Berk Hess





11:05 AM GROMACS Feature #3355 (Accepted): New PME parallel (GPU) scheme
The current DD code has separate PP and PME domain decompositions.
What could give better performance, especially ...


04:30 PM GROMACS Bug #3336 (Resolved): DD error can't be avoided with the suggested manual decomposition option
Applied in changeset commit:b4bf4c088ec42d73fb9fa7a3412c3ef294e361f0.
04:09 PM GROMACS Revision b4bf4c08: Fix DD rank count prime check
The domain decomposition would refuse to run with large prime factors
in the MPI rank count even when the grid was sp...
12:52 PM GROMACS Task #3353: Document gmx densmap output
IIRC densmap adds one grid point for each dimension. Maybe it's better to remove this and offset the grid points by h...


10:39 PM GROMACS Bug #3334: Check for DD when increasing rlist is broken
I wonder if this is really an issue.
Now rlist might limit the domain decomposition, whereas before the domain decom...
10:28 PM GROMACS Bug #3336 (Fix uploaded): DD error can't be avoided with the suggested manual decomposition option
09:58 PM GROMACS Revision 69a75c1b: Minor cleanup in constraint and shellfc code
Replaced include by forward declarations and simplified empty
ArrayRefs as function arguments.
Change-Id: I759f3f72b...
11:55 AM GROMACS Revision 2ea07ac1: Fix illegal memory access in PME communication
Depending on the compiler, mdrun could exit with an illegal
memory access error when a PME rank communicates 0 atoms ...
08:14 AM GROMACS Revision da05c565: Clarify COMM/posres grompp note
In the common case of equilibrating a macro-molecule using position
restraints, grompp will issue a note about COMM r...


04:33 PM GROMACS Revision 78e7637a: Use ArrayRef(WithPadding) in constraint code
This change is only refactoring, except for adding padding to two
buffers used for flexible constraints. This avoid p...

Also available in: Atom