[gmx-users] segmentation fault

[Justin Lemkul]

On 7/19/15 8:32 PM, Sikandar Mashayak wrote:
> Hi,
>
> I am trying to simulate a confined water system with gromacs 5.0.5,
> however, I am getting the segmentation fault. Below are the gdb backtrace
> and the build info.
>

Without an .mdp file and description of what you've done so far, there's little 
to go on here.  Follow 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

>
> Thanks,
> Sikandar
>
> backtrace::
>
> #0  0x00007ffff767d8dd in _mm_loadu_pd (tab_coul_F=0x7fffe6217100,
> tab_coul_V=0x7fffe621b560, ti_S=..., ti=0x0, ctab0_S=0x7fffea947560,
>      ctab1_S=0x7fffea947550, ctabv_S=0x7fffea947510) at
> /usr/local/gcc-4.7.1/lib/gcc/x86_64-unknown-linux-gnu/4.7.1/include/emmintrin.h:113
> #1  load_table_f_v (tab_coul_F=0x7fffe6217100, tab_coul_V=0x7fffe621b560,
> ti_S=..., ti=0x0, ctab0_S=0x7fffea947560, ctab1_S=0x7fffea947550,
>      ctabv_S=0x7fffea947510) at
> /home/mashaya1/Apps/gromacs/source/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/../nbnxn_kernel_simd_utils_x86_128d.h:168
> #2  0x00007ffff7688e9b in nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn
> (nbl=0x7fffe5800920, nbat=0x7fffe6200a80, ic=0x7fffe6205f80,
> shift_vec=0x7a7de0,
>      f=0x7fffdde37010, fshift=0x7fffe6203740, Vvdw=0x7fffe6203be0,
> Vc=0x7fffe6203c70)
>      at
> /home/mashaya1/Apps/gromacs/source/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_inner.h:628
> #3  0x00007ffff77c760f in nbnxn_kernel_simd_4xn._omp_fn.0 ()
>      at
> /home/mashaya1/Apps/gromacs/source/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c:412
> #4  0x00007ffff304681a in gomp_thread_start (xdata=Unhandled dwarf
> expression opcode 0xf3
> ) at ../../../src/gcc-4.7.1/libgomp/team.c:116
> #5  0x00007ffff2c139d1 in start_thread () from /lib64/libpthread.so.0
> #6  0x00007ffff29608fd in clone () from /lib64/libc.so.6
>
>
> Version and built info.
>
> Gromacs version:    VERSION 5.0.5-20150513-33467fd
> GIT SHA1 hash:      33467fd9bc5f94d704b071f0193da0a6ff0ea19b
> Precision:          double
> Memory model:       64 bit
> MPI library:        MPI
> OpenMP support:     enabled
> GPU support:        disabled
> invsqrt routine:    gmx_software_invsqrt(x)
> SIMD instructions:  SSE4.1
> FFT library:        fftw-3.3.3-sse2
> RDTSCP usage:       enabled
> C++11 compilation:  enabled
> TNG support:        enabled
> Tracing support:    disabled
> Built on:           Sun Jul 19 19:24:25 CDT 2015
> Built by:           mashaya1 at taub189 [CMAKE]
> Build OS/arch:      Linux 2.6.32-504.16.2.el6.x86_64 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:    Intel(R) Xeon(R) CPU           X5650  @ 2.67GHz
> Build CPU family:   6   Model: 44   Stepping: 2
> Build CPU features: aes apic clfsh cmov cx8 cx16 htt lahf_lm mmx msr
> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 sse3 sse4.1
> sse4.2 ssse3
> C compiler:         /usr/local/mpi/openmpi-1.6.5-gcc-4.7.1/bin/mpicc GNU
> 4.7.1
> C compiler flags:    -msse4.1    -Wno-maybe-uninitialized -Wextra
> -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall
> -Wno-unused -Wunused-value -Wunused-parameter  -g -fno-inline
> C++ compiler:       /usr/local/mpi/openmpi-1.6.5-gcc-4.7.1/bin/mpicxx GNU
> 4.7.1
> C++ compiler flags:  -msse4.1   -std=c++0x  -Wextra
> -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function
> -g -fno-inline
> Boost version:      1.51.0 (external)
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================