Task #2495
Task #1781: re-design benchmarking functionality
replace -noconfout with mdp option
Description
At https://gerrit.gromacs.org/#/c/7451 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
Associated revisions
History
#1 Updated by Mark Abraham over 2 years ago
- Related to Task #2569: announce deprecations in GROMACS 2019 added
#2 Updated by Mark Abraham over 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 over 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 over 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 2 years ago
Gerrit received a related patchset '1' for Issue #2495.
Uploader: Mark Abraham (mark.j.abraham@gmail.com)
Change-Id: gromacs~master~I1d00859d0f15409a472984f5a65347a50c71ad17
Gerrit URL: https://gerrit.gromacs.org/8488
#6 Updated by Mark Abraham over 2 years ago
- Target version changed from 2019 to 2020
#7 Updated by Mark Abraham over 2 years ago
- Related to Task #2169: remove 'continuation' mdp option added
#8 Updated by Paul Bauer about 1 year ago
- Status changed from New to Resolved
#9 Updated by Paul Bauer about 1 year ago
- Status changed from Resolved to Accepted
- Target version changed from 2020 to 2021
I think this should instead be kept open for 2021
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:features.
- 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:a gmx benchmark tool
Also updated release notes for functionality removed in GROMACS 2019.
Refs #2495, #1781
Fixes #2569, #1925
Change-Id: I1d00859d0f15409a472984f5a65347a50c71ad17