GROMACS development

08/21/2019

06:08 PM GROMACS Task #3031: evaluate the impact of particle order on PME

Ran this with the water boxes using either 4 tMPI ranks (3 PP and 1 PME) or 2 tMPI ranks (1 PP and 1 PME). Uisng a se...

05:10 PM GROMACS Task #2792: Improvement of PME gather and spread CUDA kernels

OK so I ran some on the RTX 2080 as well.
Looking at the total time for the spline_and_spread kernel plus the gath...

08/16/2019

12:42 PM GROMACS Task #2792: Improvement of PME gather and spread CUDA kernels

One solution would be to run with 16 threads, and fall back to the save/reload for small sizes.
From my code it w...

08/15/2019

12:11 AM GROMACS Task #2792: Improvement of PME gather and spread CUDA kernels

Ok those is a good points.
Yes there is DD on the PP side as we have 3 PP ranks and 1 PME rank.
Re-ran with 16...

04:12 PM GROMACS Task #2792: Improvement of PME gather and spread CUDA kernels

Water boxes
Command gmx mdrun -ntmpi 4 -ntomp 10 -pme gpu -nb gpu -pin on -nsteps 1000 -v -npme 1 -notunepme
V100...

08/14/2019

03:02 PM GROMACS Task #2792: Improvement of PME gather and spread CUDA kernels

To pass the unit tests it is necessary to write out the theta and grid lines information. Similarly for the gather it...

07/10/2019

11:50 AM GROMACS Task #3031: evaluate the impact of particle order on PME

What is the change/patch that implements DD sorting?
I should look at this as well.

07/04/2019

12:57 PM GROMACS Task #2792: Improvement of PME gather and spread CUDA kernels

One other question, is there a redmine for the reordering changes Berk was looking at?
Would be good to look at ho...

06/27/2019

05:57 PM GROMACS Task #2792: Improvement of PME gather and spread CUDA kernels

So there are some issues with the PME unit tests with the patch at https://gerrit.gromacs.org/8908.
With the chan...

04/11/2019

04:57 PM GROMACS Bug #2762: incorrect results with Ubuntu 18.04 / glibc 2.27 (?) and >20 threads

Note this is not specifically related to CUDA. I have seen similar problems (e.g. Gromacs crashing) when Gromacs is b...