How to solve Segmentation Fault (Core Dumped) Error in GROMACS?

User discussions
1

Dear all,

I have installed GPU GROMACS 2023 on two PCs, and one is working without errors. However, the other one gives a segmentation fault (core dumped) error during the gmx run. I launched Valgrind to check memory using the following command:

$ valgrind --leak-check=full --show-leak-kinds=all gmx mdrun -deffnm nvt -v

The results are provided in the attached text file.

Please give your valuable advice on how to solve this problem.

Sincerely,

Alisher
Valgrind_gmx.txt (919.0 KB)

2

When does the segmentation fault occur? Could you post the terminal output when you run the simulation?

3

NVT
NVT1920×1047 84.6 KB

Dear Sir,
Sorry for the late reply. The error occurred after energy minimization during NVT equilibration process.

Alisher

4

Before digging too deep into this, would you be able to test if it works in 2023.5 or 2024.3?

5

I will inform you after testing it during few days

6

Hi,
I installed gpu gromacs-2023.5 and the error occurred in the same place (The error occurred after energy minimization during NVT equilibration).
But, i can’t install gpu gromacs-2024.3 because CMake error.
CMakeError.log (8.7 KB)
CMakeOutput.log (134.1 KB)

7

Thanks. Could you make two separate issue reports at Issues · GROMACS / GROMACS · GitLab, please?

The first issue regarding the segmentation fault in 2023.5, explaining the problem and describing your system setup, preferably with input files, if you can provide that.

The second issue regarding the compilation errors you get with 2024.3.

Hopefully, someone can help you there or provide a bug fix.

8

Ok. Thank you Sir.

9

Hi,
Additionally, I tried this input file on another computer, and that computer also produced an error. Apparently, the problem is related to the input file