Bugs item #3273062, was opened at 2011-04-03 22:42
Message generated for change (Tracker Item Submitted) made by jiahao
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Category: Command-line Tools
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jiahao Chen (jiahao)
Assigned to: Nobody/Anonymous (nobody)
Summary: Segmentation fault parsing empty Gaussian input file
Initial Comment:
Parsing an empty Gaussian output file causes a segmentation fault.
$ babel -ig03 emptyfile -oreport
Segmentation fault
Running babel in gdb produces the following output:
(gdb) run
Starting program: /home/cjh/local/bin/babel -ig03 1.gjf -oreport
[Thread debugging using libthread_db enabled]
Program received signal SIGSEGV, Segmentation fault.
__strlen_sse2 () at ../sysdeps/x86_64/multiarch/../strlen.S:31
31 ../sysdeps/x86_64/multiarch/../strlen.S: No such file or directory.
in ../sysdeps/x86_64/multiarch/../strlen.S
(gdb) bt
#0 __strlen_sse2 () at ../sysdeps/x86_64/multiarch/../strlen.S:31
#1 0x00007ffff6cfa5cc in std::string::operator+=(char const*) () from
/usr/lib/libstdc++.so.6
#2 0x00007fffed87e180 in OpenBabel::GaussianOutputFormat::ReadMolecule
(this=0x7fffeda97610, pOb=0x62f040, pConv=0x7fffffffd5a0)
at /home/cjh/local/src/openbabel/src/formats/gaussformat.cpp:324
#3 0x00007ffff770ec3c in OpenBabel::OBMoleculeFormat::ReadChemObjectImpl
(pConv=0x7fffffffd5a0, pFormat=0x7fffeda97610)
at /home/cjh/local/src/openbabel/src/obmolecformat.cpp:105
#4 0x00007ffff6389d97 in OpenBabel::OBMoleculeFormat::ReadChemObject
(this=0x7fffeda97610, pConv=0x7fffffffd5a0)
at /home/cjh/local/src/openbabel/include/openbabel/obmolecformat.h:114
#5 0x00007ffff76970af in OpenBabel::OBConversion::Convert
(this=0x7fffffffd5a0) at /home/cjh/local/src/openbabel/src/obconversion.cpp:485
#6 0x00007ffff7696d99 in OpenBabel::OBConversion::Convert
(this=0x7fffffffd5a0, is=0x7fffffffcdf0, os=0x0) at
/home/cjh/local/src/openbabel/src/obconversion.cpp:418
#7 0x00007ffff769af11 in OpenBabel::OBConversion::FullConvert
(this=0x7fffffffd5a0, FileList=..., OutputFileName=..., OutputFileList=...)
at /home/cjh/local/src/openbabel/src/obconversion.cpp:1378
#8 0x000000000040573e in main (argc=4, argv=0x7fffffffd8f8) at
/home/cjh/local/src/openbabel/tools/babel.cpp:347
This problem seems specific to the Gaussian file parser; for example, this
works fine
$ babel -igamin emptyfile -oreport
0 molecules converted
2 audit log messages
This problem occurs as of r4430 on ubuntu-10.04 x86_64.
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