Error in OpenBabel package

asked 2017-03-07 06:02:18 -0500

madchem gravatar image

As I updated from FC22 to FC24, it is the same error in OpenBabel package. Till FC25 that error is present. I tried to install openbabel package from repos and compile it by myself. The results are the same: when I want to convert NWChem output file into any other format, I recieve this error:

*** Error in `babel': free(): invalid pointer: 0x00007f1852c86330 ***
======= Backtrace: =========
/usr/lib64/libc.so.6(+0x791fb)[0x7f18672ac1fb]
/usr/lib64/libc.so.6(+0x8288a)[0x7f18672b588a]
/usr/lib64/libc.so.6(cfree+0x4c)[0x7f18672b92bc]
/usr/local/lib/openbabel/2.4.1/nwchemformat.so(_ZN9OpenBabel18NWChemOutputFormat15ReadCoordinatesEPSiPNS_5OBMolE+0x1ff)[0x7f1852a7d66f]
/usr/local/lib/openbabel/2.4.1/nwchemformat.so(_ZN9OpenBabel18NWChemOutputFormat12ReadMoleculeEPNS_6OBBaseEPNS_12OBConversionE+0x1ba)[0x7f1852a7f1ea]
/usr/local/lib/libopenbabel.so.5(_ZN9OpenBabel16OBMoleculeFormat18ReadChemObjectImplEPNS_12OBConversionEPNS_8OBFormatE+0x10ed)[0x7f1866f6c57d]
/usr/local/lib/libopenbabel.so.5(_ZN9OpenBabel12OBConversion7ConvertEv+0x1d5)[0x7f1866f02005]
/usr/local/lib/libopenbabel.so.5(_ZN9OpenBabel12OBConversion7ConvertEPSiPSo+0xa9)[0x7f1866f09709]
/usr/local/lib/libopenbabel.so.5(_ZN9OpenBabel12OBConversion11FullConvertERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERS7_SA_+0x197d)[0x7f1866f0b18d]
babel(main+0xabb)[0x402d4b]
/usr/lib64/libc.so.6(__libc_start_main+0xf1)[0x7f1867253401]
babel(_start+0x2a)[0x4033ca]

On CentOS 7 and on Arch Linux all is good. So I guess it is fedora problem. You can try it out by installing openbabel package and using nwchem output file with the command:

babel -inwo file.nwo -oxyz
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Comments

can you provide a nwchem output file for testing?

fcomida gravatar imagefcomida ( 2017-03-08 07:21:37 -0500 )edit

https://www.dropbox.com/s/6cfqc4uzd8w...

This is NWChem output file. Try to install openbabel package and convert this file with

babel -inwo naoh1.out -oxyz
madchem gravatar imagemadchem ( 2017-03-11 14:17:54 -0500 )edit

It's crashing here, f24. File a bug report upstream.

fcomida gravatar imagefcomida ( 2017-03-15 10:45:51 -0500 )edit