[gmx-developers] Segfault during EM in recent git version
hess at sbc.su.se
hess at sbc.su.se
Mon Oct 5 18:20:01 CEST 2009
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.
>
More information about the gromacs.org_gmx-developers
mailing list