[gmx-users] Segmentation fault, core dumped error

Paul bauer paul.bauer.q at gmail.com
Wed May 29 12:15:58 CEST 2019


can you please open a new issue on redmine.gromacs.org for this, and 
upload your input files (if possible) and the command line you used that 
caused the error?



On 29/05/2019 01:31, Neena Susan Eappen wrote:
> 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

Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab

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