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malloc crash when building crystal supercell #824

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drew-parsons opened this issue Feb 22, 2022 · 3 comments
Closed

malloc crash when building crystal supercell #824

drew-parsons opened this issue Feb 22, 2022 · 3 comments

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@drew-parsons
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Avogadro version:

  • Avogadrolibs: 1.95.1
  • Qt: 5.15.2

Desktop version:

  • OS: Linux (Debian unstable)
  • Version linux 5.16.7-2
  • Compiler gcc 11.2.0

Describe the bug

I'm reading a pdb file of a DNA or protein fragment and trying to extend the crystal to a supercell (the aim is to extend along the longitudinal axis to get a sense of the DNA helix).

But after pressing OK in the "Build Supercell" dialog box (e.g. after selecting 2×2x2), avogadro crashes, writing to stderr

free(): invalid pointer
Aborted

To Reproduce
Steps to reproduce the behavior:

  1. Open a pdb file, e.g. 2ztb.pdb from https://www.rcsb.org/structure/2ZTB
  2. Go to 'Crystal→Build Supercell'
  3. Select '2' for A, B and C repeat.
  4. Click 'OK'
  5. See error

Expected behavior

The fragment (unit cell) should be shown repeated according to the chosen supercell.

Backtrace

Running in gdb gets a backtrace:

$ gdb avogadro2
GNU gdb (Debian 10.1-2) 10.1.90.20210103-git
...
(gdb) run 2ztb.pdb
Starting program: /usr/bin/avogadro2 2ztb.pdb
...
Open Babel formats ready:  145
[New Thread 0x7fffb23fd640 (LWP 2288197)]
[New Thread 0x7fffb0e98640 (LWP 2288198)]
[Thread 0x7fffb23fd640 (LWP 2288197) exited]
free(): invalid pointer

Thread 1 "avogadro2" received signal SIGABRT, Aborted.
__GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:49
49	../sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0  __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:49
#1  0x00007ffff6290546 in __GI_abort () at abort.c:79
#2  0x00007ffff62e7eb8 in __libc_message (action=action@entry=do_abort, fmt=fmt@entry=0x7ffff6405a78 "%s\n") at ../sysdeps/posix/libc_fatal.c:155
#3  0x00007ffff62ef91a in malloc_printerr (str=str@entry=0x7ffff640374e "free(): invalid pointer") at malloc.c:5628
#4  0x00007ffff62f0cf4 in _int_free (av=<optimized out>, p=<optimized out>, have_lock=0) at malloc.c:4398
#5  0x00007ffff62f49b4 in __GI___libc_free (mem=<optimized out>) at malloc.c:3309
#6  0x00007ffff7dd9d21 in __gnu_cxx::new_allocator<unsigned long>::deallocate(unsigned long*, unsigned long) (__t=<optimized out>, __p=0x5555569465e0, this=0x555556936bf8) at /usr/include/c++/11/ext/new_allocator.h:132
#7  std::allocator_traits<std::allocator<unsigned long> >::deallocate(std::allocator<unsigned long>&, unsigned long*, unsigned long) (__n=<optimized out>, __p=0x5555569465e0, __a=...) at /usr/include/c++/11/bits/alloc_traits.h:492
#8  std::_Vector_base<unsigned long, std::allocator<unsigned long> >::_M_deallocate(unsigned long*, unsigned long) (__n=<optimized out>, __p=0x5555569465e0, this=0x555556936bf8) at /usr/include/c++/11/bits/stl_vector.h:354
#9  std::vector<unsigned long, std::allocator<unsigned long> >::_M_realloc_insert<unsigned long const&>(__gnu_cxx::__normal_iterator<unsigned long*, std::vector<unsigned long, std::allocator<unsigned long> > >, unsigned long const&)
    (this=0x555556936bf8, __position=283446366765517) at /usr/include/c++/11/bits/vector.tcc:500
#10 0x00007ffff7cee8a7 in std::vector<unsigned long, std::allocator<unsigned long> >::push_back(unsigned long const&) (__x=@0x7fffffffcc40: 8192, this=<optimized out>) at /usr/include/c++/11/bits/stl_vector.h:1198
#11 Avogadro::Core::Array<unsigned long>::push_back(unsigned long const&) (v=@0x7fffffffcc40: 8192, this=<optimized out>) at ./avogadro/core/array.h:250
#12 Avogadro::QtGui::Molecule::addAtom(unsigned char) (this=0x7fffffffce90, number=<optimized out>) at ./avogadro/qtgui/molecule.cpp:80
#13 0x00007ffff6da8314 in Avogadro::Core::CrystalTools::buildSupercell(Avogadro::Core::Molecule&, unsigned int, unsigned int, unsigned int) (molecule=..., a=a@entry=2, b=b@entry=2, c=c@entry=2) at /usr/include/c++/11/bits/stl_vector.h:1043
#14 0x00007ffff7d05c41 in Avogadro::QtGui::RWMolecule::buildSupercell(unsigned int, unsigned int, unsigned int) (this=0x555555c960d0, a=a@entry=2, b=b@entry=2, c=c@entry=2) at ./avogadro/qtgui/rwmolecule.cpp:520
#15 0x00007ffff7dcd0e4 in Avogadro::QtPlugins::SupercellDialog::buildSupercell(Avogadro::QtGui::Molecule&) (this=this@entry=0x7fffffffd0f0, mol=...) at ./avogadro/qtplugins/crystal/supercelldialog.cpp:58
#16 0x00007ffff7dcb944 in Avogadro::QtPlugins::Crystal::buildSupercell() (this=0x555555896a30) at ./avogadro/qtplugins/crystal/crystal.cpp:200
#17 0x00007ffff69351b8 in  () at /lib/x86_64-linux-gnu/libQt5Core.so.5
#18 0x00007ffff7734dc2 in QAction::triggered(bool) () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#19 0x00007ffff77379f4 in QAction::activate(QAction::ActionEvent) () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#20 0x00007ffff78bcf22 in  () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#21 0x00007ffff78c4a01 in  () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#22 0x00007ffff777d4be in QWidget::event(QEvent*) () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#23 0x00007ffff773b6bf in QApplicationPrivate::notify_helper(QObject*, QEvent*) () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#24 0x00007ffff77431c4 in QApplication::notify(QObject*, QEvent*) () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#25 0x00007ffff68feb1a in QCoreApplication::notifyInternal2(QObject*, QEvent*) () at /lib/x86_64-linux-gnu/libQt5Core.so.5
#26 0x00007ffff7741cd3 in QApplicationPrivate::sendMouseEvent(QWidget*, QMouseEvent*, QWidget*, QWidget*, QWidget**, QPointer<QWidget>&, bool, bool) () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#27 0x00007ffff7797093 in  () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#28 0x00007ffff77997f5 in  () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#29 0x00007ffff773b6bf in QApplicationPrivate::notify_helper(QObject*, QEvent*) () at /lib/x86_64-linux-gnu/libQt5Widgets.so.5
#30 0x00007ffff68feb1a in QCoreApplication::notifyInternal2(QObject*, QEvent*) () at /lib/x86_64-linux-gnu/libQt5Core.so.5
#31 0x00007ffff7045f77 in QGuiApplicationPrivate::processMouseEvent(QWindowSystemInterfacePrivate::MouseEvent*) () at /lib/x86_64-linux-gnu/libQt5Gui.so.5
#32 0x00007ffff701c1bc in QWindowSystemInterface::sendWindowSystemEvents(QFlags<QEventLoop::ProcessEventsFlag>) () at /lib/x86_64-linux-gnu/libQt5Gui.so.5
#33 0x00007ffff1b6157a in  () at /lib/x86_64-linux-gnu/libQt5XcbQpa.so.5
#34 0x00007ffff511fcdb in g_main_context_dispatch () at /lib/x86_64-linux-gnu/libglib-2.0.so.0
#35 0x00007ffff511ff88 in  () at /lib/x86_64-linux-gnu/libglib-2.0.so.0
#36 0x00007ffff512003f in g_main_context_iteration () at /lib/x86_64-linux-gnu/libglib-2.0.so.0
#37 0x00007ffff6956154 in QEventDispatcherGlib::processEvents(QFlags<QEventLoop::ProcessEventsFlag>) () at /lib/x86_64-linux-gnu/libQt5Core.so.5
#38 0x00007ffff68fd52b in QEventLoop::exec(QFlags<QEventLoop::ProcessEventsFlag>) () at /lib/x86_64-linux-gnu/libQt5Core.so.5
#39 0x00007ffff6905800 in QCoreApplication::exec() () at /lib/x86_64-linux-gnu/libQt5Core.so.5
#40 0x000055555556b9e6 in main(int, char**) (argc=<optimized out>, argv=<optimized out>) at ./avogadro/avogadro.cpp:183

Additional context

The SIGABRT is reproducible also for other pdb examples at https://www.rcsb.org/, but sometimes with a slightly different error message

malloc(): unsorted double linked list corrupted
@ghutchis
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I'm pretty sure I know where this one is - it derives from the new layer code. I should have some time on Thursday to push a fix.

Is there a deadline for Ubuntu LTS?

@drew-parsons
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Next Ubuntu LTS release is in April, but Ubuntu 22.04 Feature Freeze: Thursday, Feb 24, 2022 . So probably too late already but can try.

@drew-parsons
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Since it's definitely a bug fix, we can probably get it approved during the feature freeze period, https://wiki.ubuntu.com/FeatureFreeze

ghutchis added a commit to ghutchis/avogadrolibs that referenced this issue Apr 28, 2022
@ghutchis
WIP to find the memory bug involved in OpenChemistry#824
b088d23 
Right now, this reverts OpenChemistry#806 but there's still some sort
of memory corruption when assigning one molecule to another

Also, it seems like File -> Import Crystal adds atoms that
don't have layer information

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>
@ghutchis ghutchis mentioned this issue Apr 29, 2022
Merged
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@ghutchis @drew-parsons