While running ptraj (AmberTools 1.5) on simulation data produced by
Amber 11 recently we found that it would reliably crash on one
particular .mdcrd file with glibc throwing an "invalid pointer" error in
free().
After running ptraj in valgrind, it appears that bufferToXYZ() is
trashing some memory out of its buffer[1]. Any ideas what might be
causing this?
The system is x86_64 running Ubuntu 11.04 with gcc 4.5.2.
Cheers,
- Ben
[1] Valgrind errors,
==10858== Invalid write of size 8
==10858== at 0x42C8B8: bufferToXYZ (trajectory.c:2471)
==10858== by 0x44CC69: ptrajProcessInputCoordinates (ptraj.c:4048)
==10858== by 0x453CE9: ptrajProcessTrajectoryFiles (ptraj.c:6954)
==10858== by 0x454CFA: ptraj (ptraj.c:7401)
==10858== by 0x439344: interface (interface.c:92)
==10858== by 0x40287F: main (main.c:218)
==10858== Address 0x65fc898 is 0 bytes after a block of size 619,688 alloc'd
==10858== at 0x4C28FAC: malloc (vg_replace_malloc.c:236)
==10858== by 0x422E01: safe_malloc (utility.c:172)
==10858== by 0x454C46: ptraj (ptraj.c:7391)
==10858== by 0x439344: interface (interface.c:92)
==10858== by 0x40287F: main (main.c:218)
==10858==
==10858== Invalid write of size 8
==10858== at 0x42C8E7: bufferToXYZ (trajectory.c:2474)
==10858== by 0x44CC69: ptrajProcessInputCoordinates (ptraj.c:4048)
==10858== by 0x453CE9: ptrajProcessTrajectoryFiles (ptraj.c:6954)
==10858== by 0x454CFA: ptraj (ptraj.c:7401)
==10858== by 0x439344: interface (interface.c:92)
==10858== by 0x40287F: main (main.c:218)
==10858== Address 0x94257f8 is 0 bytes after a block of size 619,688 alloc'd
==10858== at 0x4C28FAC: malloc (vg_replace_malloc.c:236)
==10858== by 0x422E01: safe_malloc (utility.c:172)
==10858== by 0x454C61: ptraj (ptraj.c:7392)
==10858== by 0x439344: interface (interface.c:92)
==10858== by 0x40287F: main (main.c:218)
==10858==
==10858== Invalid write of size 8
==10858== at 0x42C916: bufferToXYZ (trajectory.c:2477)
==10858== by 0x44CC69: ptrajProcessInputCoordinates (ptraj.c:4048)
==10858== by 0x453CE9: ptrajProcessTrajectoryFiles (ptraj.c:6954)
==10858== by 0x454CFA: ptraj (ptraj.c:7401)
==10858== by 0x439344: interface (interface.c:92)
==10858== by 0x40287F: main (main.c:218)
==10858== Address 0x6693d88 is 0 bytes after a block of size 619,688 alloc'd
==10858== at 0x4C28FAC: malloc (vg_replace_malloc.c:236)
==10858== by 0x422E01: safe_malloc (utility.c:172)
==10858== by 0x454C7C: ptraj (ptraj.c:7393)
==10858== by 0x439344: interface (interface.c:92)
==10858== by 0x40287F: main (main.c:218)
==10858==
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Received on Tue Aug 23 2011 - 13:30:05 PDT
