[gmx-users] Restarting a REST2 simulation

[Joseph, Benjamin Philipp]

Dear members of the mailing list,


I restarted my replica exchange with solute tempering (REST2) simulation (16 replicas on 20 = 480 cores) with the following command:

srun gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multidir rep0 rep1 rep2 rep3 rep4 rep5 rep6 rep7 rep8 rep9 rep10 rep11 rep12 rep13 rep14 rep15 -replex 10000 -hrex -cpi state.cpt -append


and am running into problems as the simulation does not run many steps after the restart. I get the following error message:


GROMACS:      gmx mdrun, version 2018.3

Executable:   /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed/bin/gmx_mpi

Data prefix:  /usr/local/software/jureca/Stages/Devel-2018b/software/GROMACS/2018.3-intel-para-2018b-plumed

Working dir:  /p/scratch/cias-5/joseph1/new/S_1/sys1/neu/topos

Command line:

  gmx_mpi mdrun -plumed plumed.dat -s topol.tpr -multidir rep0 rep1 rep2 rep3 rep4 rep5 rep6 rep7 rep8 rep9 rep10 rep11 rep12 rep13 rep14 rep15 -replex 10000 -hrex -cpi state.cpt -append



simulation part is not equal for all subsystems

  subsystem 0: 4

  subsystem 1: 4

  subsystem 2: 4

  subsystem 3: 4

  subsystem 4: 4

  subsystem 5: 4

  subsystem 6: 4

  subsystem 7: 4

  subsystem 8: 4

  subsystem 9: 3

  subsystem 10: 3

  subsystem 11: 4

  subsystem 12: 3

  subsystem 13: 4

  subsystem 14: 4

  subsystem 15: 4


-------------------------------------------------------

Program:     gmx mdrun, version 2018.3

Source file: src/gromacs/mdlib/main.cpp (line 115)

MPI rank:    0 (out of 480)


-------------------------------------------------------

Program:     gmx mdrun, version 2018.3

Source file: src/gromacs/mdlib/main.cpp (line 115)

MPI rank:    90 (out of 480)


Fatal error:


-------------------------------------------------------


...




-------------------------------------------------------

Program:     gmx mdrun, version 2018.3

Source file: src/gromacs/mdlib/main.cpp (line 115)

MPI rank:    300 (out of 480)


Fatal error:

The 16 subsystems are not compatible


When I look at every md.log file they all stopped at the same simulation step and so I do not understand why they all are not at the same simulation part. Thanks a lot in advance for your help!


Best regards,


Benjamin