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Bug #252

closed

Affinity propagation fails on large stacks

Added by Neil Voss over 14 years ago. Updated over 10 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Amber Herold
Category:
-
Target version:
Appion/Leginon 2.0.0
Start date:
03/25/2010
Due date:
% Done:

100%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
No
Workaround:

Description

The affinity propagating clustering program requires that all particles in a stack be inserted into memory for the cross-correlation matrix calculation.

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 #1

Updated by Neil Voss over 14 years ago

This needs to use my new processStack class in source:trunk/appion/appionlib/apImagicFile.py to systematically read particle subsets from the a stack.

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 #2

Updated by Neil Voss over 14 years ago

  • Target version set to Appion/Leginon 2.0.0
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 #3

Updated by Neil Voss over 14 years ago

  • Status changed from New to Assigned
  • Assignee set to Neil Voss
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 #4

Updated by Neil Voss over 14 years ago

  • Status changed from Assigned to In Code Review
  • Assignee changed from Neil Voss to Amber Herold
  • % Done changed from 0 to 100
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 #5

Updated by Neil Voss over 14 years ago

Note: program did not do a good job of comparing old version to new version.

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 #6

Updated by Amber Herold over 14 years ago

  • 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?

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 #7

Updated by Neil Voss over 14 years ago

  • 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.

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 #8

Updated by Amber Herold over 14 years ago

  • Assignee changed from Anke Mulder to Amber Herold
  • Affected Version set to Appion/Leginon 2.0.2
  • Show in known bugs set to No
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 #9

Updated by Amber Herold over 14 years ago

  • Assignee changed from Amber Herold to Dmitry Lyumkis

Dmitry, do you happen to use affinity propagation on >16GB stacks ever?

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 #10

Updated by Dmitry Lyumkis over 14 years ago

that's quite big. I don't have anything that size. I can look around other projects though

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 #11

Updated by Amber Herold over 14 years ago

  • Status changed from In Test to Closed
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 #12

Updated by Amber Herold over 14 years ago

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.

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 #13

Updated by Neil Voss about 14 years ago

  • 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.

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 #14

Updated by Neil Voss about 14 years ago

  • Status changed from Closed to In Test

see last message

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 #15

Updated by Amber Herold over 10 years ago

  • 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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