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Description of problem: Openbabel cannot convert coordinates Version-Release number of selected component (if applicable): 2.3.90-0.9.20160216git3a63a98.fc24 How reproducible: always Steps to Reproduce: 1. Try to convert nwchem output file .out to xyz: babel -inwo nwfile.out -oxyz Actual results: SegFault *** Error in `babel': free(): invalid pointer: 0x00007fb50cc50050 *** ======= Backtrace: ========= /usr/lib64/libc.so.6(+0x7566b)[0x7fb52355a66b] /usr/lib64/libc.so.6(+0x7de0a)[0x7fb523562e0a] /usr/lib64/libc.so.6(cfree+0x4c)[0x7fb52356636c] /usr/lib64/openbabel/nwchemformat.so(_ZN9OpenBabel18NWChemOutputFormat15ReadCoordinatesEPSiPNS_5OBMolE+0x21b)[0x7fb50ca47dfb] /usr/lib64/openbabel/nwchemformat.so(_ZN9OpenBabel18NWChemOutputFormat12ReadMoleculeEPNS_6OBBaseEPNS_12OBConversionE+0x1f0)[0x7fb50ca49890] /usr/lib64/libopenbabel.so.4(_ZN9OpenBabel16OBMoleculeFormat18ReadChemObjectImplEPNS_12OBConversionEPNS_8OBFormatE+0xd77)[0x7fb523225187] /usr/lib64/libopenbabel.so.4(_ZN9OpenBabel12OBConversion7ConvertEv+0x205)[0x7fb5231c8125] /usr/lib64/libopenbabel.so.4(_ZN9OpenBabel12OBConversion7ConvertEPSiPSo+0xb9)[0x7fb5231ce039] /usr/lib64/libopenbabel.so.4(_ZN9OpenBabel12OBConversion11FullConvertERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERS7_SA_+0x1edd)[0x7fb5231d003d] babel(main+0xb9e)[0x561c57211dbe] /usr/lib64/libc.so.6(__libc_start_main+0xf1)[0x7fb523505731] babel(_start+0x29)[0x561c57212489] Expected results: XYZ-matrix Additional info: I compiled code from source and GDB says: #11 0x00007ffff7701671 in OpenBabel::OBConversion::FullConvert (this=this@entry=0x7fffffffd9c0, FileList=std::vector of length 1, capacity 1 = {...}, OutputFileName="", OutputFileList=std::vector of length 0, capacity 0) at /home/madchem/openbabel-2.3.2/openbabel/src/obconversion.cpp:1486 1486 Count = Convert(pIs,pOs); (gdb) disp pOs 1: pOs = (std::ostream *) 0x0 (gdb) list 1481 } 1482 } 1483 } 1484 1485 //Single input and output files 1486 Count = Convert(pIs,pOs); 1487 1488 if(os && !os.is_open() && !OutputFileName.empty()) 1489 { 1490 //Output was written to temporary string stream. Output it to the file
I confirm that this bug is still present as of now, fc25, kernel 4.9.14, babel version 2.3.90. I also tested on Debian (in virtualbox), babel version 2.3.2 and it's working OK.
(In reply to Dmitry from comment #0) > I compiled code from source and GDB says: > #11 0x00007ffff7701671 in OpenBabel::OBConversion::FullConvert > (this=this@entry=0x7fffffffd9c0, FileList=std::vector of length 1, capacity > 1 = {...}, OutputFileName="", > OutputFileList=std::vector of length 0, capacity 0) at > /home/madchem/openbabel-2.3.2/openbabel/src/obconversion.cpp:1486 > 1486 Count = Convert(pIs,pOs); Note that this is totally unnecessary. You just need to # debuginfo-install openbabel-debuginfo after which you can run all debugging tools without problems. You didn't include the problematic output file in the report. Please try out the scratch build of the newer release at https://koji.fedoraproject.org/koji/taskinfo?taskID=18698475
(In reply to Susi Lehtola from comment #2) > (In reply to Dmitry from comment #0) > > I compiled code from source and GDB says: > > #11 0x00007ffff7701671 in OpenBabel::OBConversion::FullConvert > > (this=this@entry=0x7fffffffd9c0, FileList=std::vector of length 1, capacity > > 1 = {...}, OutputFileName="", > > OutputFileList=std::vector of length 0, capacity 0) at > > /home/madchem/openbabel-2.3.2/openbabel/src/obconversion.cpp:1486 > > 1486 Count = Convert(pIs,pOs); > > Note that this is totally unnecessary. You just need to > # debuginfo-install openbabel-debuginfo > after which you can run all debugging tools without problems. > > You didn't include the problematic output file in the report. Please try out > the scratch build of the newer release at > https://koji.fedoraproject.org/koji/taskinfo?taskID=18698475 Doesn't work for me. Same problem.
Created attachment 1268092 [details] NWChem output file babel -inwo naoh.out -oxyz must provide XYZ-matrix
Created attachment 1268093 [details] NWChem output file babel -inwo calc.nwo -oxyz must produce XYZ-matrix
Thanks for the test cases. I just checked that the last output is parsed properly with openbabel's development version. Unfortunately, as you checked before, the newest stable release, 2.4.1, still has this problem.
(In reply to Susi Lehtola from comment #6) > Thanks for the test cases. I just checked that the last output is parsed > properly with openbabel's development version. Unfortunately, as you checked > before, the newest stable release, 2.4.1, still has this problem. Yes, the development version works for me too. I guess the dev and stable version has a few changes, so you may push the new build to fedora-testing. Thank you for answer! :3
This message is a reminder that Fedora 24 is nearing its end of life. Approximately 2 (two) weeks from now Fedora will stop maintaining and issuing updates for Fedora 24. It is Fedora's policy to close all bug reports from releases that are no longer maintained. At that time this bug will be closed as EOL if it remains open with a Fedora 'version' of '24'. Package Maintainer: If you wish for this bug to remain open because you plan to fix it in a currently maintained version, simply change the 'version' to a later Fedora version. Thank you for reporting this issue and we are sorry that we were not able to fix it before Fedora 24 is end of life. If you would still like to see this bug fixed and are able to reproduce it against a later version of Fedora, you are encouraged change the 'version' to a later Fedora version prior this bug is closed as described in the policy above. Although we aim to fix as many bugs as possible during every release's lifetime, sometimes those efforts are overtaken by events. Often a more recent Fedora release includes newer upstream software that fixes bugs or makes them obsolete.
Bumping to rawhide where it still occurs. Sorry for not fixing this earlier. I'll see what I can do.
This bug appears to have been reported against 'rawhide' during the Fedora 27 development cycle. Changing version to '27'.
This message is a reminder that Fedora 27 is nearing its end of life. On 2018-Nov-30 Fedora will stop maintaining and issuing updates for Fedora 27. It is Fedora's policy to close all bug reports from releases that are no longer maintained. At that time this bug will be closed as EOL if it remains open with a Fedora 'version' of '27'. Package Maintainer: If you wish for this bug to remain open because you plan to fix it in a currently maintained version, simply change the 'version' to a later Fedora version. Thank you for reporting this issue and we are sorry that we were not able to fix it before Fedora 27 is end of life. If you would still like to see this bug fixed and are able to reproduce it against a later version of Fedora, you are encouraged change the 'version' to a later Fedora version prior this bug is closed as described in the policy above. Although we aim to fix as many bugs as possible during every release's lifetime, sometimes those efforts are overtaken by events. Often a more recent Fedora release includes newer upstream software that fixes bugs or makes them obsolete.
Fedora 27 changed to end-of-life (EOL) status on 2018-11-30. Fedora 27 is no longer maintained, which means that it will not receive any further security or bug fix updates. As a result we are closing this bug. If you can reproduce this bug against a currently maintained version of Fedora please feel free to reopen this bug against that version. If you are unable to reopen this bug, please file a new report against the current release. If you experience problems, please add a comment to this bug. Thank you for reporting this bug and we are sorry it could not be fixed.
FWIW, I cannot reproduce this on Fedora 29. Please file a new bug if it's reproducible on F28.