Program: gmx mdrun, version 2023.2
Source file: src/gromacs/mdrun/md.cpp (line 436)
Function: gmx::LegacySimulator::do_md()::<lambda()>
I am running gmx_mpi on a large system and got this error.
starting mdrun 'MergedSystem'
1000000 steps, 250.0 ps.
[nas-Precision-7820-Tower:274624] *** Process received signal ***
[nas-Precision-7820-Tower:274624] Signal: Segmentation fault (11)
[nas-Precision-7820-Tower:274624] Signal code: Address not mapped (1)
[nas-Precision-7820-Tower:274624] Failing at address: 0x55b7fddc97c4
[nas-Precision-7820-Tower:274624] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f4d95a42520]
[nas-Precision-7820-Tower:274624] [ 1] /home/nas/Desktop/gromacs-2023.2/build/bin/../lib/libgromacs_mpi.so.8(+0xc5c478)[0x7f4d96e5c478]
[nas-Precision-7820-Tower:274624] [ 2] /lib/x86_64-linux-gnu/libgomp.so.1(+0x1dc0e)[0x7f4d960ecc0e]
[nas-Precision-7820-Tower:274624] [ 3] /lib/x86_64-linux-gnu/libc.so.6(+0x94ac3)[0x7f4d95a94ac3]
[nas-Precision-7820-Tower:274624] [ 4] /lib/x86_64-linux-gnu/libc.so.6(+0x126a40)[0x7f4d95b26a40]
[nas-Precision-7820-Tower:274624] *** End of error message ***
Segmentation fault (core dumped)
Error running command: gmx_mpi mdrun -s SwellingRun/cycle_0/NVT1.tpr -c SwellingRun/cycle_0/NVT1.gro -o SwellingRun/cycle_0/NVT1.trr -x SwellingRun/cycle_0/NVT1.xtc -e SwellingRun/cycle_0/NVT1.edr -g SwellingRun/cycle_0/NVT1.log -nb cpu -pme cpu
The system contains water, membrane box and also lj walls