mdrun can exit with atom moved to far in DD or PME due to too small domains - Redmine #2614
Because of the large nstlist values that are used now, often by default
with GPUs, atom displacements are far larger than they uses to be. This
can lead to mdrun stopping with a fatal error due to particle moving too
far in DD repartitioning or PME.
Possible solutions are limiting the minimum domain size and/or maximum nstlist appropriately for the system.
(from redmine: issue id 2614, created on 2018-08-16 by berkhess, closed on 2018-08-22)
- Revision 2cb82175 by Berk Hess on 2018-08-20T23:49:56Z:
Refactor calc_verlet_buffer_size() Split of parts, which will be reused, from calc_verlet_buffer_size(). This change is only code motion. Refs #2614 Change-Id: I9cf68a2661ee10eb991240d2768c077df9f9c0c5
- Revision cd41b0fe by Berk Hess on 2018-08-21T13:10:03Z:
Ensure domains are large enough for atom motion The introduction of the dual pair list has led to larger nstlist values, which leads to larger atom displacements between domain decomposition steps. This has made it much more likely that "atom moved to far" errors appeared at DD and PME redistribution. Now minimum DD cell size setting correctly takes into account atom displacement (when there is a reference temperature). Note that this can significantly increase the minimum DD cell size for solvent systems and slighlty for systems with large molecules. Fixes #2614 Change-Id: Ie41131e9eed3ef828928516a6b8ebfb9b5ba2bdb