[gmx-developers] Segfault during EM in recent git version

Ran Friedman r.friedman at bioc.uzh.ch
Mon Oct 5 15:03:22 CEST 2009


I'm fighting these issues as well.

With the new git version I either get a segfault or really unrealistic
structures. For example, I saw that a hydrogen bound to nitrogen near a
C-terminal carboxylate group was located at the same place of a
carboxylate oxygen (!) following minimisation. As this happened in more
than one structure I guess something is broken. It's as if minimisation
doesn't take the LJ parameters into account.


Jochen Hub wrote:
> Hi,
> mdrun of the present git version stops during energy minimization in
> Segfaul/Bus error on my Mac. Gromacs 405 from a few weeks ago works
> fine with the same tpr and the same configure options. gdb reports
> some error in the assembly loops, I am not sure what the error means
> however:
> gcc version 4.0.1 (Apple Inc. build 5490)
> -------------------------------------------
> Program received signal EXC_BAD_INSTRUCTION, Illegal instruction/operand.
> _nb_kernel_ia32_3dnow_test_asm () at nb_kernel_ia32_3dnow_test_asm.s:23
> 23      nb_kernel_ia32_3dnow_test_asm.s: No such file or directory.
>        in nb_kernel_ia32_3dnow_test_asm.s
> (gdb) bt
> #0  _nb_kernel_ia32_3dnow_test_asm () at
> nb_kernel_ia32_3dnow_test_asm.s:23
> #1  0x002682a0 in nb_kernel_ia32_3dnow_test (log=0xa08834c0) at
> nb_kernel_ia32_3dnow.c:186
> #2  0x0026831f in nb_kernel_setup_ia32_3dnow (log=0xa08834c0,
> list=0x804200) at nb_kernel_ia32_3dnow.c:212
> #3  0x00268bb2 in gmx_setup_kernels (fplog=0xa08834c0) at nonbonded.c:248
> #4  0x00057899 in init_forcerec (fp=0xa08834c0, fr=0x81d000,
> fcd=0x503130, ir=0x801a00, mtop=0x501860, cr=0x500330, box=0xbfffd76c,
> bMolEpot=0, tabfn=0x500590 "table.xvg", tabpfn=0x5005b0 "tablep.xvg",
> tabbfn=0x5005d0 "table.xvg", bNoSolvOpt=0, print_force=-1) at
> force.c:1436
> #5  0x00012529 in mdrunner (fplog=0xa08834c0, cr=0x500330, nfile=27,
> fnm=0x2a06c0, bVerbose=1, bCompact=1, ddxyz=0xbfffe8e0,
> dd_node_order=1, rdd=0, rconstr=0, dddlb_opt=0x2801b1 "auto",
> dlb_scale=0.800000012, ddcsx=0x0, ddcsy=0x0, ddcsz=0x0, nstepout=100,
> ed=0x0, repl_ex_nst=0, repl_ex_seed=-1, pforce=-1, cpt_period=15,
> max_hours=-1, Flags=7168) at md.c:305
> #6  0x00018ce0 in main (argc=6, argv=0xbfffe94c) at mdrun.c:496
> Current language:  auto; currently asm
> Newer gccs (4.2 or 4.4) did not help. Compiling in 64bit did not help
> either.
> Any suggestions?
> Thanks a lot,
> Jochen

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