Task #2495

Task #1781: re-design benchmarking functionality

replace -noconfout with mdp option

Added by Mark Abraham about 2 years ago. Updated 6 months ago.

Target version:


At Berk suggested, and Erik and I agreed, that we replace mdrun -noconfout with an mdp option, which is on by default so that normal behaviour that normal users see stays the same. This option can be turned off when it is useful, e.g. in an .mdp file for benchmark tpr.

Related issues

Related to GROMACS - Task #2569: announce deprecations in GROMACS 2019Closed
Related to GROMACS - Task #2169: remove 'continuation' mdp optionNew

Associated revisions

Revision cf2d8336 (diff)
Added by Mark Abraham over 1 year ago

Deprecate various functionality in GROMACS 2019

Published a deprecation policy.

Updated the release notes to refer also to previously deprecated

Announced intent to change some functionality:
  • gmx mdrun -membed options (but not feature)
  • gmx mdrun -rerun option (but not feature)
  • integrator .mdp field will contain only integrators
  • gmx do_dssp to be replaced by gmx dssp
  • gmx trjconv and friends to be split and rewritten
List of newly deprecated functionality:
  • conversion of aromatic rings to virtual sites
  • gmx mdrun -table options (but not feature)
  • gmx mdrun -gcom option and feature
  • gmx mdrun -nsteps option and feature
  • gmx mdrun -nsteps -resetstep -resethway moved to
    a gmx benchmark tool
  • gmx mdrun -confout removed

Also updated release notes for functionality removed in GROMACS 2019.

Refs #2495, #1781
Fixes #2569, #1925

Change-Id: I1d00859d0f15409a472984f5a65347a50c71ad17


#1 Updated by Mark Abraham almost 2 years ago

  • Related to Task #2569: announce deprecations in GROMACS 2019 added

#2 Updated by Mark Abraham almost 2 years ago

The proposal to have gmx benchmark replace gmx mdrun for that use case is a natural way to have the default for -c to be on or off in the two relevant cases.

#3 Updated by Szilárd Páll almost 2 years ago

BTW, there seems to be no documentation on what is the intended use of the confout file -- and perhaps have a conversation whether those functions can be served better by other mechanism in the future (e.g. checking that a simulation has completed).

#4 Updated by Berk Hess almost 2 years ago

Having the benchmark tool removes the (short term) need for an mdp option for confout.gro.

But the confout.gro file is an awkward construct for all its current uses. For capturing the state of the system for transfer between EM and MD tng would be a better option. For transfer between MD and MD a checkpoint works, although I'm not sure what happens when you change coupling algorithms etc.
And indeed we need a proper way of signaling that a simulation has finished successfully.

#5 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '1' for Issue #2495.
Uploader: Mark Abraham ()
Change-Id: gromacs~master~I1d00859d0f15409a472984f5a65347a50c71ad17
Gerrit URL:

#6 Updated by Mark Abraham over 1 year ago

  • Target version changed from 2019 to 2020

#7 Updated by Mark Abraham over 1 year ago

  • Related to Task #2169: remove 'continuation' mdp option added

#8 Updated by Paul Bauer 7 months ago

  • Status changed from New to Resolved

#9 Updated by Paul Bauer 6 months ago

  • Status changed from Resolved to Accepted
  • Target version changed from 2020 to 2021

I think this should instead be kept open for 2021

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