Core dumped when running the nve of runall.sh

[Layne-Huang]

Hi,

I did not run the nve successfully. And it threw out the errors:

Then I ran the analyze_results.py, it threw out another error: Could you please help me solve it or give me any insights?

[xy21hb]

check your loading modules, I guess there are some modules missing, esp. those related to gmx

[luancarvalhomartins]

1. You are trying to load modules, but modules command was not found. Check your environment.
2. Core dump means GROMACS segfaulted. Can you run gmx_mpi in that env? What is your compute node exactly? Is it an HPC?

[Layne-Huang]

1. You are trying to load modules, but modules command was not found. Check your environment.
2. Core dump means GROMACS segfaulted. Can you run gmx_mpi in that env? What is your compute node exactly? Is it an HPC?

1. Which module do you mean that is not found?
2. I can run 'gmx_mpi' successfully.

[luancarvalhomartins]

1. In the beginning of your output there is a module: command not found error. Double check your environment.
2. Sure, but what about gmx_mpi mdrun? Segfault is likely not a PyAutoFEP error, but rather something concerning your GROMACS binary.

[Layne-Huang]

1. In the beginning of your output there is a module: command not found error. Double check your environment.
2. Sure, but what about gmx_mpi mdrun? Segfault is likely not a PyAutoFEP error, but rather something concerning your GROMACS binary.

1. I solved this by commenting the argument output_collecttype = python.
2. I could run other commands except nve command. Do you have any insights to test whether mdrun could run successfully?

[Layne-Huang]

1. I solved this by commenting the argument output_collecttype = python.

I solved this by commenting the argument output_collecttype = python. But it still threw out the same error.

[luancarvalhomartins]

1. I am assuming you uncommented the following line in the step2.ini: # output_runbefore = module load python3; module load cuda. You should only do that in case loading modules using module makes sense for you. It seems it don't. output_collecttype = python should not affect that.
2. There is something wrong with you GROMACS binary/compilation. Follow steps in https://manual.gromacs.org/2021.6/install-guide/index.html and make sure you compile with MPI support. Note that 2021.X is currently the last version supported by PyAutoFEP. Bumping is on going.