[gmx-users] How to set more mpi for the REMD run?

[ZHANG Cheng]

Thank you very much Paul, I got it!




------------------ Original ------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Mon, Nov 11, 2019 09:57 PM
To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;

Subject:&nbsp;Re:How to set more mpi for the REMD run?



Thank you Paul! I want to use more than one mpi processes for each of the REMD, would it be possible?




------------------ Original ------------------
From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
Date:&nbsp;Mon, Nov 11, 2019 09:39 PM
To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se&gt;;

Subject:&nbsp;How to set more mpi for the REMD run?



I am using the same files based on Mark Abraham's REMD tutorial, except using a recent Gromacs version (gromacs/2019.3).http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham%2C_Session_1B


For Stage 1 of the tutorial, when "#$ -pe mpi 4" is used, it can be run successfully:
gerun mdrun_mpi -v -multidir ./equil[0123]


However, when "#$ -pe mpi 12" is used with the same command, the error message told me as the below. Can I ask how to properly set more mpi? 




Program:&nbsp; &nbsp; &nbsp;mdrun_mpi, version 2019.3
Source file: src/gromacs/domdec/domdec.cpp (line 2403)
MPI rank:&nbsp; &nbsp; 6 (out of 12)


Fatal error:
There is no domain decomposition for 3 ranks that is compatible with the given
box and a minimum cell size of 0.8875 nm
Change the number of ranks or mdrun option -rcon or -dds or your LINCS
settings
Look in the log file for details on the domain decomposition


For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6