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

[Ran Friedman]

Hi Berk,

I've reconfigured and recompiled today, but I think this is due to older
modifications. I'm fighting with these issues for a week or so, and
until today was certain that there was something wrong in the structure
I was simulating.

I don't have 4.0.5 handy but with 4.0.2 everything works fine.

Thanks,
Ran.

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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>   


-- 
------------------------------------------------------
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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