[gmx-users] problem with REMD

[Justin Lemkul]

On Sat, Apr 6, 2013 at 7:17 AM, Shine A <shine.a at iisertvm.ac.in> wrote:

> Respected Sir,
>
>                      Now I am trying an REMD simulation on a peptide in
> cluster. The command line I used as follows
>
>         mpirun -np 6 /usr/local/gromacs/bin/mdrun_mpi -s sd_.tpr -multi 2
> -replex 1000 -reseed 175320
>
> But this command line getting error like this
>
> Wrote pdb files with previous and current coordinates
> [lilavati:27635] *** Process received signal ***
> [lilavati:27635] Signal: Segmentation fault (11)
> [lilavati:27635] Signal code: Address not mapped (1)
> [lilavati:27635] Failing at address: 0x2aaab438b8a8
> [lilavati:27635] [ 0] /lib64/libpthread.so.0 [0x357c00e4c0]
> [lilavati:27635] [ 1]
> /usr/local/gromacs/lib/libmd_mpi_d.so.6(gb_bonds_tab+0x246)
> [0x2b8f12dc1eb6]
> [lilavati:27635] [ 2]
> /usr/local/gromacs/lib/libmd_mpi_d.so.6(calc_gb_forces+0x110)
> [0x2b8f12dc18f0]
> [lilavati:27635] [ 3]
> /usr/local/gromacs/lib/libmd_mpi_d.so.6(do_force_lowlevel+0x5b5)
> [0x2b8f12d92ab5]
> [lilavati:27635] [ 4]
> /usr/local/gromacs/lib/libmd_mpi_d.so.6(do_force+0xd82) [0x2b8f12df2622]
> [lilavati:27635] [ 5] /usr/local/gromacs/bin/mdrun_mpi(do_md+0x5913)
> [0x41cbb3]
> [lilavati:27635] [ 6] /usr/local/gromacs/bin/mdrun_mpi(mdrunner+0x12ae)
> [0x41704e]
> [lilavati:27635] [ 7] /usr/local/gromacs/bin/mdrun_mpi(main+0xb4d)
> [0x41da8d]
> [lilavati:27635] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
> [0x357b41d974]
> [lilavati:27635] [ 9] /usr/local/gromacs/bin/mdrun_mpi(do_cg+0x191)
> [0x407d79]
> [lilavati:27635] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 27635 on node lilavati exited
> on signal 11 (Segmentation fault).
> --------------------------------------------------------------------------
>
>
> Why this error coming here?Can you give a solution for this? Thanks in
> advance
>

http://www.gromacs.org/Documentation/Terminology/Blowing_Up

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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