Feature #3833: Change myamiweb form default for makeDEAlignedSum.py avoid error - Appion - Electron Microscopy Group

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Feature #3833

closed

Change myamiweb form default for makeDEAlignedSum.py avoid error

Added by Anchi Cheng over 8 years ago. Updated over 6 years ago.

Status:

Closed

Priority:

Immediate

Assignee:

Scott Stagg

Category:

Target version:

Appion/Leginon 3.2

Start date:

12/15/2015

Due date:

% Done:

Estimated time:

Description

Traceback (most recent call last):
File "/opt/myamisnap/bin/makeDEAlignedSum.py", line 483, in
makeSum.run()
File "/opt/myamisnap/lib/appionlib/appionPBS.py", line 154, in run
command=self.generateCommand(targetdict)
TypeError: generateCommand() takes exactly 3 arguments (2 given)

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Updated by Anchi Cheng over 8 years ago

Project changed from 138 to Appion
Status changed from Assigned to In Code Review
Assignee changed from Anchi Cheng to Scott Stagg
Affected Version set to Appion/Leginon 3.2

r19432 fix it.

Scott, do you still use non-queuing method ? We don't. Maybe default should be changed if neither of us use that. Please review the change.

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Updated by Anchi Cheng over 8 years ago

Status changed from In Code Review to Assigned
Priority changed from Normal to Immediate

We got more error after that. It is just buggy without using queue.

NYSBC defaults different from the current:

File handling: link
Border: 60
Use Queue: True
Number of Jobs: 4
Queue ppn: 4
Queue memory 4

I really would like to Use Queue to be default. The border is also very important for us. I think it is true for all DE20 that the corner is no good.

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Updated by Scott Stagg over 8 years ago

Yes, running without the queue is terribly buggy. I would like to eventually devote some time to it. It is fine with me to have Use Queue be the default. I agree that the border should be masked, but the value varies from camera to camera. I don't know how to make a proper default for it.

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Updated by Anchi Cheng over 8 years ago

What is the border mask at your end ? If we put a default that work for both ends, it would be ok.

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Updated by Scott Stagg over 8 years ago

Our border is 70 pixels

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Updated by Anchi Cheng over 8 years ago

Tracker changed from Bug to Feature
Subject changed from makeDEAlignedSum.py error when queue is not used to Change myamiweb form default for makeDEAlignedSum.py avoid error
Status changed from Assigned to In Code Review

r19483 changes the defaults and adds validation for some obvious mistakes.
r19484 clean up buildCommand

Scott, please check if these defaults are acceptable.

Thanks.

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