 14 09:25:22 2014, original submission:

This follows the discussion in:

I am storing different runs of R2eff values into state files.
Their file size is app. 5 MB each.
The loading time is about 20-30 seconds for a state file.

After turning of comprepression, the file size reached ~70 MB.
But with no considerable increase in reading speed.

The optimization should probably be found here:

Converting between data structures in the relax data store and the XML. These are all the to_xml() and from_xml() functions you can find in the 'data_store' package.

There have been zero optimisations here and, in some parts, the code is likely to be extremely inefficient (too much looping, inefficient ordering of loop nesting, etc.).
This would be the best target for optimisations.
And the loops are where you will squeeze out the most.
To find the relevant functions/methods, just run:

$ grep -r "def to_xml\|def from_xml" . --exclude-dir=".svn"

To perform any optimisations, the test suite must be used to make sure that nothing breaks.
If you notice a breakage in a save file you are using as a test for yourself while the test suite passes, then a new
system test needs to be created using a heavily truncated save file.

Troels E. Linnet <tlinnet>
Project Member


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    Date Changed By Updated Field Previous Value => Replaced By
    Tue Jun 17 18:40:02 2014tlinnetOpen/ClosedOpen=>Closed
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