[gmx-users] Known but still domain decomposition
alexanderwien2k at gmail.com
Wed May 2 11:33:25 CEST 2018
I am doing coarse-grained bonded and nonbonded parametrization using
votca-gromacs. The "mpirun -np 64 gmx_mpi mdrun" work fine till step_021 of
parametrization where it crashes because it can not find any domain
decomposition for 64 ranks that is compatible with the system size. Even it
works in the minimization simulation in step_021.
I have been reading most of the previous discussions about the error of
domain decomposition, and I have tried different options like using
different ranks (64, 32, 16, 8, 40, 36) and also -rdd ... or -dds. However,
no success yet.
About the machine: Running on 4 nodes with total 64 cores, 64 logical
cores, Cores per node: 16.
Below I have shared the md.log files for the step_20 (which works fine) and
step_21 (minimization which works fine) and step_21 (which crashes), and I
would be so appreciated if one could help me overcome the issue.
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