[gmx-users] 3.3.2 -b option not functioning as expected

Berk Hess gmx3 at hotmail.com
Mon Apr 21 17:30:18 CEST 2008


This is a known bug caused by autoconf, which has been worked around in 3.3.3.
It turns out that a certain version of autoconf handles the definition
of fseeko incorrectly, which causes Gromacs to use the wrong file offset.
This only happens on certain system configurations.
Unfortunately this version of autoconf was used to make the 3.3.2 distribution.


> Date: Mon, 21 Apr 2008 11:17:15 -0400
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] 3.3.2 -b option not functioning as expected
> Hello,
> I find that trjconv and g_order 3.3.2 don't properly find the frame to 
> which I would like to seek via -b. I initially discovered this based on 
> the output to the command line from g_order about which frame is being 
> processed, and I have further confirmed that the incorrect frame is 
> actually getting processed by g_order. Since I believe that the routine 
> for -b is common to all programs, I tested trjconv and it shows the same 
> features. The frame is seekable by trjconv -b only with 3.3 and 3.3.1, 
> but not with 3.3.2. The simple workaround is to go through trjconv -b -e 
> with 3.3 or 3.3.1and then run g_order 3.3.2 without -b or -e.
> Perhaps I have made some mistake or perhaps this is a known problem, but 
> I couldn't find any mention of it.
> Below is the output from my tests in case anybody can verify this.
> Chris.

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