Hello,
Can you send me the project (gzipped tar) or is it too huge for email?
I mean it's likely it's going to behave differently on a different machine
in any case, but I think it's worth checking just in case it's some weird
bug that is causing this that isn't obvious.
Wayne
On Thu, 3 Dec 2009, Marcel Jurk wrote:
> Hello Wayne,
>
> I just tried to open other projects and add sequences and got no error at
> all. Following that I tried it with new projects and it seems as if the error
> is just limited to the one I am currently working on - i. e. I am only able
> to reproduce the error with this particularly project.
> Do I have to start all over again or is there a chance to fix it?
>
> Thanks so far for the answer.
>
> Cheers,
> Marcel
>
>
> Wayne Boucher wrote:
>> Hello,
>>
>> That's a new one. So it's coming from the Python code direct, rather than
>> from the C code. And I doubt if it's even doing anything particularly
>> strenuous at that line of code (which is just asking it to list the files
>> in one of the project directories). It doesn't look like a recursive
>> problem either (where it is stuck in some infinite loop). And if the
>> system claims it has 3 Gb memory free when this happens this is really
>> puzzling. So the amount of memory we allocate in the C world is limited,
>> but there is no real way to even do that in the Python world.
>>
>> Is it only on this one project, and is this project super-sized?
>>
>> Wayne
>>
>> On Wed, 2 Dec 2009, Marcel Jurk wrote:
>>
>>> Hello everyone,
>>>
>>> CCPN (2.0.6) comes up with an error message every time I am trying to
>>> build a chain after adding the sequence.
>>>
>>> It seems, CPPN is not able to allocate enough memory for this particular
>>> process. Free memory of my system is around 3 GB. Even reloading the
>>> project or restarting CCPN does not help.
>>>
>>> Does anyone understand the full error message and might explain that to
>>> me?
>>>
>>> Best wishes,
>>> Marcel
>>>
>>>
>>>
>>>>>> Exception in Tkinter callback
>>> Traceback (most recent call last):
>>> File "/home/marcel/bin/ccpnmr/python2.5/lib/python2.5/lib-tk/Tkinter.py",
>>> line 1403, in __call__
>>> return self.func(*args)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisPopup.py",
>>> line 1290, in browseAtoms
>>> popup = self.openPopup('browse_atoms', BrowseAtomsPopup)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/AnalysisPopup.py",
>>> line 1146, in openPopup
>>> transient=transient, *args, **kw)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/popups/BrowseAtoms.py",
>>> line 120, in __init__
>>> BasePopup.__init__(self, parent=parent, title="Molecules : Atom
>>> Browser", **kw)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/popups/BasePopup.py",
>>> line 91, in __init__
>>> memops.editor.BasePopup.BasePopup.__init__(self, parent, *args, **kw)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/memops/editor/BasePopup.py",
>>> line 85, in __init__
>>> memops.gui.BasePopup.BasePopup.__init__(self, parent, *args, **kw)
>>> File "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/memops/gui/BasePopup.py",
>>> line 124, in __init__
>>> self.initial_focus = self.body(frame)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/popups/BrowseAtoms.py",
>>> line 218, in body
>>> self.updateChains()
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/popups/BrowseAtoms.py",
>>> line 561, in updateChains
>>> self.updateChainAttrs(chain)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/popups/BrowseAtoms.py",
>>> line 806, in updateChainAttrs
>>> residueMapping = getResidueMapping(residue)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/MoleculeBasic.py",
>>> line 1618, in getResidueMapping
>>> makeResidueAtomSets(residue, aromaticsEquivalent=aromaticsEquivalent)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/MoleculeBasic.py",
>>> line 1853, in makeResidueAtomSets
>>> makeAtomSet(name,(atom,),None,'simple')
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/MoleculeBasic.py",
>>> line 1560, in makeAtomSet
>>> if atom.atomSet != atom0.atomSet:
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccp/api/molecule/MolSystem.py",
>>> line 1238, in getAtomSet
>>> root.refreshTopObjects('ccp.nmr.Nmr')
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py",
>>> line 16221, in refreshTopObjects
>>> for filename in os.listdir(fileLocation): OSError: [Errno 12] Cannot
>>> allocate memory: '/tango1/jurk/ccpn/PRR/BACKBONE/assignment/ccp/nmr/Nmr'
>>> Exception in Tkinter callback Traceback (most recent call last):
>>> File "/home/marcel/bin/ccpnmr/python2.5/lib/python2.5/lib-tk/Tkinter.py",
>>> line 1403, in __call__
>>> return self.func(*args)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/popups/EditMolecules.py",
>>> line 1767, in makeChain
>>> return makeChain(molSystem, molecule, code=code)
>>> File "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccp/util/Molecule.py",
>>> line 475, in makeChain
>>> chain = MolSystem.Chain(molSystem, code=code, molecule=molecule)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccp/api/molecule/MolSystem.py",
>>> line 2426, in __init__
>>> notify(self)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/Analysis.py",
>>> line 761, in initMolSystemChain
>>> residueMapping = MoleculeBasic.getResidueMapping(residue,
>>> aromaticsEquivalent=aromaticEquivalent)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/MoleculeBasic.py",
>>> line 1618, in getResidueMapping
>>> makeResidueAtomSets(residue, aromaticsEquivalent=aromaticsEquivalent)
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/MoleculeBasic.py",
>>> line 1853, in makeResidueAtomSets
>>> makeAtomSet(name,(atom,),None,'simple')
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccpnmr/analysis/core/MoleculeBasic.py",line
>>> 1560, in makeAtomSet
>>> if atom.atomSet != atom0.atomSet:
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/ccp/api/molecule/MolSystem.py",
>>> line 1238, in getAtomSet
>>> root.refreshTopObjects('ccp.nmr.Nmr')
>>> File
>>> "/home/marcel/bin/ccpnmr/ccpnmr2.0/python/memops/api/Implementation.py",
>>> line 16221, in refreshTopObjects
>>> for filename in os.listdir(fileLocation):
>>> OSError: [Errno 12] Cannot allocate memory:
>>> '/tango1/jurk/ccpn/PRR/BACKBONE/assignment/ccp/nmr/Nmr'
>>>
>>>
>>>
>>> --
>>> Marcel Jurk
>>>
>>> Leibniz Institut fuer Molekulare Pharmakologie (FMP)
>>> Solution NMR (AG Schmieder)
>>> Robert-Roessle-Str. 10
>>> 13125 Berlin
>>> Germany
>>>
>>> eMail: [log in to unmask]
>>> Phone: +49-30-94793223
>>> Fax: +49-030-94793169
>>>
>>
>
> --
> Marcel Jurk
>
> Leibniz Institut fuer Molekulare Pharmakologie (FMP)
> Solution NMR (AG Schmieder)
> Robert-Roessle-Str. 10
> 13125 Berlin
> Germany
>
> eMail: [log in to unmask]
> Phone: +49-30-94793223
> Fax: +49-030-94793169
>
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