[gmx-users] Install Problem: make check, tests failed, incompatible library version

[Mark Abraham]

Hi,

Something seems to be different between the environment when you configured
the build of GROMACS, and now, because different versions of
libxml2.2.dylib are being found.

Mark

On Mon, 8 Aug 2016 23:40 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/8/16 1:35 PM, Betty Wong wrote:
> > Hi,
> >
> > Posting again, hoping someone will help me! Much appreciated.
> >
> > I am trying to install Gromacs. (I believe that) I have successfully done
> > the following:
> >
> > tar xfz gromacs-5.1.3.tar.gz
> > cd gromacs-5.1.3
> > mkdir build
> > cd build
> > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > make
> >
> >
> > But when I get to make check, I get an error, I've copied and pasted only
> > one part of the what error output is.
> >  Start 20: MdrunMpiTests
> >
> > 20/26 Test #20: MdrunMpiTests ....................***Exception: Other
> 0.02
> > sec
> >
> > dyld: Library not loaded: libxml2.2.dylib
> >
> >   Referenced from: /Users/bwong/Desktop/gromacs-
> > 5.1.3/build/bin/mdrun-mpi-test
> >
> >   Reason: Incompatible library version: mdrun-mpi-test requires version
> > 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0
> >
>
> You need to upgrade to a newer version for this to work.
>
> -Justin
>
> > And if this helps as well:
> >
> > The following tests FAILED:
> >
> >   1 - TestUtilsUnitTests (OTHER_FAULT)
> >
> >   2 - GmxlibTests (OTHER_FAULT)
> >
> >   3 - MdlibUnitTest (OTHER_FAULT)
> >
> >   4 - CommandLineUnitTests (OTHER_FAULT)
> >
> >   5 - FFTUnitTests (OTHER_FAULT)
> >
> >   6 - MathUnitTests (OTHER_FAULT)
> >
> >   7 - RandomUnitTests (OTHER_FAULT)
> >
> >   8 - OnlineHelpUnitTests (OTHER_FAULT)
> >
> >   9 - OptionsUnitTests (OTHER_FAULT)
> >
> > 10 - UtilityUnitTests (OTHER_FAULT)
> >
> > 11 - FileIOTests (OTHER_FAULT)
> >
> > 12 - SimdUnitTests (OTHER_FAULT)
> >
> > 13 - LegacyToolsTests (OTHER_FAULT)
> >
> > 14 - GmxPreprocessTests (OTHER_FAULT)
> >
> > 15 - CorrelationsTest (OTHER_FAULT)
> >
> > 16 - AnalysisDataUnitTests (OTHER_FAULT)
> >
> > 17 - SelectionUnitTests (OTHER_FAULT)
> >
> > 18 - TrajectoryAnalysisUnitTests (OTHER_FAULT)
> >
> > 19 - MdrunTests (OTHER_FAULT)
> >
> > 20 - MdrunMpiTests (OTHER_FAULT)
> >
> > 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
> >
> > Any help? Not sure what the error is and how to fix. Thanks!
> >
> > Best,
> > Betty
> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
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