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Bug #2170

(Opt.) indication to gmx cluster -s doesn't seem to be optional

Added by Chris Neale over 2 years ago. Updated almost 2 years ago.

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

gmx cluster -h lists a topology as optional:

-s      [<.tpr/.gro/...>]  (topol.tpr)      (Opt.)

But without a topology the evaluation crashes (even with -nofit and -nopbc):

GROMACS: gmx cluster, VERSION 5.1.2
Executable: /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial/bin/gmx
Data prefix: /home/cneale/exec/GROMACS/exec/gromacs-5.1.2/serial
Command line:
gmx cluster -f OUTPUT/vbot317020ps_fit.xtc -n cindex.ndx -nofit -nopbc -method gromos -cutoff 1.0 -cl clust.xtc -wcl 10 -dist rmsd-dist.xvg -ev rmsd-eig.xvg -skip 10

Back Off! I just backed up cluster.log to ./#cluster.log.1#
Using gromos method for clustering

-------------------------------------------------------
Program gmx cluster, VERSION 5.1.2
Source code file: /home/cneale/exec/GROMACS/source/gromacs-5.1.2/src/gromacs/fileio/gmxfio.c, line: 476

Can not open file:
topol.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

Associated revisions

Revision f6e66d9b (diff)
Added by Erik Lindahl almost 2 years ago

Require TPR file for gmx cluster

The program crashes without it, so it wasn't
optional.

Fixes #2170.

Change-Id: I63af728eea047dd4c3b11d890d507473109a7279

History

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

Gerrit received a related patchset '1' for Issue #2170.
Uploader: Erik Lindahl ()
Change-Id: gromacs~release-2018~I63af728eea047dd4c3b11d890d507473109a7279
Gerrit URL: https://gerrit.gromacs.org/7335

#2 Updated by Erik Lindahl almost 2 years ago

  • Status changed from New to Resolved

Not critical, so to save time I won't push it in 2016 and then pull forward, but at least it will be required for release-2018.

#4 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Resolved to Closed

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