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

Thu Jan 24 15:23:44 CET 2013

oh that was simply solved by upgrading of G++ :)

the only problem which remains is the missing of support of mu GPU :(
That time I've tried to start simulation on simply 2 cores CPU + geforce 9500

>From md run I've obtained

NOTE: Error occurred during GPU detection:
      CUDA driver version is insufficient for CUDA runtime version
      Can not use GPU acceleration, will fall back to CPU kernels.

ED sampling will be performed!
ED: Reading edi file new_a2a_pca_biased.edi
ED: Note: Reference and average structure are composed of the same atom indices.
ED: Found 1 ED group.
Using 1 MPI thread
Using 2 OpenMP threads

No GPUs detected

I've installed cuda-5.0 with driver
NVRM version: NVIDIA UNIX x86_64 Kernel Module  304.54  Sat Sep 29
00:05:49 PDT 2012

that system works fine with the recent nvidia GPU's but has no support
for GeForce 9500.

James

2013/1/24, James Starlight <jmsstarlight at gmail.com>:
> 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
>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>>>>> * 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/>
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
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>>>
>> --
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>