r2018 docs tweaks/corrections necessary
These are short notes compiled from the first glance, feel free to improve/add more.
- Install guide
- Add NVML to optional components, look through its other mentions.
- Mention cuFFT in the FFT section.
- "GPU support" overall facelift, Volta, etc.
- SIMD: AVX2_128 missing; add hints on AVX_512 vs AVX2_256.
- File names descriptions of builds (full/mdrun-only/MPI/prefixes).
- Tested platforms: add Cray XC50+ThunderX2.
- User guide
- Review NB/cutoff schemes (tolerance, nstlist).
- Examples of "-gputasks" are outdated in multiple spots, as initially it just replaced "-gpu_id" everywhere, including the docs, and only later started requiring all the other parameters to be specified.
- "Good performance" best effort update.
- Performance checklist update.
- Clean up env.vars section (there be dinosaurs, Szilard has a WIP https://gerrit.gromacs.org/7375).
- Some empty TODO sections at the end (?), like "Terminology".
- Figure out version's URLs, try to have a current version URL (e.g. manual.gromacs.org/documentation/current/index.html), remove the duplication of minor releases.
- Make the overview versioning page http://manual.gromacs.org/documentation/ more user-friendly; have "up" links on the sub-pages.
Environment variable docs maintenance
Removed deprecated variables (some ancient, some recent), corrected some
Added undocumented environment variables.
Left a comment with handy one-liner to discover leftovers as well as
Install guide updates
Updated install guide to reflect chnges in for the 2018 release.
User guide updates to GPU section
Clarify the mdrun GPU options docs
Fixed documentation typo
This version is true to the original text.
Updated links in user guide
Made sure links in the terminology section of the user guide point
directly to the html reference manual instead of to the pdf version.
Added small part for MD section in terminology woth link to reference
#11 Updated by Mark Abraham about 1 year ago
- Target version changed from 2018 to 2018.1
I had a few patches that made it into version 2018 that addressed things that didn't reference this issue.
There's still an open question of how we want release notes to work and look on the webpage. https://gerrit.gromacs.org/#/c/7444/ adds those for all 2016.x. I can import the earlier ones in semi-bulk once we have some agreement on the approach.
Are there remaining thoughts people have for things to document / update for release 2018?
#17 Updated by Oliver Stueker 11 months ago
I noticed in the Performance guide's Run Setup section1, the second bullet point is a bit mangled:
When using a time-step of 2 fs, use cutoff-scheme = constraints=h-bonds (and not constraints=all-bonds), since this is faster, [...]
I assume it's supposed to be:
[...] use `cutoff-scheme=verlet` and `constraints=h-bonds` [...]
#21 Updated by Paul Bauer 6 months ago
- NVML support is listed under CUDA GPU acceleration but not explicitly as optional -> should this be changed?
- cuFFT is mentioned in the correct section
- GPU support is updated and also mentions OpenCL
- SIMD section is correctly updated
- File name changing and explaining (I think) has been added
- Tested platforms has been updated
- NB/cut-off schemes has been updated
- GPU task has been updated
- Good performance section has been updated as far as I can see
- Performance checklist has been updated
- Env vars have been updated
- Terminology has been updated but can use a change to some links to the relevant reference manual sections in master (not in release-2018)
- Website versioning has been updated
- Up page is not included, but I don't know how this can be added in sphinx