[gmx-users] Gromacs 2018 installation failed

[Qinghua Liao]

Hello Elton,

Thanks a lot for your help! I just tried to load a binutils library (it 
was installed on the cluster) and install Gromacs 2018 again,
it works now!


All the best,
Qinghua


On 02/09/2018 11:33 PM, Elton Carvalho wrote:
> If you are in a hurry, you can download the binutils package from here
> https://www.gnu.org/software/binutils/ and compile it on your own, setting
> the PREFIX to a directory in your home, then use $PATH to make your binary
> the highest priority.
>
> Cheers,
> Elton
>
> On Fri, Feb 9, 2018 at 8:17 PM, Qinghua Liao <scorpio.liao at gmail.com> wrote:
>
>> Hello Elton,
>>
>> Thanks a lot for your information, I already sent an e-mail to the
>> administrator,
>> hopefully they will fix it.
>>
>>
>> All the best,
>> Qinghua
>>
>>
>> On 02/09/2018 08:03 PM, Elton Carvalho wrote:
>>
>>> Hello, Qinghua,
>>>
>>> The error message refers to the standard library. I believe the package
>>> that provides this in ubuntu is glibc. Check that it's a current enough
>>> version.
>>>
>>> Another thing is that the liker (ld) needs to support C++11. That's the
>>> binutils package. I've had success with version 2.29. Not sure which is
>>> the
>>> lowest version required.
>>>
>>> Good luck,
>>> Elton
>>>
>>> On Fri, Feb 9, 2018 at 12:25 PM, Qinghua Liao <scorpio.liao at gmail.com>
>>> wrote:
>>>
>>> Dear GMX developers,
>>>> I am trying to install Gromacs2018 with cuda on clusters, the
>>>> installation
>>>> was successful on one cluster,
>>>> but failed on the other cluster. I guess there might be some library
>>>> missing on the other cluster.
>>>>
>>>> For the succeeded one, the operating system is openSUSE 42.2 (GNU/Linux
>>>> 4.4.27-2-default), the compilers are gcc and c++ 4.8.5,
>>>> the CUDA version is 9.0.176, the MPI is openMPI 1.10.3
>>>>
>>>> For the failed one, the operating system is Ubuntu 16.04.3 (GNU/Linux
>>>> 4.4.0-109-generic x86_64), I tried CUDA 9.1.85  and 9.0.176,
>>>> together with gcc/c++ version 6.4, icc/icpc 2017.4, all were failed. The
>>>> error is the same:
>>>>
>>>>
>>>> -- Performing Test CXX11_STDLIB_PRESENT
>>>> -- Performing Test CXX11_STDLIB_PRESENT - Failed
>>>> CMake Error at cmake/gmxTestCXX11.cmake:210 (message):
>>>>     This version of GROMACS requires C++11-compatible standard library.
>>>> Please
>>>>     use a newer compiler, and/or a newer standard library, or use the
>>>> GROMACS
>>>>     5.1.x release.  Consult the installation guide for details before
>>>> upgrading
>>>>     components.
>>>> Call Stack (most recent call first):
>>>>     CMakeLists.txt:168 (gmx_test_cxx11)
>>>>
>>>>
>>>> Here is my command:
>>>> CC=gcc CXX=c++ .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON
>>>> -DCMAKE_INSTALL_PREFIX=/--PATH--/Programs/Gromacs2018
>>>>
>>>> I am confused here that the old compilers worked but the new ones did
>>>> not,
>>>> while the error message suggests to use newer compilers.
>>>> Could some one help me with fixing it? Thanks a lot!
>>>>
>>>>
>>>> All the best,
>>>> Qinghua
>>>> --
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>>>
>>>
>>>
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