[gmx-developers] Segfault during EM in recent git version
Jochen Hub
jochen at xray.bmc.uu.se
Mon Oct 5 17:20:47 CEST 2009
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
> 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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>>>>
>>>>
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--
---------------------------------------------------
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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