[gmx-users] Problem with gromacs-4.6 compilation on Debian

[Szilárd Páll]

On Thu, Jan 24, 2013 at 7:09 PM, Christoph Junghans <junghans at votca.org>wrote:

> > Date: Thu, 24 Jan 2013 01:07:04 +0100
> > From: Szil?rd P?ll <szilard.pall at cbr.su.se>
> > Subject: Re: [gmx-users] Problem with gromacs-4.6 compilation on
> >         Debian
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID:
> >         <CANnYEw522dfPw5ELOr=
> XWQyN3XWOeUjjpUbh4bfc1r7YnHsB8Q at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Hi all,
> >
> > Let me clarify one thing: I highly doubt that the *gcc version* upgrade
> is
> > what fixes your the issue, but rather the standard C++ library's version,
> > as you can see the undefined symbols refer to "GLIBCXX_3.4.15".
> Usually that is the case but for std::, the symbols are defined in
> libstdc++, which is part of the gcc package.
>
> $ strings /usr/lib/gcc/i686-pc-linux-gnu/4.6.3/libstdc++.so | grep _M_hook
> _ZNSt6__norm15_List_node_base7_M_hookEPS0_
> _ZNSt15_List_node_base7_M_hookEPS_
> _ZNSt8__detail15_List_node_base7_M_hookEPS0_
> _ZNSt9__cxx199815_List_node_base7_M_hookEPS0_
>

Christoph, you're right I was just looking at the Ubuntu setup where
libstdc++ comes as a separate package - although it is in a similar
location as the one you suggest and it is a hard dependency for g++.

So folks & fellow gooooglers: the conclusion is that if you see the
initially reported errors, you should update your g++ (which will get you
new libstdc++).

Cheers,
--
Szilárd



>
> Christoph
>
> >
> > Of course, updating the compiler is a perfectly fine solution if you get
> > the new (enough version of the) standard C++ library by doing so.
> >
> > Just wanted to clarify this for users bumping into this issue later.
> >
> > Cheers,
> >
> > --
> > Szilárd
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
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