Bug #1538
limited length of dynamic selection arguments
Description
The argument used for dynamic selection (in the -select option of several analysis commands of gmx) has a very limited maximum length. I run across this problem while trying to calculate many different distances with 'gmx distance' without prior preparation of the index file. Since the trajectories that I have are rather big (hundreds of milions of frames), I wanted to calculate what I needed with only one pass, and collect the results in one big xvg file. Please see the files attached for reproduction of the error. At first the error manifested itself by the message like:
- Error in `gmx': realloc(): invalid next size: 0x0000000000fa57e0 ***
Abort
With files that I've attached here, I just get a segfault. However, if I remove only one from among the segments connected with 'plus' in the command line, it works flawlessly. I wonder, if the command will work for anybody. If it works, it is probably enough to add few other distances into the command line to see the error. I know that the selection can be done more sparsely (without 'resname SOL') in this example, but its just illustration of the limitation of argument length...
Gregorz Wieczorek
Associated revisions
History
#1 Updated by Teemu Murtola over 6 years ago
- Category changed from analysis tools to selections
- Status changed from New to In Progress
- Assignee set to Teemu Murtola
- Target version set to 5.0
#2 Updated by Gerrit Code Review Bot over 6 years ago
Gerrit received a related patchset '1' for Issue #1538.
Uploader: Teemu Murtola (teemu.murtola@gmail.com)
Change-Id: I1112b5ccae526cf3b8fd079bbabf8d7f61e52635
Gerrit URL: https://gerrit.gromacs.org/3721
#3 Updated by Teemu Murtola over 6 years ago
- Status changed from In Progress to Fix uploaded
There were some places where the length of an individual selection (not the whole input string) was limited to 1024 characters. Fixed a few, which makes this case work.
#4 Updated by Erik Lindahl over 6 years ago
- Status changed from Fix uploaded to Resolved
#5 Updated by Erik Lindahl over 6 years ago
- Status changed from Resolved to Closed
Remove some hardcoded selection string buffers
This removes some arbitrary limitations on the length of the input
string. The error handling would still be in the need of a bigger
overhaul (all of these were in the error handling parts).
Fixes #1538, related to #655.
Change-Id: I1112b5ccae526cf3b8fd079bbabf8d7f61e52635