[gmx-users] 2016.3 installation

Mark Abraham mark.j.abraham at gmail.com
Tue May 2 10:36:17 CEST 2017 

Hi,

That seems like you're now running in a different environment from the one
in which you compiled. I can't be specific, because I don't know anything
about your machine, but you need to load the same compiler module,
devtoolset, or something like that.

Mark

On Tue, May 2, 2017 at 9:43 AM RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> Dear Mark,
>
> I executed the test files from bin and I et the following error
>
> ./analysisdata-test
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20'
> not found (required by ./analysisdata-test)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not
> found (required by ./analysisdata-test)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21'
> not found (required by ./analysisdata-test)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15'
> not found (required by ./analysisdata-test)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20'
> not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not
> found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18'
> not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14'
> not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21'
> not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
> ./analysisdata-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15'
> not found (required by /gromacs-2016.1/build/lib/libgromacs.so.2)
>
>
> Await your precious response
>
> On Mon, May 1, 2017 at 5:25 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
> > Dear Mark
> >
> > First apology that I am unaware how to run the test programs.
> >
> > Next, I tried to simulate a protein and i get the following error.
> >
> >
> > *[user at mqml rahul]$* source /usr/local/gromacs/bin/GMXRC
> > *[user at mqml rahul]$* gmx pdb2gmx -f 99nsInput.pdb -o 99nsInput.gro -p
> > 99nsInput.top
> > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found
> > (required by gmx)
> > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found
> > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > gmx: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found
> (required
> > by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found
> > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found
> > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found
> > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > gmx: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found
> > (required by /usr/local/gromacs/bin/../lib64/libgromacs.so.2)
> > *[user at mqml rahul]$*
> >
> >
> >
> >
> >
> >
> > On Mon, May 1, 2017 at 12:58 AM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> We can't tell. Run one of the test programs you can see in the
> $build/bin
> >> did
> >>
> >> Mark
> >>
> >> On Sat, 29 Apr 2017 12:40 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:
> >>
> >> > Dear Users
> >> >
> >> > I am trying to install Gromacs 2016.3
> >> >
> >> > For make check command I am getting the following errors.
> >> >
> >> > I need your assistance to overcome this issue.
> >> >
> >> >
> >> > 22% tests passed, 21 tests failed out of 27
> >> >
> >> > Label Time Summary:
> >> > GTest                 =   0.02 sec (18 tests)
> >> > IntegrationTest       =   0.00 sec (2 tests)
> >> > MpiIntegrationTest    =   0.00 sec (1 test)
> >> > UnitTest              =   0.02 sec (18 tests)
> >> >
> >> > Total Test time (real) =   0.82 sec
> >> >
> >> > The following tests FAILED:
> >> >       1 - TestUtilsUnitTests (Failed)
> >> >       2 - MdlibUnitTest (Failed)
> >> >       3 - CommandLineUnitTests (Failed)
> >> >       4 - FFTUnitTests (Failed)
> >> >       5 - HardwareUnitTests (Failed)
> >> >       6 - MathUnitTests (Failed)
> >> >       7 - OnlineHelpUnitTests (Failed)
> >> >       8 - OptionsUnitTests (Failed)
> >> >       9 - RandomUnitTests (Failed)
> >> >      10 - UtilityUnitTests (Failed)
> >> >      11 - FileIOTests (Failed)
> >> >      12 - PullTest (Failed)
> >> >      13 - SimdUnitTests (Failed)
> >> >      14 - LegacyToolsTests (Failed)
> >> >      15 - GmxPreprocessTests (Failed)
> >> >      16 - CorrelationsTest (Failed)
> >> >      17 - AnalysisDataUnitTests (Failed)
> >> >      18 - SelectionUnitTests (Failed)
> >> >      19 - TrajectoryAnalysisUnitTests (Failed)
> >> >      20 - MdrunTests (Failed)
> >> >      21 - MdrunMpiTests (Failed)
> >> > Errors while running CTest
> >> > make[3]: *** [CMakeFiles/run-ctest] Error 8
> >> > make[2]: *** [CMakeFiles/run-ctest.dir/all] Error 2
> >> > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> >> > make: *** [check] Error 2
> >> > [root at mqml build]#
> >> >
> >> > --
> >> > *Regards,*
> >> > *Rahul Suresh*
> >> > *Research Scholar*
> >> > *Bharathiar University*
> >> > *Coimbatore*
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
> >> >
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> >> >
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> >> > send a mail to gmx-users-request at gromacs.org.
> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/Support
> >> /Mailing_Lists/GMX-Users_List before posting!
> >>
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> >>
> >
> >
> >
> > --
> > *Regards,*
> > *Rahul Suresh*
> > *Research Scholar*
> > *Bharathiar University*
> > *Coimbatore*
> >
>
>
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
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>
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