GROMACS development

03/23/2020

02:10 PM GROMACS Bug #3440: Multi-nodes run exits with error with openmpi/4.0.0

The linked output seems to indicate an hwloc crash, so probably not GROMACS-related. Can you try to build against a d...

01:54 PM GROMACS Bug #3448: GMX 2020.1 - Multidir simulations can stop at different times when killed by job manager

Daniel Kozuch wrote:
> Related to Bug #2440 (https://redmine.gromacs.org/issues/2440). I am using GROMACS 2020.1 pat...

03/19/2020

04:27 PM GROMACS Revision e25e880d: Fix DLB initial state reporting

Missing entry in the array of state strings means that the initial "on"
and "auto" states were incorrectly reported.
...

03:30 PM GROMACS Task #3446: apply maintainability updates across all GPU kernels

Mark Abraham wrote:
> The first point is partly done already - see pme_gpu_program.cl
Thanks for the correction.

03/18/2020

03:57 PM GROMACS Task #3446 (New): apply maintainability updates across all GPU kernels

Before the CUDA and OpenCL GPU device code greatly diverges, in order to improve maintainability, we need to refactor...

03/17/2020

12:12 PM GROMACS Task #3445: create heuristic for c_skipNeutralAtoms

I don't think we need to test all of those inputs. We should think of what are the conditions that have an impact on ...

03/16/2020

09:50 PM GROMACS Task #3445 (New): create heuristic for c_skipNeutralAtoms

Skipping zero-charge atoms can have significant performance benefit (measured ~10-15% spread+gather time a while ago ...

03/15/2020

08:15 PM GROMACS Bug #3443: Bonded GPU kernel performance regression with 2020

"Ref users' list discussion":https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg40653.html as ...

03/11/2020

08:51 PM GROMACS Revision ee15399a: Reorganize dipole calculation in do_force

Encapsulated dipole used in do_force in a struct and eliminated
fr->mu_tot and moved code into a separate reduction f...

03/04/2020

06:59 PM GROMACS Bug #3385: FindLibStdCpp.cmake - wrong sanity check for clang

Erik Lindahl wrote:
> Anton Shterenlikht wrote:
>
> > The other flags are all fairly standard - nothing special.
...