[gmx-users] Errors in building GMX 5.1.x on Redhat 6.5 (a lot of "Undefined reference to ..")

[Qing Lv]

Thank you, Mark. I am now trying to install devtoolset-2.


Regarding Cygwin version, I must clarify that, although the compilation is successful, I got an error message when performing "make check":
95% tests passed, 1 tests failed out of 20
The following tests FAILED:
12 - SimdUnitTests (SEGFAULT)
Will it be a serious problem?
Thanks.


Qing


At 2017-02-03 13:08:50, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>Hi,
>
>These are linking errors that look like they are from not linking the
>appropriate version of the C++ standard library. I highly recommend leaving
>the system libraries alone on redhat systems, and instead compiling with
>the devtoolset packages.
>
>Thanks for the Cygwin report. People often report problems that look like
>they come from broken systems, and we rarely hear of a resolution.
>
>Mark
>
>On Fri, 3 Feb 2017 05:55 Qing Lv <lvqingjiejie at 163.com> wrote:
>
>> Hi Colleagues,
>>
>>
>> I am trying to build GMX 5.1.x (tried 5.1.4, 5.1.1, & 5.1) on a Redhat 6.5
>> server; I have updated GCC compiler and all dependent libraries (tried GCC
>> 4.9.4 and GCC 6.3.0). (The built-in compiler of Redhat 6.5 is GCC 4.4.7,
>> which is too old.)
>> I used the commmand
>> export CC=gcc
>> export CXX=gcc
>> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
>>         # No errors reported till now
>> make
>> When 100% completed, I got a lot of error messages like
>> ../../lib/libgromacs.so.1.0.0: Undefined reference to
>> ‘std::runtime_error::what() const’
>> ../../lib/libgromacs.so.1.0.0: Undefined reference to ........
>> ../../lib/libgromacs.so.1.0.0: Undefined reference to ........
>> And the error messages finished with
>> collect2: Error: ld returns 1
>> make[2]: *** [bin/template] Error 1
>> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> make: *** [all] Error 2
>>
>>
>> Any friends can help? Thanks
>> BTW, I have just successfully compiled GMX 5.1.4 on Cygwin.
>>
>>
>> Qing
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