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

[Qing Lv]

Mark,


The results are:
$ ./simd-test.exe
Segmentation fault (core dumped)


Thanks,
Qing


At 2017-02-03 19:46:35, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>Hi,
>
>Unlikely, given that the other tests passed. But what is the output from
>running that manually, e.g. $builddir/bin/simd-test
>
>Mark
>
>On Fri, Feb 3, 2017 at 6:52 AM Qing Lv <lvqingjiejie at 163.com> wrote:
>
>> 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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