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Task #2359

r2018 docs tweaks/corrections necessary

Added by Szilárd Páll 9 months ago. Updated about 1 month ago.

Status:
Closed
Priority:
Normal
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Category:
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Target version:
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uncategorized
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Description

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    - Examples of "-gputasks" are outdated in multiple spots, as initially it just replaced "-gpu_id" everywhere, including the docs, and only later started requiring all the other parameters to be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".
  • Website
    - 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.

Associated revisions

Revision 2fd09ca5 (diff)
Added by Szilárd Páll 9 months ago

Environment variable docs maintenance

Removed deprecated variables (some ancient, some recent), corrected some
misspelled ones.

Added undocumented environment variables.

Left a comment with handy one-liner to discover leftovers as well as
undocumented variables.

Refs #2359

Change-Id: Icb80cf661e2a53c5049fe18d687b987fb2c025f1

Revision d7d9b85f (diff)
Added by Szilárd Páll 9 months ago

Install guide updates

Updated install guide to reflect chnges in for the 2018 release.

Refs #2359

Change-Id: Ic679e7d7e96392c2c28185db1f71928146cd742d

Revision 01de2421 (diff)
Added by Szilárd Páll 9 months ago

User guide updates to GPU section

Refs #2359

Change-Id: Ied4945f83dc19f93a51aa78f51b7cea18021f5b8

Revision 192c73a7 (diff)
Added by Aleksei Iupinov 6 months ago

Clarify the mdrun GPU options docs

Refs #2359

Change-Id: If112077a59f875ffb1c689b2ac67dad7cdf2adb9

Revision 5bb6743d (diff)
Added by Mark Abraham 3 months ago

Fixed documentation typo

This version is true to the original text.

Refs #2359

Change-Id: I3c2ab7a30109a397999883d5147346f1244a77f0

Revision c445a37b (diff)
Added by Paul Bauer about 1 month ago

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
manual.

Refs #2359

Change-Id: Ie21d177c722fcc4b548d8c2d2fa228bff9bce2c8

Revision 775c42cb (diff)
Added by Paul Bauer 27 days ago

Transfer information from old how-to section

Transfer information from the old how-to section to the new website and
perform some updates/deletions where needed.

Refs #2359

Change-Id: I474f4161003f07f92ba23d8183ac058fec4dc17b

History

#1 Updated by Mark Abraham 9 months ago

  • Target version set to 2018

#2 Updated by Aleksei Iupinov 9 months ago

  • Description updated (diff)

#3 Updated by Aleksei Iupinov 9 months ago

  • Description updated (diff)

#4 Updated by Mark Abraham 9 months ago

Szilard has some WIP

#5 Updated by Gerrit Code Review Bot 9 months ago

Gerrit received a related patchset '3' for Issue #2359.
Uploader: Szilárd Páll ()
Change-Id: gromacs~release-2018~Icb80cf661e2a53c5049fe18d687b987fb2c025f1
Gerrit URL: https://gerrit.gromacs.org/7375

#6 Updated by Gerrit Code Review Bot 9 months ago

Gerrit received a related patchset '3' for Issue #2359.
Uploader: Szilárd Páll ()
Change-Id: gromacs~release-2018~Ic679e7d7e96392c2c28185db1f71928146cd742d
Gerrit URL: https://gerrit.gromacs.org/7429

#7 Updated by Gerrit Code Review Bot 9 months ago

Gerrit received a related DRAFT patchset '2' for Issue #2359.
Uploader: Szilárd Páll ()
Change-Id: gromacs~release-2018~Ied4945f83dc19f93a51aa78f51b7cea18021f5b8
Gerrit URL: https://gerrit.gromacs.org/7430

#8 Updated by Mark Abraham 9 months ago

Ill organize updates to the user guide. I can see some stubs that Paul added that should be removed in 2018 branch, and probably some re-ordering of content is in order, too.

#9 Updated by Mark Abraham 9 months ago

Also, I added the release notes to the repo and organize it to build RELEASENOTES plain text into the tarball. See https://gerrit.gromacs.org/#/c/7433/

#10 Updated by Mark Abraham 9 months ago

  • Status changed from New to Fix uploaded

#11 Updated by Mark Abraham 8 months 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?

#12 Updated by Paul Bauer 8 months ago

I'm working on some more things for master (transferring stuff from the old pages), but I don't think those need to get in release-2018

#13 Updated by Gerrit Code Review Bot 8 months ago

Gerrit received a related patchset '1' for Issue #2359.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~I474f4161003f07f92ba23d8183ac058fec4dc17b
Gerrit URL: https://gerrit.gromacs.org/7487

#14 Updated by Gerrit Code Review Bot 7 months ago

Gerrit received a related patchset '3' for Issue #2359.
Uploader: Mark Abraham ()
Change-Id: gromacs~release-2018~If112077a59f875ffb1c689b2ac67dad7cdf2adb9
Gerrit URL: https://gerrit.gromacs.org/7639

#15 Updated by Gerrit Code Review Bot 7 months ago

Gerrit received a related patchset '1' for Issue #2359.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~If112077a59f875ffb1c689b2ac67dad7cdf2adb9
Gerrit URL: https://gerrit.gromacs.org/7650

#16 Updated by Mark Abraham 6 months ago

  • Target version changed from 2018.1 to 2018.2

#17 Updated by Oliver Stueker 5 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` [...]

right?

[1] http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html#run-setup

#18 Updated by Gerrit Code Review Bot 3 months ago

Gerrit received a related patchset '1' for Issue #2359.
Uploader: Mark Abraham ()
Change-Id: gromacs~release-2018~I3c2ab7a30109a397999883d5147346f1244a77f0
Gerrit URL: https://gerrit.gromacs.org/7998

#19 Updated by Mark Abraham 3 months ago

Thanks Oliver, fixed that

#20 Updated by Mark Abraham 3 months ago

  • Status changed from Fix uploaded to Feedback wanted
  • Target version changed from 2018.2 to 2018.3

If there's remaining issues to address here, somemone needs to work out what they are for 2018.3

#21 Updated by Paul Bauer about 1 month ago

I think most of the issues listed here are actually addressed already with the patches that went into the latest version. Listing them below
  • 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

#22 Updated by Gerrit Code Review Bot about 1 month ago

Gerrit received a related patchset '1' for Issue #2359.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~Ie21d177c722fcc4b548d8c2d2fa228bff9bce2c8
Gerrit URL: https://gerrit.gromacs.org/8185

#23 Updated by Paul Bauer about 1 month ago

I'll close this for now as the issues have been addressed in general as I mentioned above. If any more changes are urgently needed for the documentation please open it again and let me know.

#24 Updated by Paul Bauer about 1 month ago

  • Status changed from Feedback wanted to Closed

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