Bug #4212
closedTemplate Picking - Unknown commandline options
0%
Removing the string shown after Unknown command line options and running it via command line works.
Updated by Sargis Dallakyan almost 8 years ago
- Assignee set to Anchi Cheng
- Workaround updated (diff)
Appion command and the error log is at /gpfs/appion/jbrasch/16may20b/extract/tmplrun20
[root@SEMC-head tmplrun20]# more tmplrun20.appionsub.log
... Time stamp: 16may24s57
... Function name: templateCorrelator
... Appion directory: /opt/myamisnap/lib
... Processing hostname: node11
Traceback (most recent call last):
File "/opt/myamisnap/bin/templateCorrelator.py", line 7, in <module>
imgLoop = apTemplateCorrelator.TemplateCorrelationLoop()
File "/opt/myamisnap/lib/appionlib/particleLoop2.py", line 92, in __init__
appionLoop2.AppionLoop.__init__(self)
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 27, in __init__
appionScript.AppionScript.__init__(self)
File "/opt/myamisnap/lib/appionlib/appionScript.py", line 67, in __init__
self.setParams(optargs,useglobalparams)
File "/opt/myamisnap/lib/appionlib/appionScript.py", line 341, in setParams
self.params = apParam.convertParserToParams(self.parser)
File "/opt/myamisnap/lib/appionlib/apParam.py", line 374, in convertParserToParams
apDisplay.printError("Unknown commandline options: "+str(args))
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 ***
Unknown commandline options: ['0', '0strt=0', '0end=360', '0incr=10', '1', '1strt=0', '1end=360', '1incr=10', '2',
'2strt=0', '2end=360', '2incr=10', '3', '3strt=0', '3end=360', '3incr=10', '4', '4strt=0', '4end=360', '4incr=5', '
5', '5strt=0', '5end=360', '5incr=10', '6', '6strt=0', '6end=360', '6incr=10', '7', '7strt=0', '7end=360', '7incr=1
0', '8', '8strt=0', '8end=360', '8incr=10', '9', '9strt=0', '9end=360', '9incr=10', '1', '1strt=0', '1end=360', '1i
ncr=10', '2', '2strt=0', '2end=360', '2incr=10', '3', '3strt=0', '3end=360', '3incr=10', '4', '4strt=0', '4end=360'
, '4incr=10', '5', '5strt=0', '5end=360', '5incr=10', '6', '6strt=0', '6end=360', '6incr=10', '7', '7strt=0', '7end
=360', '7incr=10', '8', '8strt=0', '8end=360', '8incr=10', '9', '9strt=0', '9end=360', '9incr=10', '0', '0strt=0',
'0end=360', '0incr=10', '1', '1strt=0', '1end=360', '1incr=10', '2', '2strt=0', '2end=360', '2incr=10', '--expid=21
48']
Not sure, if this is related to template correlator runAppionLoop.php form conversion #3859 or this bug was there before the conversion.
Updated by Anchi Cheng almost 8 years ago
- Target version set to Appion/Leginon 3.3
- Affected Version changed from Appion/Leginon 3.2 to Appion/Leginon 3.3
It is a parsing error in runAppionLoop when there are more than 9 template chosen. Can use the old interface by replacing the url where it says runAppionLoop.php with runTemplateCorrelator.php to use the old one.
Updated by Sargis Dallakyan almost 8 years ago
Thanks Anchi. It's good to know where this bug is coming from. I was having hard time trying to reproduce this.
Updated by Anchi Cheng almost 8 years ago
- Status changed from New to In Test
- Assignee changed from Anchi Cheng to Julia Brasch
Fixed in r19828 and merged into beta. The problem is in removing the commands generated for the template selections. It searches for "template1" so it picked up both 10 and 1 but only clean up the former partially. Reversed the order of iteration fixes the problem.
Julia, it should be fine once the change takes effect tomorrow.
Updated by Julia Brasch over 7 years ago
update: template picking has been working smoothly since the update. Thanks! Julia