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

[Jochen Hub]

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.
>   


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