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

[Mark Abraham]

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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