Bug #252
closed
Affinity propagation fails on large stacks
Added by Neil Voss over 14 years ago.
Updated over 10 years ago.
Affected Version:
Appion/Leginon 2.2.0
Description
The affinity propagating clustering program requires that all particles in a stack be inserted into memory for the cross-correlation matrix calculation.
This needs to use my new processStack class in source:trunk/appion/appionlib/apImagicFile.py to systematically read particle subsets from the a stack.
- Target version set to Appion/Leginon 2.0.0
- Status changed from New to Assigned
- Assignee set to Neil Voss
- Status changed from Assigned to In Code Review
- Assignee changed from Neil Voss to Amber Herold
- % Done changed from 0 to 100
Note: program did not do a good job of comparing old version to new version.
- Status changed from In Code Review to In Test
- Assignee changed from Amber Herold to Neil Voss
Looks ok. Not a fan of using simf as a shorthand for similarfile but OK.
Can you assign to someone to test?
- Assignee changed from Neil Voss to Anke Mulder
- Priority changed from Low to Normal
You'll need to run on amibox after Friday, May 20. Try it on a large stack > 16GB.
- Assignee changed from Anke Mulder to Amber Herold
- Affected Version set to Appion/Leginon 2.0.2
- Show in known bugs set to No
- Assignee changed from Amber Herold to Dmitry Lyumkis
Dmitry, do you happen to use affinity propagation on >16GB stacks ever?
that's quite big. I don't have anything that size. I can look around other projects though
- Status changed from In Test to Closed
This one is too difficult to test bc we don't have any large stacks that will work. Since Neil logged it I'm assuming it worked for the data that he was having trouble with.
- Assignee changed from Dmitry Lyumkis to Amber Herold
I think Joel reported this issue to me for data at NIS. In the past it would probably fail on stacks > 2GB. The algorithm has changed so all stacks are treated equally, so if it works on a 200kB stack it should also work on a 200GB stack.
- Status changed from Closed to In Test
- Status changed from In Test to Closed
- Affected Version changed from Appion/Leginon 2.0.2 to Appion/Leginon 2.2.0
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