Failure to continue a simulation using domain decomposition
I am running a simulation using 2021.1 without domain decomposition and then I tried to extend it using domain decomposition but I get the error reported below both using the native thread mpi version of gromacs as well as the mpi version (both with -nb gpu and with -nb cpu) while it works fine if instead of restarting from the CPT I start from scratch using the TPR.
I am attaching the TPR/CPT and LOG files.topol.tprstate.cptmd.part0018.log
On host nid02360 1 GPU selected for this run.
Mapping of GPU IDs to the 2 GPU tasks in the 2 ranks on this node:
PP:0,PP:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 2 MPI threads
Using 6 OpenMP threads per tMPI thread
Not all bonded interactions have been properly assigned to the domain decomposition cells
A list of missing interactions:
Bond of 1408 missing 6
Angle of 5044 missing 53
Proper Dih. of 8359 missing 126
Improper Dih. of 1564 missing 10
LJ-14 of 7258 missing 69
Molecule type 'Protein_chain_A'
the first 10 missing interactions, except for exclusions:
Proper Dih. atoms 1329 1331 1333 1334 global 1329 1331 1333 1334
LJ-14 atoms 1329 1334 global 1329 1334
Angle atoms 1331 1333 1334 global 1331 1333 1334
Proper Dih. atoms 1332 1331 1333 1334 global 1332 1331 1333 1334
LJ-14 atoms 1332 1334 global 1332 1334
Angle atoms 1334 1333 1336 global 1334 1333 1336
LJ-14 atoms 1334 1337 global 1334 1337
LJ-14 atoms 1334 1338 global 1334 1338
LJ-14 atoms 1334 1339 global 1334 1339
Proper Dih. atoms 1339 1331 1333 1334 global 1339 1331 1333 1334
Molecule type 'Protein_chain_B'
the first 10 missing interactions, except for exclusions:
LJ-14 atoms 373 378 global 2161 2166
Angle atoms 375 377 378 global 2163 2165 2166
LJ-14 atoms 376 378 global 2164 2166
Proper Dih. atoms 377 379 382 384 global 2165 2167 2170 2172
Angle atoms 378 377 379 global 2166 2165 2167
Angle atoms 378 377 390 global 2166 2165 2178
Proper Dih. atoms 378 377 379 380 global 2166 2165 2167 2168
Proper Dih. atoms 378 377 379 381 global 2166 2165 2167 2169
Proper Dih. atoms 378 377 379 382 global 2166 2165 2167 2170
Proper Dih. atoms 378 377 390 391 global 2166 2165 2178 2179
Edited by Mark Abraham