problem with crashes in Hole Targeting in Leginon 1.4.1
Added by Anonymous over 17 years ago
I'm getting Leginon 1.4.1 crashing when I press the submit targets button in the Square Targeting node (after picking some targets, of course) in the MSI-Edge application. The crash seems to happen when Leginon gets to the Hole Targeting node. (The Hole Targeting node has the option to check the targets manually turned on and queuing turned off.) I get no traceback in the Python code, unfortunately. The only error message output is: "Illegal instruction",
William
Replies (3)
- Added by Anonymous over 17 years ago
A different problem happens in MSI-T. It doesn't actually bring down Leginon but it hangs and I get the following output:
File "/usr/lib64/python2.5/threading.py", line 460, in __bootstrap
self.run()
File "/usr/lib64/python2.5/threading.py", line 440, in run
self.__target(*self.__args, **self.__kwargs)
File "/usr/local/lib64/python2.5/site-packages/Leginon/databinder.py", line 13
1, in handleData
method(args)
File "/usr/local/lib64/python2.5/site-packages/Leginon/watcher.py", line 35, i
n handleEvent
self.processEvent(pubevent)
File "/usr/local/lib64/python2.5/site-packages/Leginon/watcher.py", line 46, i
n processEvent
self.processData(newdata)
File "/usr/local/lib64/python2.5/site-packages/Leginon/imagewatcher.py", line
46, in processData
self.processImageData(idata)
File "/usr/local/lib64/python2.5/site-packages/Leginon/targetfinder.py", line
196, in processImageData
self.findTargets(imagedata, targetlist)
File "/usr/local/lib64/python2.5/site-packages/Leginon/jahcfinder.py", line 42
8, in findTargets
self.everything()
File "/usr/local/lib64/python2.5/site-packages/Leginon/jahcfinder.py", line 35
4, in everything
self.correlateTemplate()
File "/usr/local/lib64/python2.5/site-packages/Leginon/jahcfinder.py", line 11
8, in correlateTemplate
self.hf.create_template()
File "/usr/local/lib64/python2.5/site-packages/Leginon/jahcfinderback.py", lin
e 176, in create_template
tempim = self.read_hole_template(filename)
File "/usr/local/lib64/python2.5/site-packages/Leginon/jahcfinderback.py", lin
e 164, in read_hole_template
im = mrc.read(filename)
File "/usr/local/lib64/python2.5/site-packages/pyami/mrc.py", line 421, in rea
d
f = open(filename, 'rb')
IOError: [Errno 2] No such file or directory: '/usr/lib/python2.4/site-packages/
Leginon/holetemplate.mrc'
For some reason it is looking in the directory /usr/lib/python2.4 although Python 2.4 has never been installed on the relevant system (a SUSE 10.3 machine). Also, if I create the expected directory and then put holetemplate.mrc into it then I get the same problem as occurs with MSI-Edge - Leginon just crashes with an "Illegal Instruction" error without any other error messages or output to indicate what has gone wrong,
William
- Added by Anonymous over 17 years ago
I do get a core from Python (from the above crash in MSI-T which gives the "Illegal Instruction" error) and it turns out the traceback from the core as revealed by gdb is in Py_Histogram in nd_image in scipy, if that's any help,
William
- Added by Anonymous over 17 years ago
"WVNicholson" wrote: I do get a core from Python (from the above crash in MSI-T which gives the "Illegal Instruction" error) and it turns out the traceback from the core as revealed by gdb is in Py_Histogram in nd_image in scipy, if that's any help,
William
I fixed the problem with crashes with an "Illegal Instruction" error by changing to an earlier version of scipy. (I had the current 0.6.x version and went to the last 0.5.x version I think. The Leginon manual does mention that just 0.5.1 of scipy has been tested at Scripps.)
Also, I think the incorrect path for holetemplate.mrc is picked up from the defaults for Hole Targeting in the database, usually obtained from the previous user choices for the template correlation settings. (In the case the settings started off wrong because the database was copied from another system with the file in a different directory.) I suppose Leginon could give a more helpful error message. Anyway, everything works okay when I put the correct path in the field in the template correlation settings node in Hole Targetting for MRC file with the template,
William