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Bug #3250

Continuing (appending) from checkpoint makes energy files corrupt

Added by Magnus Lundborg 2 months ago. Updated 2 months ago.

Status:
Closed
Priority:
High
Assignee:
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

If restarting from a checkpoint energy files can no longer be opened (with 'gmx energy' or 'gmx awh').
The guilty commit is ec205c721f49c918b0a92c2a084a905d14209e87 (Change-Id: I0fe517f4ce3f6630e589a65d106ca67bcb14765b), i.e. broken since right after v2020-beta1.

Associated revisions

Revision 6c0b8d31 (diff)
Added by Berk Hess 2 months ago

Fix mdrun appending invalidating energy files

When appending at mdrun restarts, energy files would become
unreadable at the appending point.

Fixes #3250

Change-Id: I7683e1a954fb8865acb5e77aae028ae717ae0ab3

History

#1 Updated by Magnus Lundborg 2 months ago

To clarity, gmx energy can open the file, but not read the data past the checkpoint append. The message is:
"Fatal error:
Energy header magic number mismatch, this is not a GROMACS edr file
If you want to use the correct frames before the corrupted frame and avoid
this fatal error set the env.var. GMX_ENX_NO_FATAL"

#2 Updated by Berk Hess 2 months ago

  • Status changed from New to Fix uploaded
  • Assignee set to Berk Hess

#3 Updated by Berk Hess 2 months ago

  • Status changed from Fix uploaded to Resolved

#4 Updated by Paul Bauer 2 months ago

  • Status changed from Resolved to Closed

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