Bug #4595: parallel unlock failure - Appion - Electron Microscopy Group

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Bug #4595

closed

parallel unlock failure

Added by Giovanna Scapin over 7 years ago. Updated over 7 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Category:

Target version:

Appion/Leginon 3.3

Start date:

11/14/2016

Due date:

% Done:

Estimated time:

Affected Version:

Appion/Leginon 3.3

Show in known bugs:

Workaround:

Description

I tried to run CTFFIND4 on the SEMC-head from appion, it failed with

Traceback (most recent call last):
File "/opt/myamisnap/bin/ctffind4.py", line 451, in <module>
imgLoop.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 108, in run
self.finishLoopOneImage(imgdata)
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 124, in finishLoopOneImage
self.unlockParallel(imgdata.dbid)
File "/opt/myamisnap/lib/appionlib/appionScript.py", line 545, in unlockParallel
apDisplay.printError('Parallel unlock failed')
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 65, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
Parallel unlock failed

All files are in /gpfs/appion/gscapin/16nov11d/ctf

Related issues 1 (0 open — 1 closed)

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Updated by Giovanna Scapin over 7 years ago

A bit more specifics: I run it once, (in /gpfs/appion/gscapin/16nov11d/ctf/ctffind4run1) and the ACE button on the viewer did not display any rings, or 0.8, 0.5 best values. Also, under the GUI, the summary talks about 28 CTFs completed. When I tried to generate a stack file after template picking, it failed (in /gpfs/appion/gscapin/16nov11d/stacks/stack1 and stack2; see below). A second attempt to run ctffind4 caused the error above. It may as well be something I did,but I cannot figure out what it could be.

Thanks - Giovanna

......................
.!!! WARNING: no best CTF value for image 16nov11d_IrIn10_022gr_04sq_02hln_05enn-a
.!!! WARNING: no best CTF value for image 16nov11d_IrIn10_022gr_04sq_02hln_04enn-a
.!!! WARNING: no best CTF value for image 16nov11d_IrIn10_022gr_04sq_02hln_02enn-a
.!!! WARNING: no best CTF value for image 16nov11d_IrIn10_022gr_04sq_02hln_03enn-a
.!!! WARNING: no best CTF value for image 16nov11d_IrIn10_028gr_01sq_02hln_02enn-a
.
... finished skipping in 11.76 sec

!!! WARNING: skipped 1115 of 1115 images
... [[ 1115 no reprocess | 0 rejected | 0 wrong tilt | 0 in donedict ]]
... Process images old to new
!!! WARNING: Checking for dd
!!! WARNING: No images were found to process

Beginning Main Loop
!!! WARNING: skipped total of 1115 images.
... to process them again, remove 'continue' option and run makestack2 again.
!!! WARNING: 0 files with the patterns '/gpfs/appion/gscapin/16nov11d/stacks/stack1/16nov11d*.dwn.mrc' will be removed
... Removed 0 of 0 files
!!! WARNING: 0 files with the patterns '/gpfs/appion/gscapin/16nov11d/stacks/stack1/16nov11d*mrc.corrected.mrc' will be removed
... Removed 0 of 0 files
COMPLETE LOOP: 6.01 sec for -1 images
... Closing out function log: makestack2.log
... Ended at Mon, 14 Nov 2016 07:05:43
Total run time: 32.84 sec
... Run directory:
/gpfs/appion/gscapin/16nov11d/stacks/stack1
(

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Updated by Anchi Cheng over 7 years ago

Status changed from New to Closed
Target version set to Appion/Leginon 3.3
Affected Version changed from Appion/Leginon 3.2 to Appion/Leginon 3.3

The parallel unlock problem is a timing issue. The lock file has been removed by another unlock call but a fraction of the second delay caused it wanting to do it again. e2c473fd adds some wait time for it. Should fix it.

Stack generation with no best ctf value is caused by ctfdisplay not generating the diagnosis result. It is a SEMC internal problem of bad .matplotlib cache saved at user's home directory.