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

[Szilárd Páll]

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".

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


On Wed, Jan 23, 2013 at 5:47 PM, Ricardo <rsoares at fcfrp.usp.br> wrote:

> On 01/22/2013 06:02 PM, Christoph Junghans wrote:
>
>> Message: 5
>>> Date: Tue, 22 Jan 2013 19:42:01 +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:
>>>          <CANnYEw5=t=25hnZPfHpdJot7=3YN**CU1AeGv7HCAc3mut_75w8Q at mail.**
>>> gmail.com <3YNCU1AeGv7HCAc3mut_75w8Q at mail.gmail.com>>
>>> Content-Type: text/plain; charset=ISO-8859-1
>>>
>>> On Tue, Jan 22, 2013 at 12:45 PM, James Starlight<jmsstarlight at gmail.**
>>> com <jmsstarlight at gmail.com>>wrote:
>>>
>>>  Szilárd,
>>>>
>>>> Today I've tried to re-install cuda+gromacs and do apt-get
>>>> distr-upgrade but the same error was obtained during gromacs
>>>>
>>>>  I'm don't see how does the distribution upgrade relate to the issues
>>> you
>>> had (except if you have updated glibs to a newer version which is *still*
>>> incompatible with libcuda. You should probably try getting a more recent
>>> glibc and GCC version, one that libcuda is linked against. However, I'm
>>> not
>>> sure what the source of your problem is, so I can't suggest a certain
>>> solution.
>>>
>> I had a similar problem on Gentoo Linux
>> (https://bugs.gentoo.org/show_**bug.cgi?id=452386<https://bugs.gentoo.org/show_bug.cgi?id=452386>),
>> it helped to use a
>> newer version of gcc (>=4.6).
>>
>> Cheers,
>>
>> Christoph
>>
>
>
>
> I also had this problem, and found that (manually) updating GCC to version
> 4.6 or higher has fully solved some installation issues with GROMACS 4.6.
> Please note that, for older linux dists, updating via console 'apt-get
> update' does not assure that you'd get newer versions of GCC, therefore, in
> this case, it should be downloaded and installed manually.
>
> Cheers
>
>
>  compilation. By the way where I could provide --add-needed option ?
>>>>
>>> CMAKE_EXE_LINKER_FLAGS=-wl,--**add-needed
>>>
>>> Cheers,
>>> Szilárd
>>>
>>>
>>>
>>>> James
>>>>
>>>>
>>>> 2013/1/21 Szilárd Páll<szilard.pall at cbr.su.se>:
>>>>
>>>>> Szilárd
>>>>>
>>>> --
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>>>>
>>>>  --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>
> Ricardo O S Soares
> http://fisbio.fcfrp.usp.br/**joomla/ <http://fisbio.fcfrp.usp.br/joomla/>
>
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