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

[Qing Lv]

Dear Mark,


I built and ran it on the same machine.
The test conclusion of $builddir/bin/mdrun-test is:
[----------] Global test environment tear-down
[==========] 24 tests from 8 test cases ran. (5206 ms total)
[  PASSED  ] 24 tests.


I searched the complete test result of mdrun-rest (which is quite long), but did not find "SIMD" (or Simd, simd).
Thanks.


Qing


At 2017-02-03 21:12:15, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>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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