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Bug #126

Problem with skipping large chunks of trajectory

Added by Alan Dodd almost 13 years ago. Updated over 12 years ago.

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

Description

When using the -b option with a variety of Gromacs programs - currently all
tested - g_density, g_traj, trjconv - to skip a large part of a suitably large
XTC, the program crashes with one of a variety of errors:

Source code file: xtcio.c, line: 233

Fatal error:
Frame contains more atoms (1865562167) than expected (42549)
---------------------------------------------
Source code file: xtcio.c, line: 83

Fatal error:
Magic Number Error in XTC file (read 121802304, should be 1995)
--------------------------------------------

Source code file: trxio.c, line: 635

Fatal error:
Specified frame doesn't exist or file not seekable

at frame 0. The files I have testing this on are generally quite large, and
skipping a chunk larger than ~2GB results in a crash. Suggesting use of a
different variable size?
3.2.1 programs do not suffer the same problem.

History

#1 Updated by Chris Neale over 12 years ago

I have also seen this problem. Only in single precision, and only after the time
begins to drift (in the small decimal places) from what might be expected.
Perhaps it is a problem with seeking a timestamp and not giving a large enough
window to accept the correct time? If so, a new input flag might solve this
problem

#2 Updated by David van der Spoel over 12 years ago

Fixed in CVS.

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