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

Jochen Hub jochen at xray.bmc.uu.se
Mon Oct 5 14:49:05 CEST 2009


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 
#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 
#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 

Any suggestions?

Thanks a lot,


Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755

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