Project

General

Profile

Feature #1446

suboptimal error message from grompp when a required group is not defined in the mdp file

Added by Chris Neale about 3 years ago. Updated almost 3 years ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
-
Target version:
Difficulty:
uncategorized
Close

Description

When pull_ngroups = N , but pull_groupN is undefined, the error message in the output from grompp seems cryptic (although it is technically correct). In this case, grompp complains that a group reference in the .mdp was not found in the index file. It would be more useful for the user if grompp noticed that the group was not defined at all and, if this is the case, modifies the error message.

Here is the error message I get from the test system that I upload in this post:

Program grompp, VERSION 4.6.5
Source code file: /home/nealec/exe/gromacs-4.6.5/source/src/kernel/readir.c, line: 2316

Fatal error:
Group referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

############

I think that the following message would be more useful:

Fatal error:
Group pull_group2 required by grompp was undefined

Or, if that is too much work (e.g., the information about the name of the "empty" group-name is not available at that place int he code), then:

Fatal error:
Group referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.
Note that this error can also occur when you forget to define a required group

############

Note that, adding the following to the .ndx file doesn't fix the error, so now I think that technically even the error message is incorrect, although the below usage is admittedly absurd (empty name for index group)

[ ]
7 8 9

tarball.tgz - files to demonstrate error message (2.43 KB) Chris Neale, 02/28/2014 06:26 PM

Associated revisions

Revision d3ce9e70 (diff)
Added by Rossen Apostolov almost 3 years ago

More clear message for undefined pullgroups.

When a pull group was not defined in the index file,
grompp didn't report in a clear way where the problem was.

Fixes #1446.

Change-Id: If571b46b91f6ad28213808b6e18d96e1da0be79d

History

#1 Updated by Rossen Apostolov almost 3 years ago

  • Status changed from New to Accepted
  • Target version set to 4.6.6

#2 Updated by Gerrit Code Review Bot almost 3 years ago

Gerrit received a related patchset '1' for Issue #1446.
Uploader: Rossen Apostolov ()
Change-Id: If571b46b91f6ad28213808b6e18d96e1da0be79d
Gerrit URL: https://gerrit.gromacs.org/3617

#3 Updated by Rossen Apostolov almost 3 years ago

  • Status changed from Accepted to Fix uploaded

#4 Updated by Erik Lindahl almost 3 years ago

  • Status changed from Fix uploaded to Resolved

#5 Updated by Erik Lindahl almost 3 years ago

  • Status changed from Resolved to Closed

Also available in: Atom PDF