[gmx-developers] Segfault during EM in recent git version
Jochen Hub
jochen at xray.bmc.uu.se
Tue Oct 6 12:33:59 CEST 2009
Hi,
this fixes the Segfault, thanks! However, there are still LINCS warnings
in the lysines, and sometimes also at isoleucines and at the OH-group of
Tyr. Typically after 20-40 EM steps which look fine according to the
decreasing Fmax etc. They always appear if the the cases with C in one
cg, and the 2 heavy vsites plus one vsite (such as N) together in one cg:
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
Where the warning looks like that:
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1291 1294 36.8 0.1583 0.1576 0.1583 -> C--MNH3
1291 1295 37.6 0.1583 0.1587 0.1583 -> C--MNH3
1294 1295 35.4 0.0802 0.0805 0.0802 -> MNH3-MNH3
Cheers,
Jochen
hess at sbc.su.se wrote:
> Ah, this is in the vsite fix I made for the bug you
> reported previously.
> This code is quite obviously incorrect.
> But I realize now it can be done simpler.
> if (atom[a].ptype != eptVSite || pbc_set[a]) {
> can be replaced by
> if (pbc_set[a]) {
>
> This will certainly solve your last crash.
> Just to be sure, could you check that this still fixes
> the bug you reported previously?
>
> Berk
>
>
>
>> Sorry, here a few more details:
>>
>> (gdb) list
>> 1498 }
>> 1499 if (vsite_pbc_f[vsi] == -1) {
>> 1500 /* Check if this is the first processed atom of a
>> vsite only cg */
>> 1501 bViteOnlyCG_and_FirstAtom = TRUE;
>> 1502 for(a=cgs->index[cg_v]; a<cgs->index[cg_v+1]; a++) {
>> 1503 if (atom[a].ptype != eptVSite || pbc_set[a]) {
>> 1504 bViteOnlyCG_and_FirstAtom = FALSE;
>> 1505 break;
>> 1506 }
>> 1507 }
>>
>> The problem is that the atom[a=0] is not defined.
>>
>> Jochen
>>
>>
>>
>> Berk Hess wrote:
>>
>>> 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
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> gmx-developers mailing list
>>>>>>>>> gmx-developers at gromacs.org
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>>> interface or send it to gmx-developers-request at gromacs.org.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> gmx-developers mailing list
>>>>>>> gmx-developers at gromacs.org
>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>>>> interface or send it to gmx-developers-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> gmx-developers mailing list
>>>>> gmx-developers at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>>> interface or send it to gmx-developers-request at gromacs.org.
>>>>>
>>>>>
>>>>>
>>> _______________________________________________
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-developers-request at gromacs.org.
>>>
>>>
>> --
>> ---------------------------------------------------
>> 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
>> ---------------------------------------------------
>>
>> _______________________________________________
>> gmx-developers mailing list
>> gmx-developers at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-developers-request at gromacs.org.
>>
>>
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>
--
---------------------------------------------------
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
---------------------------------------------------
More information about the gromacs.org_gmx-developers
mailing list