[gmx-developers] Segfault during EM in recent git version
Jochen Hub
jochen at xray.bmc.uu.se
Mon Oct 5 17:05:36 CEST 2009
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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