Re: [AMBER] buffer overflow in tleap, AmberTools21, gcc 9.3

From: David A Case <>
Date: Wed, 13 Oct 2021 11:55:28 -0400

On Fri, Oct 01, 2021, Alessandro Contini wrote:
>I'm experiencing a buffer overflow issue in tleap from AmberTools21
>(amber20), compiled under Ubuntu 20.04 with gcc 9.3.0. All files to
>reproduce the issue (including leap.log) are attached here (run "tleap
>-f h-remd.leaprc.01"). The error do not occur when using amber18
>(Ubuntu 18.04; gcc 7.4.0) and with amber20 but compiled with gcc 4.8.5
>(CentOs 7). The amber distribution has been updated to the last patch
>available on Sept. 30th 21.

I can't reproduce the problem on my Ubuntu 20.04 installation. My tleap run
with your inputs exits with no errors or warnings.

Can you say why you think this is buffer overflow? I don't see anything about
that in your leap.log file. Was there some message on the terminal?

The problem appears to be in reading the frcmod file, but I don't see a
problem there. You might try reading in an almost empty frcmod file, then
slowly adding back in real entries until you can spot the problem.


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Received on Wed Oct 13 2021 - 09:00:02 PDT
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