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
>
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