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

[Mark Abraham]

Hi,

Surprising, but we don't test on (or officially support) Cygwin, so could
happen. It would be most likely to happen if you built on a different
machine than you were running on... Does $builddir/bin/mdrun-test pass?
Does the terminal output mention SIMD?

Mark

On Fri, Feb 3, 2017 at 1:29 PM Qing Lv <lvqingjiejie at 163.com> wrote:

> 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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