[gmx-users] Free energy, domain decomposition and gmx 465 v 505

[Gmx QA]

Hi all

I am running some free energy tutorial calculations to learn more about how
those are set up in gromacs, but have run into a problem when using
different versions.

I am following the free energy tutorial on the Gromacs website
(fe-tutorial-4.6), so not Justin's tutorial.

With vmx 4.6.5 everything goes according to the tutorial, and I can run
with four thread on my laptop.
Please find what I think is the relevant section of the log file below:

$/usr/local/gmx465/bin/mdrun -v -deffnm topol_465

Initializing Domain Decomposition on 4 nodes

Dynamic load balancing: auto

Will sort the charge groups at every domain (re)decomposition

Initial maximum inter charge-group distances:

    two-body bonded interactions: 0.239 nm, LJC-14 q, atoms 4 7

  multi-body bonded interactions: 0.239 nm, Angle, atoms 2 6

Minimum cell size due to bonded interactions: 0.263 nm

Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.497 nm

Estimated maximum distance required for P-LINCS: 0.497 nm

This distance will limit the DD cell size, you can override this with -rcon

Using 0 separate PME nodes, as there are too few total

 nodes for efficient splitting

Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25

Optimizing the DD grid for 4 cells with a minimum initial size of 0.622 nm

The maximum allowed number of cells is: X 3 Y 3 Z 2

Domain decomposition grid 2 x 2 x 1, separate PME nodes 0

PME domain decomposition: 2 x 2 x 1

Domain decomposition nodeid 0, coordinates 0 0 0


Using 4 MPI threads



While on the other hand, when I am using v 5.0.5 I cannot start simulations
using more than one thread, otherwise the domain decomposition complains,
even though the excerpt from the log file from that run is (almost)
identical


$/usr/local/gmx505/bin/mdrun -v -deffnm topol_505


Initializing Domain Decomposition on 4 ranks

Dynamic load balancing: auto

Will sort the charge groups at every domain (re)decomposition

Initial maximum inter charge-group distances:

    two-body bonded interactions: 0.239 nm, LJC-14 q, atoms 4 7

  multi-body bonded interactions: 0.239 nm, Angle, atoms 2 6

Minimum cell size due to bonded interactions: 0.263 nm

Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.497 nm

Estimated maximum distance required for P-LINCS: 0.497 nm

This distance will limit the DD cell size, you can override this with -rcon

Using 0 separate PME ranks, as there are too few total

 ranks for efficient splitting

Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25

Optimizing the DD grid for 4 cells with a minimum initial size of 0.622 nm

The maximum allowed number of cells is: X 3 Y 3 Z 2


-------------------------------------------------------

Program gmx, VERSION 5.0.5

Source code file:
/Users/pk/source/gromacs-5.0.5/src/gromacs/mdlib/domdec.c, line: 6902


Fatal error:

There is no domain decomposition for 4 ranks that is compatible with the
given box and a minimum cell size of 0.62175 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

-------------------------------------------------------



Is there something that I have overlooked in v 5 that needs to be taken
into consideration? I am not that familiar with the new parallelization
scheme of v5, maybe there is something there?


Thanks

/PK