[gmx-developers] Segfault during EM in recent git version

[Ran Friedman]

Hi Jochen,

IIRC I had a segfault also with MD on single precision, apparently
because of  large forces. This may be due to minimisation issues though.
Personally, I'm not using the git version until I understand what's
going on.

Best,
Ran

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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>
>


-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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