[gmx-developers] Segfault during EM in recent git version
Berk Hess
hess at cbr.su.se
Mon Oct 5 17:21:46 CEST 2009
Jochen Hub wrote:
> Berk Hess wrote:
>> Did you use cut-off's?
>> New all-versus-all loops have been added for simulations without
>> cut-off's.
>>
>
> Yes, for both coulomb and vdw:
>
> coulombtype = Cut-off
> vdw-type = Cut-off
>
> Jochen
Sorry, maybe my question was a but unclear.
Do you have finite cut-off lengths, or do you have pbc=no and cut-off's
set to 0 (infinity).
Berk
>
>> 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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