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Feature #1054

Feature #1292: mdrun features to deprecate for 5.0

Feature #1500: Post-5.0 feature clean-up plan

implicit solvent parallelization

Added by Justin Lemkul about 7 years ago. Updated almost 2 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
mdrun
Target version:
Difficulty:
uncategorized
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Description

Currently, all implicit solvent simulations are restricted to a maximum of 2 processors when run on CPU. If OpenMM support is dropped (as mentioned by Szilard on the mailing list), the implicit code is largely useless since simulations are very slow on only 1-2 CPU, while their explicit solvent counterparts run orders of magnitude faster on a moderate number of processors. The 2-processor limitation was introduced to solve #777, but greater flexibility would be a significant improvement.

Associated revisions

Revision 93c6b6d6 (diff)
Added by Mark Abraham almost 2 years ago

Remove support for implicit solvation

Mdp files with implicit-solvent = no can still be read, and formerly
valid related fields are now ignored, so that default mdp files from
previous versions of GROMACS will work. Anything else for the
implciit-solvent mdp value gives an error in grompp.

grompp can now only write a tpr file that has a false value for
ir->implicit_solvent, but can read older versions. When mdrun is
presented with an older tpr file that did such a simulation, it
refuses to run, presenting a useful error message. Such tpr files are
still useful for other purposes, so can still be read, except that the
fields specific to these methods are ignored.

grompp now ignores the topology directives for related parameters,
which means that force-field folders that are the same as, or
modifications of folders formerly supported by GROMACS still
work. However, the versions currently distributed have none of those
fields.

The group-scheme kernels have been removed, and generation
infrastructure updated so that they do generate the code that's in the
repo. However, now that the python generation scripts no longer
generate GB kernels, the dictionary ordering changes, which changes
the generated output. That output is not sensitive to the order of the
declarations or data-structure elements, so this is only a cosmetic
issue.

Documentation has been removed.

Unit tests on .mdp file handling have had to be updated.

Also removed unused enbcoul enumeration

Refs #1500
Refs #1971
Fixes #1054

Change-Id: Ib241555ff3d8e60012ba0e628ab0f9a3f91eca9e

History

#1 Updated by Berk Hess about 7 years ago

  • Assignee changed from Berk Hess to Erik Lindahl

#2 Updated by Mark Abraham over 6 years ago

  • Parent task set to #1292

#3 Updated by Mark Abraham over 5 years ago

  • Target version changed from 5.0 to future
  • Parent task changed from #1292 to #1500

#4 Updated by Mark Abraham almost 2 years ago

  • Assignee changed from Erik Lindahl to Mark Abraham
  • Target version changed from future to 2019

"Fixing" this by removing the support for it.

#5 Updated by Gerrit Code Review Bot almost 2 years ago

Gerrit received a related patchset '1' for Issue #1054.
Uploader: Mark Abraham ()
Change-Id: gromacs~master~Ib241555ff3d8e60012ba0e628ab0f9a3f91eca9e
Gerrit URL: https://gerrit.gromacs.org/7477

#6 Updated by Mark Abraham almost 2 years ago

  • Tracker changed from Feature to Task

#7 Updated by Mark Abraham almost 2 years ago

  • Tracker changed from Task to Feature
  • Subject changed from Improve implicit solvent parallelization to implicit solvent parallelization
  • Status changed from New to Closed

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