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

[James Starlight]

After switching to gcc-4.6 I've obtained that error on the first step
of gromacs compilation

[  0%] Building NVCC (Device) object
src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
CMake Error at gpu_utils_generated_gpu_utils.cu.o.cmake:198 (message):
  Error generating
  /home/own/distr/gromacs-4.6/src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir//./gpu_utils_generated_gpu_utils.cu.o


make[2]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/./gpu_utils_generated_gpu_utils.cu.o]
Error 1
make[1]: *** [src/gmxlib/gpu_utils/CMakeFiles/gpu_utils.dir/all] Error 2
make: *** [all] Error 2


2013/1/24, Szilárd Páll <szilard.pall at cbr.su.se>:
> 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
>>>>>>
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before
>>>>> posting!
>>>>> * Please don't post (un)subscribe requests to the list. Use the
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>>>>> * Can't post? Read
>>>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>>>>
>>>>>  --
>>> 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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>>
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