GROMACS version:gromacs2023
GROMACS modification: Yes/No
Here post your question
The server is using 200g of RAM, there shouldn’t be an out of memory problem, I used the command submitted by sbatch：
#!/bin/bash
#SBATCH -J gromacs2023
#SBATCH -p amd
#SBATCH -N 1
#SBATCH --ntasks-per-node=128
#SBATCH --mem=200G
module purge
#module load compiler/intel/2017.5.239
#module load mpi/intelmpi/2017.4.239
#module load mpi/hpcx/2.4.1/intel-2017.5.239
#module load apps/gromacs/2019.5/hpcx-2.4.1-intel2017
module load compiler/intel-compiler/2021.3.0
module load mpi/intelmpi/2021.3.0
module load apps/cmake/3.26.3
module load compiler/gcc/9.3.0
module load mathlib/fftw/intelmpi/3.3.9_single
module load apps/gromacs/2023/cpu-intelmpi-intel2021
echo -e “1\n13” | gmx_mpi hbond -f md.xtc -s md.tpr -n index.ndx -num -hbm -hbn
I successfully ran mdrun for 25ns, generating files: md.tpr, md.xtc. Here is the command I executed:
Select a group: Selected 1: ‘Protein’
Select a group: Selected 13: ‘MOL’
Checking for overlap in atoms between Protein and MOL
Calculating hydrogen bonds between Protein (11283 atoms) and MOL (65 atoms)
Found 982 donors and 2019 acceptors
Making hbmap structure…done.
Reading frame 0 time 0.000
Will do grid-search on 25x25x25 grid, rcut=0.34999999
Frame loop parallelized with OpenMP using 128 threads.
Reading frame 12000 time 24000.000
Found 52 different hydrogen bonds in trajectory
Found 114 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
325/982[comput24:41390:0:41390] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace (tid: 41390) ====
0 0x0000000000014070 .annobin_sigaction.c() sigaction.c:0
1 0x0000000000fffbc3 _INTERNALb7fb3a0b::do_merge() gmx_hbond.cpp:0
2 0x0000000000fff4c9 _INTERNALb7fb3a0b::merge_hb() gmx_hbond.cpp:0
3 0x0000000000ff7fc5 gmx_hbond() ???:0
4 0x0000000000e17207 gmx::CommandLineModuleManager::run() ???:0
5 0x000000000040aa8a main() ???:0
6 0x0000000000027453 __libc_start_main() ???:0
7 0x000000000040a929 _start() ???:0
/opt/gridview/slurm/spool/slurmd/job15569/slurm_script: line 20: 41389 Done echo -e “1\n13”
41390 Segmentation fault (core dumped) | gmx_mpi hbond -f md.xtc -s md.tpr -n index.ndx -num -hbm -hbn