GROMACS development

03/16/2018

12:53 AM GROMACS Bug #2421: EwaldUnitTests and SimdUnitTests fail on ppc64le with gcc-8.0.1

Based on the IBM feedback, it's only version 8 that will get the ABI change.
I would suggest that we simply add a ...

02/28/2018

11:27 PM GROMACS Bug #2370 (Closed): pdb2gmx does not report why chains of residues are teminated

02/26/2018

08:14 PM GROMACS Bug #2419: Asserting failure in simd gatherLoadUTranspose with DDT

PS Paul: Could you try to move the declaration of those two (aligned) variables to the very start of the routine, ins...

08:03 PM GROMACS Bug #2419: Asserting failure in simd gatherLoadUTranspose with DDT

This appears to be caused by the declarations on lines 457-458 of clincs.cpp not generating properly aligned variable...

04:02 PM GROMACS Bug #2388: inconsistent pinning behavior due to missing SMT info on AMD Zen

Note: Even with the patch to add more AMD SMT detection, there *will* be cases where we do not perfectly detect SMT o...

03:14 PM GROMACS Task #2412: attempt to do better FFTW planning

My concern with different plan options is that it would lead to even more complications in the code and normal users ...

03:04 PM GROMACS Bug #2421: EwaldUnitTests and SimdUnitTests fail on ppc64le with gcc-8.0.1

This appears to be bugs in the very basic load/store operations. Unfortunately I've seen those before, and although i...

01/31/2018

02:49 PM GROMACS Bug #2388: inconsistent pinning behavior due to missing SMT info on AMD Zen

Well, it's not technically a bug since the hardware info module properly detects that we can't see it, and correctly ...

01/15/2018

04:24 PM GROMACS Feature #1842: Replace XML with JSON

Mark and I had another chat about JSON and our best strategies for it, partly based on recent development in JSON lib...

01/10/2018

12:39 PM GROMACS Bug #2370 (Resolved): pdb2gmx does not report why chains of residues are teminated

Applied in changeset commit:541e7d05da570755b263f5ada97215b96e61781c.