Sorry - a typo:
" To make it easier for us to identify the problem, could you provide
the simplest possible program that causes the problem? Could you name
a PDB file that causes the problem?"
On 22 February 2010 18:39, Noel O'Boyle <baoille...@gmail.com> wrote:
> Hello Alexey,
>
> To make it easier for us to identify the problem, could you provide
> the simplest possible program that causes the program? Could you name
> a PDB file that causes the problem?
>
> - Noel
>
> On 22 February 2010 17:32, Alexey Nesternko <comcona...@gmail.com> wrote:
>> This is the part of program, which also crashes in the same way:
>>
>> #!/usr/bin/python -d
>> import openbabel, sys, math, random
>> import numpy
>>
>> try:
>> def add(x, y): return x+y
>> obC = openbabel.OBConversion()
>> obC.SetInAndOutFormats("pdb", "pdb")
>>
>> mols = []
>> verts = []
>> probs = []
>>
>> # initializing structures
>> if True:
>> nmol = openbabel.OBMol()
>> obC.ReadFile(nmol, "dppsnew.pdb")
>> mols.append( nmol )
>> nmol = openbabel.OBMol()
>> obC.ReadFile( nmol, "chlnew.pdb")
>> mols.append( nmol )
>>
>> # init values for grid
>> numconformers = 50
>>
>> # =================================================
>> # crashes because of this block!!!
>> # =================================================
>> for mol in mols:
>> for i in range(0,numconformers):
>> nmol = openbabel.OBMol(mol)
>> for torl in openbabel.OBMolTorsionIter(nmol):
>> atlist = [nmol.GetAtom(torl[0]+1),
>> nmol.GetAtom(torl[1]+1), nmol.GetAtom(torl[2]+1),
>> nmol.GetAtom(torl[3]+1)]
>> if (atlist[1].IsInRing() and
>> atlist[2].IsInRing() ):
>> continue
>> tor = nmol.GetTorsion(atlist[0],
>> atlist[1], atlist[2], atlist[3])
>> tor = random.gauss(tor, 3)*math.pi/180
>> nmol.SetTorsion(atlist[0], atlist[1],
>> atlist[2], atlist[3], tor)
>> mol.AddConformer(nmol.GetConformer(0))
>> # =================================================
>> # end of block
>> # =================================================
>> finally:
>> print 'Bue!'
>>
>>
>>
>> crash message:
>>
>> *** glibc detected *** /usr/bin/python2.6: double free or corruption
>> (out): 0x0000000000d4bd20 ***
>> ======= Backtrace: =========
>> /lib/libc.so.6[0x7f5f621f14ce]
>> /lib/libc.so.6(cfree+0x75)[0x7f5f621f2dbb]
>> /usr/local/lib/libopenbabel.so.3(_ZN9OpenBabel5OBMolD0Ev+0xd0)[0x7f5f61a135e0]
>>
>>
>> Program crashes at end everywhere - in debian, gento and cygwin.
>> Program works absolutely normally. The only error - is the crush on
>> the end, while destructing. What I does wrong with conformers?
>>
>> Thank you.
>>
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>
------------------------------------------------------------------------------
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proactively, and fine-tune applications for parallel performance.
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