Difference between single rank and multiple rank when pulling using constraints relative to rest of the system - Redmine #2397
I noticed that I get completely different e.g. pull forces and temperature on a run started on a GPU server running NB and PME on GPU and then continued from a restart file on the PDC Beskow supercomputer running MPI (no GPUs).
Continuing from a checkpoint on a different hardware would not make the results binary identical, but in this case the difference is remarkable. The pull forces and temperature fluctuations are a lot higher on Beskow. I guess something is going wrong and I guess the output from the GPU server is correct, based only on the fact that it is more stable.
I’m attaching the pull force and temperature output and the log file from a run where the first 100 ps are run on a GPU server, the next 200 ps on Beskow and then 200 ps on the GPU server again.
(from redmine: issue id 2397, created on 2018-02-02 by magnus.lundborg, closed on 2018-11-08)
- Revision aa102e69 by Berk Hess on 2018-08-18T19:45:13Z:
Add check for pull group PBC to grompp Pull groups that use a reference atom for periodic boundary treatment should have all their atoms well within half the box size of this reference. When this is not the case, grompp will now issue a warning. Refs #2397 Change-Id: Ida7004624a470981d9ce22a1ef921daebad83364
- Revision 2a77f97d by Magnus Lundborg on 2018-09-21T07:14:41Z:
Fixes a bug in pull group size calculation The wrong atom indexes were used when checking the coordinates of atoms in a pull group (commit aa102e691d59b4de37c8e4). That lead to false reports of too large pull group (and presumably false negatives). This fixes the problem. Refs #2397 Change-Id: Ib7d7e648204c0d1b219714610de7fb5842713048