Re: [AMBER-Developers] AmberTools15 + gcc-4.8.4

From: Jason Swails <jason.swails.gmail.com>
Date: Sat, 30 May 2015 22:18:16 -0400

On Sat, May 30, 2015 at 2:19 PM, Gerald Monard <
Gerald.Monard.univ-lorraine.fr> wrote:

> As a follow-up and after some internet digging:
> I have:
> $ cat /etc/redhat-release
> CentOS Linux release 7.1.1503 (Core)
> $ gcc --version
> gcc (GCC) 4.8.4
> $ python
> Python 2.7.5 (default, Jun 17 2014, 18:11:42)
> [GCC 4.8.2 20140120 (Red Hat 4.8.2-16)] on linux2
>
> But it seems that the gcc -fstack-protector-strong option has been
> available only since gcc-4.9!
> I guess that it is a CentOS or RHEL7.1 related problem, but I'm not sure
> how to fix it.
>

​This is indeed strange. What Python does when it builds extensions is to
use the same compiler flags that were used to build Python itself.

You should be able to override this with the CFLAGS environment variable.
Or perhaps that is set on your system for some reason?​ It's really rather
perplexing that the system Python for Red Hat would fail to build
extensions with the standard compiler released with it. That would
represent a significant flaw in their product.

​And the Python signature suggests that it was built with GCC 4.8.2-16, so
something must be going on in your system's environment that I can't
discern from the available information.

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat May 30 2015 - 19:30:05 PDT
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