Bugs item #3347962, was opened at 2011-06-30 19:19
Message generated for change (Tracker Item Submitted) made by jiahao
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Category: Command-line Tools
Group: 2.3.x
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Jiahao Chen (jiahao)
Assigned to: Nobody/Anonymous (nobody)
Summary: babel hang during file conversion
Initial Comment:
The head version of OB hangs while parsing a file for file conversions. I have
tried several file formats (xyz, mopout and qcout) and they all hang in the
same place in the main loop of the file parser.
$ gdb babel
Reading symbols from /home/cjh/local/bin/babel...done.
(gdb) set args -ixyz -oreport geom.xyz
(gdb) run
Starting program: /home/cjh/local/bin/babel -ixyz -oreport geom.xyz
[Thread debugging using libthread_db enabled]
^C
Program received signal SIGINT, Interrupt.
0x00007ffff7b324a0 in __read_nocancel () at
../sysdeps/unix/syscall-template.S:82
82 ../sysdeps/unix/syscall-template.S: No such file or directory.
in ../sysdeps/unix/syscall-template.S
(gdb) bt
#0 0x00007ffff7b324a0 in __read_nocancel () at
../sysdeps/unix/syscall-template.S:82
#1 0x00007ffff7acd348 in _IO_new_file_underflow (fp=0x7ffff7dd76a0) at
fileops.c:606
#2 0x00007ffff7aceeee in _IO_default_uflow (fp=0x0) at genops.c:440
#3 0x00007ffff7ac5c7b in _IO_getc (fp=0x7ffff7dd76a0) at getc.c:41
#4 0x00007ffff6cecadd in __gnu_cxx::stdio_sync_filebuf<char,
std::char_traits<char> >::uflow() () from /usr/lib/libstdc++.so.6
#5 0x00007ffff6cd2d90 in std::istream::get() () from /usr/lib/libstdc++.so.6
#6 0x00007ffff769ec89 in zlib_stream::basic_unzip_streambuf<char,
std::char_traits<char> >::check_header (this=0x674cc0)
at /home/cjh/local/src/openbabel/src/zipstreamimpl.h:819
#7 0x00007ffff769d8f8 in basic_zip_istream (this=0x674cc0, istream=...,
window_size=-15, read_buffer_size=4096,
input_buffer_size=4096, __in_chrg=<value optimized out>, __vtt_parm=<value
optimized out>)
at /home/cjh/local/src/openbabel/src/zipstreamimpl.h:744
#8 0x00007ffff7696ef4 in OpenBabel::OBConversion::Convert
(this=0x7fffffffd570, is=0x0, os=0x7fffffffd1d0)
at /home/cjh/local/src/openbabel/src/obconversion.cpp:421
#9 0x00007ffff769b16f in OpenBabel::OBConversion::FullConvert
(this=0x7fffffffd570, FileList=..., OutputFileName=...,
OutputFileList=...) at
/home/cjh/local/src/openbabel/src/obconversion.cpp:1410
#10 0x000000000040573e in main (argc=4, argv=0x7fffffffd8c8) at
/home/cjh/local/src/openbabel/tools/babel.cpp:347
>From the trace it seems that something is going on with the zlib interface,
>but clearing the ZLIB related variables in cmake and setting -D
>DISABLE_WRITE_COMPRESSION in CPPFLAGS did not appear to solve the problem.
This problem occurs as of r4519 on ubuntu-10.04 x86_64, compiled with Debug
settings.
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