[gmx-users] segmentation fault

[Sikandar Mashayak]

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.


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)