Segmentation fault - core dumped

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1

GROMACS version: 2023.1
GROMACS modification: Yes/No

I am currently trying the Martini M3 tutorial (M3-tutorials), which basically starts with the a CG simulation of a soluble protein. I have done everything according to the tutorial, but when i want to perform a simple energy minimization i get following error:

gmx mdrun -deffnm minimization-vac -v
:-) GROMACS - gmx mdrun, 2023.1 (-:

Executable: /usr/local/bin/gmx
Data prefix: /usr/local
Working dir: /home/qoraj/Documents/CG_simulations/tutorial_protein_part1/tutorial_2/template/tut1
Command line:
gmx mdrun -deffnm minimization-vac -v

Back Off! I just backed up minimization-vac.log to ./#minimization-vac.log.2#
Reading file minimization-vac.tpr, VERSION 2023.1 (single precision)
Update groups can not be used for this system because an incompatible virtual site type is used

Using 1 MPI thread
Using 8 OpenMP threads

Segmentation fault (core dumped)

Does anybody have experience with this kind of problem? I am by far no expert in this field and i am not really familiar with “virtual sites”. I also downloaded the “worked” tutorial and the files i generated match the “worked” files and also when i try to simulate the “worked” files with my setup i get the same error so i guess it has something to do with my setup?? Maybe my gromacs version? Has anybody experiences with a similar problem?

2

Hi!

Update groups can not be used for this system because an incompatible virtual site type is used

It is nothing to worry about, that’s a just an information message. Update groups are needed for some performance-relevant features, but there’s nothing you can do here, since it’s just how the system is set up.

The segmentation fault, though, is definitely indicative of some bug in GROMACS.

I also downloaded the “worked” tutorial and the files i generated match the “worked” files and also when i try to simulate the “worked” files with my setup i get the same error so i guess it has something to do with my setup??

Could you share what exactly you downloaded? Or your input files?

Maybe my gromacs version?

Please share the output of gmx -version. There’s unlikely something wrong with your GROMACS version per se, but the bug you’re encountering might be version/build specific, so the full version info will be helpful.

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Hey @al42and thanks for the fast reply :)

At this website: 3: Proteins - Part I: Basic and Martinize 2 there is a link in the beginning “The files required for this tutorial (including worked files) can be downloaded from [here.]”. I used that link to download the file and the given tutorial for the simulation.

Today i tried the same on another computer and there everything worked fine so it is most likely a software issue? I wanted to try the tutorial on my own computer, which should be possible i guess since it is a small system to simulate?

Thank you very much for help!

My gromacs version (quick and dirty installation):


gmx --version
                         :-) GROMACS - gmx, 2023.1 (-:

Executable:   /usr/local/bin/gmx
Data prefix:  /usr/local
Working dir:  /home/qoraj/Documents/CG_simulations/tutorial_protein_part1 (1)/tutorial_2/martini3_worked/test
Command line:
  gmx --version

GROMACS version:    2023.1
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support:        disabled
SIMD instructions:  AVX2_256
CPU FFT library:    fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library:    none
Multi-GPU FFT:      none
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 11.3.0
C compiler flags:   -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 11.3.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp 
BLAS library:       Internal
LAPACK library:     Internal

And i will upload my used input files and the .log file.

Thank you already!!

minimization-vac.log (13.2 KB)

4

Hi! Thank you, I can reproduce your bug. We will look into it.

5

Thank you very much!

Would it make sense to install an slightly older version of gromacs and try the simulations with that version?

6

Yes, if you can test with an older version, that would be nice. I suspect 2022.5 might work, but had not had time to check it myself.

7

Hello there,

So i used gromacs 2022.5 now and it works fine. Did you manage to find out what the problem with gromacs 2023.1 is/was?

Kind regards

8

Hi! We’re still looking into it. The bug is filed at SegFault in MARTINI minimization (#4814) · Issues · GROMACS / GROMACS · GitLab, if you’re interested

1 Like
9

Hi. The problem will be fixed in the upcoming 2023.3 release.