[AMBER] tleap problems in Fedora Core 12

From: case <case.biomaps.rutgers.edu>
Date: Fri, 14 May 2010 15:58:27 -0400

A user (Omair Khan) has reported tleap segfaults in Fedora Core 12, with gcc
version 4.4.3 20100127 (Red Hat 4.4.3-4).

We found a person in the lab with a laptop using Fedora Core 12, and can
reproduce what looks like the same error (segfault on loading in standard
off files from the Amber library). Like the original poster, the owner of
the laptop is not familiar with debugging problems like this, but can loan
it next week to someone who can investigate more fully. But if any Amber guru
has Fedora Core 12 (x86_64) [or wants to set up a virtual machine]
you might also look to see what happens there. But now that we can reproduce
the problem, we have a good shot at fixing it, presumably.

[This note also gives Scott time to prepare his usual post about how this
all could have been avoided if we had just waited a few years (way back when)
for C++ to be developed into a useful language....]

Perhaps related: Ubuntu 10.04 is also using gcc 4.4.3 (in this case
Ubuntu 4.4.3-4ubuntu5). On a 32-bit virtual machine, this compiler/OS combo
seems fine. So it is not strictly just the compiler version; Fedora Core 12
seems to be exposing problems with our older codes.

[One thing to look for: this may(!?!) be related to the bug found by Andreas
Svrcek-Seiler with the same compiler:

   http://dev-archive.ambermd.org/201004/0148.html

In that case, the culprit was strcpy() being used with overlapping memory,
something that seems only to fail with Fedora, even though the standard says
you can't rely on that.]

cc-ing this to Andreas in case he knows -- do you see any tleap failures
with your Fedora installation?

...thanks...dave


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Received on Fri May 14 2010 - 13:00:06 PDT
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