Hello,
you have set the -mpi option correctly (I think), but the small test
system used for the tutorial can not be split up over more domains (as
the error message tells you).
The idea of the tutorial are here to run on system for each mpi process.
Are you trying to do the same (and run 12 different simulations), or do
you want to use several mpi processes for each of the REMD simulations?
Cheers
Paul
On 11/11/2019 14:39, ZHANG Cheng wrote:
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: mdrun_mpi, version 2019.3
Source file: src/gromacs/domdec/domdec.cpp (line 2403)
MPI rank: 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
--
Paul Bauer, PhD
GROMACS Release Manager
KTH Stockholm, SciLifeLab
0046737308594
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