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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