Berk Hess





09:16 AM GROMACS Bug #2317: Incorrect warning about PME ranks during cpt restart
I think I noticed this issue as well around the time this got filed. But now I can not reproduce it with the code fro...
08:54 AM GROMACS Bug #2323 (Fix uploaded): avx512 implementation of operator << requires immediate with gcc 6.4
08:54 AM GROMACS Bug #2327 (Accepted): AVX2_128 and AVX_128_FMA double precision PME gather regression
It seems that on AMD Zen AVX2_256 is always faster than AVX2_128 when we anyway have sufficient operands for the widt...
08:47 AM GROMACS Task #2328 (Resolved): assess AVX2 128 vs 256 on AMD Zen and change defaults
This seems to be resolved for the moment. But (unfortunately) we will need to keep checking this when code changes or...
06:41 AM GROMACS Revision 011eec72: Add grompp note for PR pcouple + position restraints
Refs #2330
Change-Id: I299e39247d69214d9b54c47874d522ac7b00a30e


07:59 PM GROMACS Revision cacb3b41: Remove SIMD warning for AMD Zen
After choosing nbnxn 2xNN kernels and changing the to tabulated Ewald
nonbonded kernels, AVX2_256 is only a few perce...
05:20 PM GROMACS Revision 7bc4ec9b: Tone down note about not pinning threads
The note mdrun prints to stderr and log file when not pinning
threads is now a short note instead of the old failure ...


12:50 PM GROMACS Feature #2339 (Closed): sum of two largest charge group is enormous and bigger than rlist
There are no charge groups with the Verlet scheme or you can view it a single atom charge groups, so this can't happe...
12:47 PM GROMACS Bug #2331 (Closed): Lost particles while sorting Gromacs 2016.4
Duplicate of #2330.
12:34 PM GROMACS Bug #2333 (Rejected): mdrun crash with high density of particles and SD integrator
Have you even looked at the energy output at step 0? I get:
Large VCM(group rest): 505.20956, -0.00001, -...

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