[gmx-developers] Segfault during EM in recent git version
Jochen Hub
jochen at xray.bmc.uu.se
Mon Oct 5 17:41:08 CEST 2009
Ok, here's the bad memory access:
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_PROTECTION_FAILURE at address: 0x00000014
0x000a7c6a in get_vsite_pbc (iparams=0x3ca000, ilist=0x81f21c, atom=0x0,
md=0x403400, cgs=0x81f694, a2cg=0x163f000) at vsite.c:1503
1503 if (atom[a].ptype != eptVSite || pbc_set[a]) {
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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
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>>>>>>>
>>>>>>
>>>>>>
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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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