[gmx-developers] Segfault during EM in recent git version
Berk Hess
hess at cbr.su.se
Mon Oct 5 17:11:56 CEST 2009
Did you use cut-off's?
New all-versus-all loops have been added for simulations without cut-off's.
Berk
Jochen Hub wrote:
> Hi Berk,
>
> yes, I have always reconfigured with distclean and everything. And
> checked that no CC variables or similar were messing up something. I
> could well imagine that the problem is again due to virtual sites
> which I have in my structure.
>
> In addition, I am getting LINCS warnings during EM with the 405 from a
> few weeks ago, but *not* related to the bug you fixed recently (with
> CGs with only vsites). These lincs warnings appear typically in
> lysines, somewhere between the last carbon and the NH3 in the lysine
> chain. Noteworthy, the warnings did not appear with steepest descent,
> but with conjugate gradient. Higher lincs-order did not help, but even
> increased the large changes in angles. For example:
>
> atom 1 atom 2 angle previous, current, constraint length
> 886 889 34.3 0.1583 0.1582 0.1583
> 886 890 33.8 0.1583 0.1580 0.1583
> 889 890 34.0 0.0802 0.0805 0.0802
> 1291 1294 33.8 0.1583 0.1578 0.1583
> 1291 1295 34.3 0.1583 0.1586 0.1583
> 1294 1295 32.3 0.0802 0.0803 0.0802
>
> where the respective atoms are:
> 886 amber99_11 55 LYP CE 822 -0.0143 14.026 ;
> qtot -3.006
> 887 amber99_28 55 LYP HE1 823 0.1135 0 ;
> qtot -2.893
> 888 amber99_28 55 LYP HE2 824 0.1135 0 ;
> qtot -2.779
> 889 MNH3 55 LYP MNZ1 825 0 8.517 ;
> qtot -2.779
> 890 MNH3 55 LYP MNZ2 825 0 8.517 ;
> qtot -2.779
> 891 amber99_39 55 LYP NZ 825 -0.3854 0 ;
> qtot -3.165
> 892 amber99_17 55 LYP HZ1 826 0.34 0 ;
> qtot -2.825
> 893 amber99_17 55 LYP HZ2 827 0.34 0 ;
> qtot -2.485
> 894 amber99_17 55 LYP HZ3 828 0.34 0 ;
> qtot -2.145
>
> The atoms around nr 1291 are also the tip of a lysine side chain.
> 1291 amber99_11 80 LYP CE 1189 -0.0143 14.026 ;
> qtot -4.006
> 1292 amber99_28 80 LYP HE1 1190 0.1135 0 ;
> qtot -3.893
> 1293 amber99_28 80 LYP HE2 1191 0.1135 0 ;
> qtot -3.779
> 1294 MNH3 80 LYP MNZ1 1192 0 8.517 ;
> qtot -3.779
> 1295 MNH3 80 LYP MNZ2 1192 0 8.517 ;
> qtot -3.779
> 1296 amber99_39 80 LYP NZ 1192 -0.3854 0 ;
> qtot -4.165
> 1297 amber99_17 80 LYP HZ1 1193 0.34 0 ;
> qtot -3.825
> 1298 amber99_17 80 LYP HZ2 1194 0.34 0 ;
> qtot -3.485
> 1299 amber99_17 80 LYP HZ3 1195 0.34 0 ;
> qtot -3.145
>
> Jochne
>
>
>
> Berk Hess wrote:
>> Hi,
>>
>> Did you try to rerun configure and recompile everything?
>> I just compared EM to an older version and got exactly the same results.
>>
>> Berk
>>
>> Jochen Hub wrote:
>>
>>> Hi Ran,
>>>
>>> did you also have these problems only during energy minimization? I
>>> asking since I want to use the present git for longer production runs?
>>>
>>> Best,
>>> Jochen
>>>
>>>
>>>
>>> Ran Friedman wrote:
>>>
>>>> Hi,
>>>>
>>>> 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.
>>>>
>>>> Ran.
>>>>
>>>> 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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