Multidir and continuing simulations using cpt file

User discussions
1

GROMACS version: 2020
GROMACS modification: Yes/No

Dear all,
As below I like to continue four independent simulations together using multidir:

gmx_mpi mdrun -multidir 1 2 3 4 -s topol.tpr -deffnm md -g md.log -cpi md.cpt -noappend

The md.cpt file corresponding to each simulation exists inside each directory, each single simulation can be continued individually, but with multidir the simulation do not work with below error:

simulation checkpoint files were from the following respective
simulation parts:
Simulation 0: 7
Simulation 1: 9
Simulation 2: 11
Simulation 3: 10

Multi-simulations must all start in the same way, either a new
simulation, a restart with appending, or a restart without appending.
MPT ERROR: Rank 0(g:0) is aborting with error code 1.
Process ID: 47980, Host: r4i0n6, Program: /p/app/gromacs/gromacs-2020.1/bin/gmx_mpi
MPT Version: HPE MPT 2.20 08/30/19 04:33:45

MPT: --------stack traceback-------
For more information and tips for troubleshooting, please check the GROMACS
website at Errors - Gromacs

However, the checkpoint files you specified were from different
simulation parts. Either remove the checkpoint file from each directory,
or ensure each directory has a checkpoint file from the same simulation
part (and, if you want to append to output files, ensure the old output
files are present and named as they were when the checkpoint file was
written).

Would you please let me know what might be the reason?

Thank you
Alex

2

We check for identical simulation parts as in many cases something is wrong when they don’t match and the user might get simulations that run out of sync.

If you want to avoid this check, remove the “if (!identicalSimulationParts)” conditional in src/gromacs/mdrunutility/handlerestart.cpp

3

Thanks for the response.

What does identical simulation means here?
The four simulations I want to continue have the same number of atoms and atom-types and all had previously simulated for 300 ns want to be continued for identical times. And I use the “-cpi an.cpt -noappend” to continue all the same way.

I wonder if I should then recompile the source if I remove the "if (!identicalSimulationParts)” from the handlerestart.cpp?

BTW, without the “-cpi an.cpt -noappend”, the multidir works just fine.

Thanks

4

No, I meant identical “simulation part numbers”, so only the number that mdrun complains about.

Yes, you will need to compile.