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Bug #2634

rerun function returns fault error on trajectory which passed gmx check

Added by zhiyi wu 10 months ago. Updated 7 months ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
Close

Description

I tried to run mdrun rerun on a trajectory which has been generated previously, using gmx mdrun -deffnm prod -rerun prod.trr.
And I have encountered:
Fatal error:
Number of atoms in trajectory (-1) does not match the run input file (91497)

I have used gmx check to check the status of the trajectory, which seems perfectly fine.
gmx check -f prod.trr
Checking file prod.trr
trr version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
  1. Atoms 91497
    Last frame 2 time 4.000
    Item #frames Timestep (ps)
    Step 3 2
    Time 3 2
    Lambda 3 2
    Coords 3 2
    Velocities 1
    Forces 1
    Box 3 2

The trajectory can be reproduced by running prod.tpr which is a 5ps simulation.
gmx mdrun -deffnm prod

prod.tpr (3.99 MB) prod.tpr zhiyi wu, 09/04/2018 05:15 PM
prod.trr (5.24 MB) prod.trr zhiyi wu, 09/04/2018 05:15 PM

Associated revisions

Revision 33fa9d43 (diff)
Added by Paul Bauer 7 months ago

Give error when rerun with identical file names

Fixes #2634

Change-Id: If3985274b3e74910c9ddefbddcfb52d1b01a3fba

History

#1 Updated by Mark Abraham 9 months ago

  • Category set to mdrun
  • Status changed from New to Accepted
  • Priority changed from High to Low
  • Target version set to 2018.4

Thanks for the report.

Using gmx mdrun -deffnm prod -rerun prod.trr causes the output trajectory to be named prod.trr, which is apparently interfering with reading the rerun file of the same name. gmx mdrun -s prod -rerun prod.trr works, and is how I suggest Zhiyi proceeds.

mdrun should refuse to start the rerun if either trajectory output filename matches the rerun input filename.

#2 Updated by Gerrit Code Review Bot 7 months ago

Gerrit received a related patchset '1' for Issue #2634.
Uploader: Paul Bauer ()
Change-Id: gromacs~release-2018~If3985274b3e74910c9ddefbddcfb52d1b01a3fba
Gerrit URL: https://gerrit.gromacs.org/8673

#3 Updated by Paul Bauer 7 months ago

  • Status changed from Accepted to Resolved

#4 Updated by Paul Bauer 7 months ago

  • Status changed from Resolved to Closed

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