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Bug #1605

grompp does not generate PME grid size 84

Added by Berk Hess over 2 years ago. Updated over 2 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Category:
preprocessing (pdb2gmx,grompp)
Target version:
Affected version - extra info:
>=4.6 (since cc33f2)
Affected version:
Difficulty:
uncategorized
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Description

If the fourier-spacing chosen in the mdp file is too fine for a grid of size 80, grompp will skip to 96, ignoring the perfectly fine value of 84. This results in high FFT and FFT communication costs.

Associated revisions

Revision b7bcff77 (diff)
Added by Berk Hess over 2 years ago

Fix calc_grid avoiding PME grid factor 84

Due to an indexing issue, it was unlikely that calc_grid, and thus
grompp, would choose a PME grid of 84*2^n and instead use a factor 96.
For a cubic box, this could increase the FFT cost by a factor 1.5.
Fixes #1605.

Change-Id: I8d6a85a98267af053b66867722fc5626ef907964

History

#1 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #1605.
Uploader: Berk Hess ()
Change-Id: I8d6a85a98267af053b66867722fc5626ef907964
Gerrit URL: https://gerrit.gromacs.org/4103

#2 Updated by Berk Hess over 2 years ago

  • Status changed from In Progress to Fix uploaded

#3 Updated by Szilárd Páll over 2 years ago

  • Affected version - extra info set to >=4.6 (since cc33f2)

#4 Updated by Mark Abraham over 2 years ago

  • Status changed from Fix uploaded to Closed

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