[gmx-users] Segmentation fault, core dumped error

[Neena Susan Eappen]

Hi Paul Bauer,

I do not have an account on redmine.gromacs.org neither that page allows me to create an account. Please let me know what to do.

Hi Najamuddin,

I tried xtc file instead of trr, still same error shows up.

Thank you,
Neena

________________________________
From: Neena Susan Eappen
Sent: Wednesday, May 29, 2019 5:25 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Segmentation fault, core dumped error


Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr

Specify 2 groups to analyze:

Group     0 (System) has   130 elements

Group     1 (Protein) has   130 elements

Group     2 (Protein-H) has    63 elements

Group     3 (C-alpha) has    11 elements

Group     4 (Backbone) has    34 elements

Group     5 (MainChain) has    47 elements

Group     6 (MainChain+Cb) has    58 elements

Group     7 (MainChain+H) has    58 elements

Group     8 (SideChain) has    72 elements

Group     9 (SideChain-H) has    16 elements


Select a group: 1 Selected 1: 'Protein'

Select a group: 1 Selected 1: 'Protein'

Output: Calculating hydrogen bonds in Protein (130 atoms)

Found 13 donors and 25 acceptors

trr version: GMX_trn_file (single precision)

Reading frame       0 time    0.000

Will do grid-seach on 2374x2374x2374 grid, rcut=0.35

Segmentation fault (core dumped)

________________________________
From: Neena Susan Eappen
Sent: Tuesday, May 28, 2019 11:31 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users,

Is there a reason why segmentation fault appeared when gmx hbond command was used?

Thank you,
Neena

________________________________
From: Neena Susan Eappen
Sent: Friday, May 24, 2019 12:40 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Segmentation fault, core dumped error

Hello gromacs users,

I got an error message when I used gmx hbond command: Segmentation fault, core dumped. Shown below is my gmx version details (if that can point to my problem). Any insight would be appreciated.

GROMACS version:        2018.4
Precision:      single
Memory model:   64 bit
MPI library:    thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:    disabled
SIMD instructions:      AVX2_256
FFT library:    fftw-3.3.8-sse2-avx-avx2-avx2_128-avx512
RDTSCP usage:   enabled
TNG support:    enabled
Hwloc support:  disabled
Tracing support:        disabled
Built on:       2019-01-12 0:35
Built by:       name at HP-PC [CMAKE]<mailto:name at HP-PC%20[CMAKE]>
Build OS/arch:  Linux 4.4.0-17134-Microsoft x86_64
Build CPU vendor:       Intel
Build CPU brand:        Intel(R) Core(TM) i3-5010U CPU @ 2.10GHz
Build CPU family:       6   Model: 61   Stepping: 4
Build CPU features:     aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler:     /usr/bin/cc GNU 7.3.0
C compiler flags:       march=core-AVX2     -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast
C++ compiler:   /usr/bin/c++ GNU 7.3.0
C++ compiler flags:     -march=core-avx2    -std=c++11   -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast

Thank you,
Neena