Dear Ben,
The error while saving does (indeed) mean that the program ran out of
memory. It is hard to say what might have caused it (Wayne might have a
better idea) but I guess one could try to close down other applications.
What computer are you runnign on, and how much memory does it have?
The error while loading means that the file ends in the middle of the
data. Most likely the writing was interrupted during save. Try to look
into the relevant file ccp/Nmr.xml and see how it ends. A correct file
ends with </_StorageUnit> - most likely it will be clear what is wrong.
Unfortunately it is unlikely that your data will be reccoverable, so
better look to your backups.
Yours,
Rasmus
---------------------------------------------------------------------------
Dr. Rasmus H. Fogh Email: [log in to unmask]
Dept. of Biochemistry, University of Cambridge,
80 Tennis Court Road, Cambridge CB2 1GA, UK. FAX (01223)766002
On Fri, 16 Jun 2006, Ben Goult wrote:
> Hi,
>
> After peak picking a spectrum upon trying to save my project it fails and I
> get the following traceback
>
> ERROR saving xml ccp.Nmr ccp/Nmr.xml
> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 1345, in __call__
> return self.func(*args)
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py", line
> 1395, in closeProject
> if (not self.checkSaving()):
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py", line
> 1383, in checkSaving
> if (not self.quitSaveProject()):
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py", line
> 1335, in quitSaveProject
> return self.saveFile()
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py", line
> 1369, in saveFile
> self.project.saveModified()
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 26469, in saveModified
> storage.save()
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 8939, in save
> ioModule.save(stream, self.project)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccp/xml/Nmr.py", line 135, in
> save
> GeneralXmlIO.save(
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py",
> line 116, in save
> doSave(stream, parent, saveObjects, mapping, comment, simplified)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py",
> line 200, in doSave
> classID[obj] = _ID
> MemoryError
>
> Is this project permanently broken or can it be saved? Also is there
> anything I can do to prevent this happening? The peak list is pretty big
> (20000 peaks) but I am not sure the cause is the size of the peak list as I
> have a peak list in the project that has 40000peaks and it doesnt prevent
> it from saving.
>
> On a similar vein, I tried to reopen a project after seeing this error but
> this failed as well giving this traceback:
>
> ERROR loading xml ccp.Nmr ccp/Nmr.xml
> Exception in Tkinter callback
> Traceback (most recent call last):
> File "/usr/lib64/python2.4/lib-tk/Tkinter.py", line 1345, in __call__
> return self.func(*args)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/gui/ScrolledMatrix.py",
> line 571, in mouseDoubleClick
> self.selectDoubleCell(row,col)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/gui/ScrolledMatrix.py",
> line 546, in selectDoubleCell
> self.doubleCallback(self.currentObject, objRow, objCol)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/gui/FileSelect.py", line
> 395, in doubleCallback
> self.double_callback(file)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/gui/BasePopup.py", line
> 224, in ok
> if (not self.apply()):
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/memops/editor/OpenProjectPopup.py",
> line 142, in apply
> self.callback(self.project)
> File
> "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/AnalysisPopup.py", line
> 904, in initProject
> Analysis.initProject(self, project)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py",
> line 206, in initProject
> self.initResonances()
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccpnmr/analysis/Analysis.py",
> line 1059, in initResonances
> resonances = self.project.resonances
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 17466, in getResonances
> otherStorage.load()
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/api/Implementation.py",
> line 8904, in load
> ioModule.load(stream, self.project)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/ccp/xml/Nmr.py", line 113, in
> load
> return GeneralXmlIO.load(stream, mapping, parentObject)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py",
> line 370, in load
> result = doLoad(stream, mapping, headObject)
> File "/data/prog/ccpnmr/ccpnmr1.0/python/memops/format/xml/XmlIO.py",
> line 907, in doLoad
> raise ApiError(
> ApiError: Error loading fileNot (correct) XMLNo </_StorageUnit> element
> found
> S
>
> Any ideas on what this means and how I can avoid it?
>
> Cheers
>
> Ben
>
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