GROMACS development

07/09/2019

03:36 PM GROMACS Task #2983: better suited data-types for bonded GPU kernels

It seems to me like it would be best to split iatoms into std::vector<int> InteractionTypes and std::vector<int4> Int...

07/04/2019

08:14 AM GROMACS Task #2983: better suited data-types for bonded GPU kernels

I made an attempt at preloading the data, but I just shifted the problem earlier. The problem was that I did not come...

07/03/2019

04:02 PM GROMACS Revision 5854b8da: Vectorize GPU bonded data.

Loads data for bonds, angles, UB angles and pairs in blocks
of 3, 4, 4 and 3 ints respectively.
Refs: #2983
Change-...

06/30/2019

11:09 PM GROMACS Revision ec176323: Cleaning up the GPU bonded kernel

Improved variable names
Removed unnecessary includes
Refs #2988
Change-Id: Ife5f50e68f27994203305e376f2781a076052b64

06/28/2019

12:37 PM GROMACS Revision 01b2f20b: Fused GPU bonded kernels

To reduce the GPU kernel launch times the
GPU bonded kernels have been fused to a single kernel.
Refs #2818
Change-...

06/20/2019

12:53 PM GROMACS Task #2983: better suited data-types for bonded GPU kernels

Since I'm far from an expert at GPU programming (I just try to learn as I go along) I'm afraid I can't say what alter...

06/18/2019

09:33 PM GROMACS Task #2983: better suited data-types for bonded GPU kernels

I'll be happy to try to help with this as well, but I must admit I don't know how to prefetch the data in a suitable ...

05/23/2019

04:36 PM GROMACS Bug #2958: Compiling master (to become 2020) using CUDA 9.0

With CUDA-9.2 I can compile with gcc-7, but not gcc-6 (I haven't tested gcc-5).

04:26 PM GROMACS Bug #2958 (New): Compiling master (to become 2020) using CUDA 9.0

When compiling master with CUDA 9.0 (gcc-5 or gcc-6) I get the following type of errors:
/usr/lib/gcc/x86_64-linux...

05/21/2019

02:44 PM GROMACS Task #2818: bonded GPU kernel fusion

I'm assigning this to myself for now. Hopefully I can do this, but will probably need some advice along the way.
S...