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gmx tools dump core for fatal errors - Redmine #1866

Archive from user: Viveca Lindahl

Recently I’ve been getting a core dump when a gmx tool exits with a fatal error, e.g. if I put a typo in my mdp file and run gmx gromp I’ve gotten it also e.g. for make_ndx. This is mostly an annoyance… but I guess it’s not what is supposed to happen. Here is an example backtrace:

#0 0x00007f654bffdcc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
56 ../nptl/sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0 0x00007f654bffdcc9 in __GI_raise (sig=sig@entry=6) at ../nptl/sysdeps/unix/sysv/linux/raise.c:56
#1 0x00007f654c0010d8 in __GI_abort () at abort.c:89
#2 0x0000000000701dcf in gmx_exit_on_fatal_error (exitType=ExitType_Abort, returnValue=1) at /data/viveca/gromacs/src/gromacs/utility/fatalerror.cpp:251
#3 0x0000000000701ea5 in gmx_fatal_mpi_va(int, const char , int, gmx_bool, gmx_bool, const char, typedef _va_list_tag_va_list_tag *) (file=0x1ccf698 “/data/viveca/gromacs/src/gromacs/gmxpreprocess/readir.cpp”, line=2640, bMaster=1, bFinalize=0,
fmt=0x1cd5fd0 “Group %s referenced in the .mdp file was not found in the index file.\nGroup names must match either [moleculetype] names or custom index group\nnames, in which case you must supply an index file to the”…, ap=0x7ffd5262d428) at /data/viveca/gromacs/src/gromacs/utility/fatalerror.cpp:270
#4 0x0000000000701f63 in gmx_fatal (f_errno=0, file=0x1ccf698 “/data/viveca/gromacs/src/gromacs/gmxpreprocess/readir.cpp”, line=2640,
fmt=0x1cd5fd0 “Group %s referenced in the .mdp file was not found in the index file.\nGroup names must match either [moleculetype] names or custom index group\nnames, in which case you must supply an index file to the”…) at /data/viveca/gromacs/src/gromacs/utility/fatalerror.cpp:277

(from redmine: issue id 1866, created on 2015-11-30 by gmxdefault, closed on 2016-05-14)

  • Changesets:
    • Revision 1c83c6c0 by Roland Schulz on 2016-05-13T17:53:59Z:
Don't use abort for fatal errors

Fixes #1866

Change-Id: I44330ef3769c684fbd0c8ffd7e8987d733006a67