本帖最后由 17-li 于 2025-7-8 11:19 编辑
我的软件版本信息为:-) GROMACS - gmx, 2022.5-plumed_2.9.0 (-:
生成 tpr 文件的命令为：
gmx grompp -f metad_plumed.mdp-c system.gro -p topol.top -n metad.ndx -o metad.tpr-maxwarn 2
，运行该命令后生成文件 mdout.mdp 和 mdout.mdp
后台运行模拟的命令为：
nohup gmx mdrun -s metad.tpr -deffnm metadout -plumed metad.dat -ntmpi 1 -ntomp 16 -pin on -v >> metad.out &
metad.out文件中的完整内容如下，没有出现Fatal error：
:-) GROMACS - gmx mdrun, 2022.5-plumed_2.9.0 (-:
Executable: /home/xxx/softs/install/gromacs-2022.5/bin/gmx
Data prefix: /home/xxx/softs/install/gromacs-2022.5
Working dir: /home/xx/0707METAD
Command line:
gmx mdrun -s metad.tpr -deffnm metadout -plumed metad.dat -ntmpi 1 -ntomp 16 -pin on -v
Reading file 0707metad.tpr, VERSION 2022.5-plumed_2.9.0 (single precision)
Changing nstlist from 10 to 100, rlist from 1 to 1.158
1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 1 rank on this node:
PP:0,PME:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
PME tasks will do all aspects on the GPU
Using 1 MPI thread
Using 16 OpenMP threads
starting mdrun 'Birds22 in water'
500000 steps, 1000.0 ps.
但是输出 nvidia-smi命令后发现该任务并没有运行，而是出现报错 segmentation fault
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发表于 Post on 2025-7-8 11:19:54
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